Transgenic plants with increased photosynthesis efficiency and growth

Abstract

The present disclosure provides a transgenic plant comprising one or more nucleotide sequences encoding polypeptides selected from photosystem II subunit S (PsbS), zeaxanthin epoxidase (ZEP), and violaxanthin de-epoxidase (VDE), operably linked to at least one expression control sequence. Expression vectors for making transgenic plants, and methods for increasing biomass production and/or carbon fixation and/or growth in a plant comprising increasing expression of at least one of PsbS, ZEP and VDE polypeptides are also provided.

Claims

1. A genetically modified higher plant comprising genetic modifications that increase expression of both a zeaxanthin epoxidase (ZEP) polypeptide and a violaxanthin de-epoxidase (VDE) polypeptide as compared to expression of the ZEP polypeptide and the VDE polypeptide in a control plant without the genetic modifications grown under the same conditions, wherein the genetically modified higher plant is a tracheophyte, wherein the genetically modified plant comprises at least endogenous levels of an endogenous photosystem II subunit S (PsbS) polypeptide, wherein the expression of the VDE polypeptide is increased by expressing a transfected nucleotide sequence encoding the VDE polypeptide in the genetically modified plant and/or by a genetic modification in a promoter of a nucleotide sequence encoding the VDE polypeptide, and wherein the expression of the ZEP polypeptide is increased by expressing a transfected nucleotide sequence encoding the ZEP polypeptide in the genetically modified plant and/or by a genetic modification in a promoter of a nucleotide sequence encoding the ZEP polypeptide.

2. The genetically modified higher plant of claim 1, wherein the expression of the VDE polypeptide is increased by expressing the transfected nucleotide sequence encoding the VDE polypeptide, and wherein the transfected nucleotide sequence is operably linked to at least one expression control sequence; and wherein the expression of the ZEP polypeptide is increased by expressing the transfected nucleotide sequence encoding the ZEP polypeptide, and wherein the transfected nucleotide sequence is operably linked to at least one expression control sequence.

3. The genetically modified higher plant of claim 1, wherein one or both of the transfected nucleotide sequences are derived from a dicot or a monocot.

4. The genetically modified higher plant of claim 3, wherein the dicot is selected from Arabidopsis thaliana, Beta vulgaris (sugar beet), Glycine max (soybean), Vigna unguiculata (cowpea), and Manihot esculenta (cassava), or wherein the monocot comprises Saccharum officinarum (sugarcane).

5. The genetically modified higher plant of claim 1, wherein: (a) the ZEP polypeptide is encoded by a nucleotide sequence having at least 70% identity to SEQ ID NO: 2; the ZEP polypeptide has an amino acid sequence having at least 70% identity to SEQ ID NO: 5, KRH28470.1, NP_001241348.1, or XP_010666612.1; or the ZEP polypeptide comprises an amino acid sequence having at least 70% identity to SEQ ID NO: 8; and/or (b) the VDE polypeptide is encoded by the nucleotide sequence having at least 70% identity to SEQ ID NO: 3 or a conserved domain thereof; the VDE polypeptide has an amino acid sequence having at least 70% identity to SEQ ID NO: 6, SEQ ID NO: 67 (XP_021623226.1), XP_006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, XP_006576257.1, XP_010674199.1, or a conserved domain thereof; or the VDE polypeptide comprises a conserved domain having at least 70% identity to SEQ ID NO: 9 or a conserved domain thereof.

6. The genetically modified higher plant of claim 5, wherein: (a) the ZEP is encoded by the nucleotide sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 2; the ZEP polypeptide has an amino acid sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 5, KRH28470.1, NP_001241348.1, or XP_010666612.1; or the ZEP polypeptide comprises an amino acid sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 8; and/or (b) the VDE polypeptide is encoded by the nucleotide sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 3 or a conserved domain thereof; the VDE polypeptide has an amino acid sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 6, SEQ ID NO: 67 (XP_021623226.1), XP_006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, XP_006576257.1, XP_010674199.1, or a conserved domain thereof; or the VDE polypeptide comprises a conserved domain having at least 80%, 90%, or 100% identity to SEQ ID NO: 9 or a conserved domain thereof.

7. The genetically modified higher plant of claim 1, wherein: the ZEP is encoded by a nucleotide sequence of SEQ ID NO: 2, and the VDE polypeptide is encoded by a nucleotide sequence of SEQ ID NO: 3; the ZEP polypeptide is encoded by a nucleotide sequence having at least 90% identity to SEQ ID NO: 2, and the VDE polypeptide is encoded by a nucleotide sequence having at least 90% identity to SEQ ID NO: 3; the ZEP polypeptide is encoded by a nucleotide sequence having at least 70% identity to SEQ ID NO: 2, and the VDE polypeptide is encoded by a nucleotide sequence having at least 70% identity to SEQ ID NO: 3; the ZEP polypeptide has an amino acid sequence of SEQ ID NO: 5, and the VDE polypeptide has an amino acid sequence of SEQ ID NO: 6; the ZEP polypeptide has an amino acid sequence at least 90% identical to SEQ ID NO: 5, and the VDE polypeptide has an amino acid sequence at least 90% identical to SEQ ID NO: 6; the ZEP polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 5, and the VDE polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 6; and/or the ZEP polypeptide comprises the amino acid sequence of SEQ ID NO: 8, and the VDE polypeptide comprises a conserved domain of SEQ ID NO: 9.

8. The genetically modified higher plant of claim 1, wherein: the ZEP polypeptide has the amino acid sequence of KRH28470.1 or NP_001241348.1, and the VDE polypeptide has the amino acid sequence of XP_006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, or XP_006576257.1; the ZEP polypeptide has an amino acid sequence at least 90% identical to KRH28470.1 or NP 001241348.1, and the VDE polypeptide has an amino acid sequence at least 90% identical to XP_006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, or XP 006576257.1; the ZEP polypeptide has an amino acid sequence at least 70% identical to KRH28470.1 or NP 001241348.1, and the VDE polypeptide has an amino acid sequence at least 70% identical to XP 006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, or XP 006576257.1; the ZEP polypeptide comprises the amino acid sequence of KRH28470.1 or NP_001241348.1, and the VDE polypeptide comprises a conserved domain of XP_006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, or XP_006576257.1; the ZEP polypeptide has the amino acid sequence of XP_010666612.1, and the VDE polypeptide has the amino acid sequence of XP_010674199.1; the ZEP polypeptide has an amino acid sequence at least 90% identical to XP_010666612.1, and the VDE polypeptide has an amino acid sequence at least 90% identical to XP_010674199.1; the ZEP polypeptide has an amino acid sequence at least 70% identical to XP_010666612.1 or NP_001241348.1, and the VDE polypeptide has an amino acid sequence at least 70% identical to XP 010674199.1; the ZEP polypeptide comprises the amino acid sequence of XP_010666612.1, and the VDE polypeptide comprises a conserved domain of XP_010674199.1; the VDE polypeptide has the amino acid sequence of SEQ ID NO: 67; the VDE polypeptide has an amino acid sequence at least 90% identical to SEQ ID NO: 67; the VDE polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 67; and/or the VDE polypeptide comprises a conserved domain of SEQ ID NO: 67.

9. The genetically modified higher plant of claim 8, further comprising a genetic modification that increases expression of a photosystem II subunit S (PsbS) polypeptide as compared to expression of the endogenous PsbS polypeptide in a control plant without the genetic modification grown under the same conditions, wherein the expression of the PsbS polypeptide is increased by expressing a transfected nucleotide sequence encoding the PsbS polypeptide in the genetically modified plant and/or by a genetic modification in a promoter of a nucleotide sequence encoding the endogenous PsbS polypeptide, and wherein the PsbS polypeptide is encoded by the nucleotide sequence of SEQ ID NO: 1; the PsbS polypeptide is encoded by a nucleotide sequence at least 90% identical to SEQ ID NO: 1; the PsbS polypeptide is encoded by a nucleotide sequence at least 70% identical to SEQ ID NO: 1; the PsbS polypeptide has the amino acid sequence of SEQ ID NO: 4; the PsbS polypeptide has an amino acid sequence at least 90% identical to SEQ ID NO: 4; the PsbS polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 4; and/or the PsbS polypeptide comprises a conserved domain of SEQ ID NO: 1, SEQ ID NO: 4, or SEQ ID NO: 7; the PsbS polypeptide has an amino acid sequence of XP_003523444.1, NP_001276237.1, or ACU23291.1; the PsbS polypeptide has an amino acid sequence at least 90% identical to XP_003523444.1, NP_001276237.1, or ACU23291.1; the PsbS polypeptide has an amino acid sequence at least 70% identical to XP_003523444.1, NP_001276237.1, or ACU23291.1; the PsbS polypeptide comprises a conserved domain of SEQ ID NO: 4, XP_003523444.1, NP_001276237.1, or ACU23291.1; the PsbS polypeptide has an amino acid sequence of SEQ ID NO: 28; the PsbS polypeptide has an amino acid sequence at least 90% identical to SEQ ID NO: 28; the PsbS polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 28; and/or the PsbS polypeptide comprises a conserved domain of SEQ ID NO: 28.

10. The genetically modified higher plant of claim 9, wherein the expression of the PsbS polypeptide is increased by expressing the transfected nucleotide sequence encoding the PsbS polypeptide, and wherein the transfected nucleotide sequence is operably linked to at least one expression control sequence.

11. The genetically modified higher plant of claim 1, wherein the plant is a crop plant, a model plant, a monocotyledonous plant, a dicotyledonous plant, a plant with Crassulacean acid metabolism (CAM) photosynthesis, a plant with C3 photosynthesis, a plant with C4 photosynthesis, an annual plant, a greenhouse plant, a horticultural flowering plant, a perennial plant, a switchgrass plant, a maize plant, a biomass plant, or a sugarcane plant.

12. The genetically modified higher plant of claim 1, wherein the plant is selected from the group of tobacco, corn, rice, sorghum, soybean, cowpea, poplar, eucalyptus, cassava, barley, potato, sugarcane, alfalfa, sugar beet, or wherein the plant is selected from the group consisting of switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, sugar beet, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop and a biomass crop.

13. The genetically modified higher plant of claim 12, wherein the plant is: sugar beet, the ZEP polypeptide has an amino acid sequence at least 70% identical to XP 010666612.1 or NP_001241348.1, the VDE polypeptide has an amino acid sequence at least 70% identical to XP_010674199.1; soybean, the ZEP polypeptide has an amino acid sequence at least 70% identical to KRH28470.1 or NP_001241348.1, the VDE polypeptide has an amino acid sequence at least 70% identical to XP_006576259.1, XP_014628869.1, XP_014628868.1, NP_001241404.1, NP_001240949.1, or XP_006576257.1; cassava and the VDE polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 67; cowpea; or sugarcane.

14. The genetically modified higher plant of claim 1, wherein: the plant has improved growth under fluctuation light conditions as compared to the control plant grown under the same fluctuating light conditions; the plant has increased photosynthetic efficiency under fluctuating light conditions as compared to the control plant grown under the same fluctuating light conditions; the plant has improved photoprotection efficiency under fluctuating light conditions as compared to the control plant grown under the same fluctuating light conditions; the plant has an increased rate of relaxation of non-photochemical quenching (NPQ) under fluctuating light conditions as compared to the control plant grown under the same fluctuating light conditions; and/or the plant has improved quantum yield and CO.sub.2 fixation under fluctuating light conditions as compared to the control plant grown under the same fluctuating light conditions.

15. The genetically modified higher plant of claim 1, wherein the plant further comprises expression of at least one additional polypeptide that provides herbicide resistance, insect or pest resistance, disease resistance, modified fatty acid metabolism, and/or modified carbohydrate metabolism.

16. The genetically modified higher plant of claim 1, wherein: the transcript level of the VDE polypeptide is increased 3-fold as compared to the control plant, and wherein the transcript level of the ZEP polypeptide is increased 8-fold as compared to the control plant; the transcript level of the VDE polypeptide is increased 10-fold as compared to the control plant, and wherein the transcript level of the ZEP polypeptide is increased 6-fold as compared to the control plant; the transcript level of the VDE polypeptide is increased 4-fold as compared to the control plant, and wherein the transcript level of the ZEP polypeptide is increased 7-fold as compared to the control plant; the protein level of the VDE polypeptide is increased 16-fold as compared to the control plant, and wherein the protein level of the ZEP polypeptide is increased 80-fold as compared to the control plant; the protein level of the VDE polypeptide is increased 30-fold as compared to the control plant, and wherein the protein level of the ZEP polypeptide is increased 74-fold as compared to the control plant; the protein level of the VDE polypeptide is increased 47-fold as compared to the control plant, and wherein the protein level of the ZEP polypeptide is increased 75-fold as compared to the control plant; the increase of transcript level as compared to the control plant between the VDE polypeptide and the ZEP polypeptide has a ratio selected from the group consisting of 3:8, 10:6, and 4:7; the increase of protein level as compared to the control plant between the VDE polypeptide and the ZEP polypeptide has a ratio selected from the group consisting of 16:80, 30:74, and 47:75; the increase of transcript level of the VDE polypeptide as compared to the control plant is from about 3-fold to about 10-fold, and wherein the increase of transcript level of the ZEP polypeptide as compared to the control plant is from about 6-fold to about 8-fold; or the increase of protein level of the VDE polypeptide as compared to the control plant is in from about 16-fold to about 47-fold, and wherein the increase of protein level of the ZEP polypeptide as compared to the control plant is from about 74-fold to about 80-fold.

17. The genetically modified higher plant of claim 5, further comprising a genetic modification that increases expression of a photosystem II subunit S (PsbS) polypeptide as compared to expression of the endogenous PsbS polypeptide in a control plant without the genetic modification grown under the same conditions, wherein the expression of the PsbS polypeptide is increased by expressing a transfected nucleotide sequence encoding the PsbS polypeptide in the genetically modified plant and/or by a genetic modification in a promoter of a nucleotide sequence encoding the endogenous PsbS polypeptide, wherein the PsbS polypeptide: (i) is encoded by a nucleotide sequence having at least 70% identity to SEQ ID NO: 1 or a conserved domain thereof; (ii) has an amino acid sequence having at least 70% identity to SEQ ID NO: 4, XP_003523444.1, NP_001276237.1, ACU23291.1, SEQ ID NO: 28 (XP_010692414.1), or a conserved domain thereof; or (iii) comprises a conserved domain having at least 70% identity to SEQ ID NO: 7 or a conserved domain thereof.

18. The genetically modified higher plant of claim 17, wherein the PsbS polypeptide: (i) is encoded by a nucleotide sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 1 or a conserved domain thereof; (ii) has an amino acid sequence having at least 80%, 90%, or 100% identity to SEQ ID NO: 4, XP_003523444.1, NP_001276237.1, ACU23291.1, SEQ ID NO: 28 (XP_010692414.1), or a conserved domain thereof; or (iii) comprises a conserved domain having at least 80%, 90%, or 100% identity to SEQ ID NO: 7 or a conserved domain thereof.

19. The genetically modified higher plant of claim 13, wherein the plant is sugar beet, and wherein the plant further comprises a genetic modification that increases expression of a PsbS polypeptide as compared to expression of the endogenous PsbS polypeptide in a control plant without the genetic modification grown under the same conditions, wherein the expression of the PsbS polypeptide is increased by expressing a transfected nucleotide sequence encoding the PsbS polypeptide in the genetically modified plant and/or by a genetic modification in a promoter of a nucleotide sequence encoding the endogenous PsbS polypeptide, and the PsbS polypeptide has an amino acid sequence at least 70% identical to SEQ ID NO: 28.

20. The genetically modified higher plant of claim 13, wherein the plant is soybean, and wherein the plant further comprises a genetic modification that increases expression of a PsbS polypeptide as compared to expression of the endogenous PsbS polypeptide in a control plant without the genetic modification grown under the same conditions, wherein the expression of the PsbS polypeptide is increased by expressing a transfected nucleotide sequence encoding the PsbS polypeptide in the genetically modified plant and/or by a genetic modification in a promoter of a nucleotide sequence encoding the endogenous PsbS polypeptide, and the PsbS polypeptide has an amino acid sequence at least 70% identical to XP_003523444.1, NP_001276237.1, or ACU23291.1.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) The features, objects and advantages other than those set forth above will become more readily apparent when consideration is given to the detailed description below. Such detailed description makes reference to the following drawings, wherein:

(2) FIG. 1. (A) Non-photochemical quenching in young seedlings of wild-type and three (VDE-PsbS-ZEP) VPZ overexpressing lines during 10 min illumination with 1000 mol m.sup.2 s.sup.1 PFD, followed by 10 min of dark relaxation. (B) Non-photochemical quenching and (C) PSII efficiency in young seedlings during repeated cycles of 3 min illumination with 2000 mol m.sup.2 s.sup.1 PFD, followed by 2 min of 200 mol m.sup.2 s.sup.1 PFD. Error bars indicate se (n=18), asterisks indicate significant differences between VPZ lines and wild-type (=0.05).

(3) FIG. 2. mRNA and protein expression of native (Nt) and transgenic (At) violaxanthin de-epoxidase (VDE), photosystem II subunit S (PsbS) and zeaxanthin epoxidase (ZEP). (A-C) mRNA levels relative to actin and tubulin, (D-F) protein levels relative to wild-type, determined from densitometry on western blots, error bars indicate se (n=5) asterisks indicate significant differences between VPZ lines and wild-type (=0.05), (G) Example of western blots for VDE, PsbS and ZEP.

(4) FIG. 3. Non-photochemical quenching during gas exchange as a function of absorbed light intensity in fully-expanded leaves of wild-type and VPZ-overexpressing lines. Light intensity was either increased from low to high PFD, while waiting for steady state at each step (A), or varied from high to low PFD with 4 min of 2000 mol m.sup.2 s.sup.1 before each light intensity change (B). Error bars indicate se (n=6), asterisks indicate significant differences between VPZ lines and wild-type (=0.05).

(5) FIG. 4. (A-B) Linear electron transport (J) and net assimilation rate (An) as a function of light intensity and corresponding parameter fits for initial slope (C-D). Light intensity was varied from high to low PFD with 4 min of 2000 mol m.sup.2 s.sup.1 PFD before each light intensity change. Error bars indicate se (n=6), asterisks indicate significant differences between VPZ lines and wild-type (=0.05).

(6) FIG. 5. Photo-protection index after exposure of (A) one hour or (B) two hours to 2000 mol m.sup.2 s.sup.1 PFD (.sub.max=470 nm) in seedlings of VPZ overexpression lines and wild-type. Index values less than one indicate occurrence of photo-inhibition. (C) PSII efficiency plotted against residual NPQ in young seedlings after exposure to one hour (Upward pointing trianglesVPZ, CircleWT) or two hours (Downward pointing trianglesVPZ, SquareWT) of 2000 mol m.sup.2 s.sup.1 and 10 min of subsequent dark relaxation. Error bars indicate se (n=18), asterisks indicate significant differences between VPZ lines and wild-type (=0.05).

(7) FIG. 6. Final plant size and weight in greenhouse experiments relative to WT. (A) Total dry-weight per plant, (B) leaf area per plant, (C) Plant height, (D) Leaf dry-weight per plant, (E) Stem dry-weight per plant, (F) Root dry-weight per plant. Error bars indicate se (n=20 and n=19 for experiment 1 and 2), asterisks indicate significant differences between VPZ lines and wild-type (=0.05).

(8) FIG. 7. Linear electron transport and net assimilation rate as a function of light intensity. Light intensity was varied from high to low PFD with 4 min of 2000 mol m.sup.2 s.sup.1 PFD before each light intensity change. (A-B) Linear electron transport (J) and net assimilation rate (An) and corresponding parameter fits for initial slope (C-D), convexity (E-F) and asymptote (G-H). Error bars indicate se (n=6).

(9) FIG. 8. Convexity (A-B) and asymptote (C-D) parameter fits to linear electron transport (J) and net assimilation rate (An) as a function of light intensity. Light intensity was varied from high to low PFD with 4 min of 2000 mol m.sup.2 s.sup.1 PFD before each light intensity change. Error bars indicate se (n=6).

(10) FIG. 9. Plasmid map of VDE-PsbS-ZEP construct.

(11) FIG. 10. The intended goal to increase speed in which photoprotection responds to changes in light intensity and the role VDE, PsbS and ZEP play in this process. Blue lines represent transgenic plants compared to orange lines (wild type).

(12) FIG. 11. Fast high throughput screening of phenotypes. Chlorophyll fluorescence of leaf discs (left) and chlorophyll fluorescence of young seedlings (right).

(13) FIG. 12. Growth experiment comparing VPZ-23 and VPZ-34 transgenic to wild type plants.

(14) FIG. 13. Greenhouse experiment showing significantly increased growth in all lines.

(15) FIG. 14. Results of quantum yield and CO.sub.2 fixation at various light intensities, after prior exposure of the leaf to 2000 mol m.sup.2s.sup.1 PFD.

(16) FIG. 15. NPQ kinetics under fluctuating light.

(17) FIG. 16. Time constants of NPQ in the first induction/relaxation.

(18) FIG. 17. NPQ components (qE, qZ, and qI) association with conversion of violaxanthin to zeaxanthin.

(19) FIG. 18. Transient overexpression of NPQ-related genes in Nicotiana benthamiana. The upper left panel shows NPQ measurements on leaf spots overexpressing FLAG-tagged PsbS, VDE, ZEP, and GUS as a negative control, during 13 min illumination at 600 mol photons m-2 s-1 (white bar), followed by 10 min of dark (black bar). Error bars represent standard deviation (n=6). The upper right panel shows the false-color image of NPQ of a leaf expressing PSBS, VDE, ZEP and GUS 10 min after high light exposure. Rainbow bar indicates relative amount of NPQ. The lower panel shows the immunoblot analysis of tissue collected from the leaf in the upper right panel and probed with anti-FLAG.

(20) FIG. 19. Transient co-overexpression of VDE and ZEP in Nicotiana benthamiana speeds up NPQ induction and relaxation. Error bars represent standard error (n=4).

(21) FIG. 20. NPQ kinetics of transgenic T.sub.1 progeny. NPQ measurements with DUAL PAM were taken on the youngest fully developed leaf of T.sub.1 adult plants for three different lines: one wild-type segregant (Null), one overexpressing ZEP (ZEP) and one overexpressing ZEP and VDE (ZEP-VDE), during 10 min illumination at 600 mol photons m-2 s-1 (white bar), followed by 10 min of dark (black bar). Each curve corresponds to the average NPQ measurement of three different plants; error bars indicate standard error (n=3).

(22) FIG. 21. Photosystem II quantum yield (YID of stable transgenic T.sub.1 plants of Nicotiana tabacum cv. Petite Havana.

(23) FIG. 22. Growth experiment in the greenhouse. Four sets of plants are shown in the figure, one per transgenic line. Each set contains 36 plants.

(24) FIG. 23. Transient overexpression of NbPsbS and RbcslaAtZEP+GapalAtPsbS+Fba2AtVDE constructs in N. benthamiana.

(25) FIG. 24. Amino acid alignment of NPQ genes in representative plant species for (A) PsbS, (B) ZEP and (C) VDE.

(26) FIG. 25. Levels of mRNA and protein of VDE, PsbS, and ZEP in leaves of transgenic tobacco plants grown under greenhouse conditions. (A, C, and E) mRNA levels relative to actin and tubulin. (B, D, and F) Protein levels relative to wild type (WT), determined from densitometry on immunoblots. Error bars indicate standard error of measurement (SEM) (n=5 biological replicates), and asterisks indicate significant differences between VPZ lines and WT (=0.05). (G) Representative immunoblots for VDE, PsbS, and ZEP.

(27) FIG. 26. Levels of mRNA and protein of VDE, PsbS, and ZEP in leaves of transgenic tobacco plants grown under field conditions. (A, C, E) mRNA levels relative to actin and tubulin. (B, D, F) Protein levels relative to wild type (WT), determined from densitometry on immunoblots. Error bars indicate SEM (n=4), and asterisk indicates significant differences between VPZ lines and WT (=0.05).

(28) FIG. 27. NPQ relaxation kinetics in transgenic cowpea 1643B1. X-axis is time in seconds. Y-axis is normalized NPQ.

(29) FIG. 28. NPQ induction and relaxation kinetics in transgenic cowpea 1643B1. X-axis is time. Y-axis is NPQ divided by 4.

(30) FIG. 29. Normalized NPQ induction and relaxation kinetics under fluctuating light in transgenic cowpea 1643B1. X-axis is time. Y-axis is NPQ divided by 4. Data is normalized to the highest NPQ within each set.

(31) FIG. 30. NPQ induction and relaxation kinetics in transgenic cowpea CP472A. X-axis is time. Y-axis is NPQ divided by 4.

(32) FIG. 31. NPQ induction and relaxation kinetics in nine transgenic rice lines.

(33) FIG. 32. Average NPQ induction and relaxation kinetics in transgenic rice.

DETAILED DESCRIPTION

(34) The plants, vectors, and methods now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the invention are shown. Indeed, the invention may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements.

(35) Likewise, many modifications and other embodiments of the plants, vectors, and methods described herein will come to mind to one of skill in the art to which the invention pertains having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the invention is not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

(36) Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of skill in the art to which the invention pertains. Although any methods and materials similar to or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described herein.

Definitions

(37) Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Lewin, Genes VII, 2001 (Oxford University Press), The Encyclopedia of Molecular Biology, Kendrew et al, eds., 1999 (Wiley-Interscience) and Molecular Biology and Biotechnology, a Comprehensive Desk Reference, Robert A. Meyers, ed., 1995 (VCH Publishers. Inc), Current Protocols In Molecular Biology, F. M. Ausubel et al., eds., 1987 (Green Publishing), Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3rd edition, 2001.

(38) The terms polynucleotide, nucleotide, nucleotide sequence, nucleic acid, gene, and oligonucleotide are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.

(39) As used herein, a vector is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. The vectors described herein can be expression vectors.

(40) As used herein, an expression vector is a vector that includes one or more expression control sequences.

(41) As used herein, an expression control sequence or expression cassette is a DNA sequence that controls and regulates the transcription and/or translation of another DNA sequence. The expression control sequence can comprise a heterologous or non-heterologous promoter.

(42) As used herein, operably linked means incorporated into a genetic construct so that expression control sequences effectively control expression of a coding sequence of interest.

(43) As used herein, transformed and transfected encompass the introduction of a nucleic acid (e.g., a vector) into a cell by a number of techniques known in the art.

(44) Plasmids are designated by a lower case p preceded and/or followed by capital letters and/or numbers.

(45) As used herein, the term level of expression refers to the measurable expression level of a given nucleic acid or polypeptide. The level of expression of a given nucleic acid or polypeptide is determined by methods well known in the art. The term differentially expressed or differential expression refers to an increase or decrease in the measurable expression level of a given a given nucleic acid or polypeptide. Differentially expressed or differential expression means a 1-fold, or more, up to and including 2-fold, 5-fold, 10-fold, 20-fold, 50-fold or more difference in the level of expression of a given nucleic acid or polypeptide in two samples used for comparison. A given nucleic acid or polypeptide is also said to be differentially expressed in two samples if one of the two samples contains no detectable expression of a given nucleic acid or polypeptide.

(46) Polymorphism refers to variation in nucleotide sequences within a genome that may or may not have a functional consequence. These variants can be developed as genetic markers and used in all aspects of genetic investigation including the analysis of associating genetic differences with variation in traits of interest. As used herein, the term polymorphism includes, but is not limited to, single nucleotide polymorphism (SNP), insertion/deletion (InDel), simple sequence repeats (SSR), presence/absence variation (PAV), and copy number variation (CNV). Polymorphisms can be naturally occurring or artificially induced. The methods of inducing and detecting polymorphisms are well known in the art.

(47) As used herein, the term promoter refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. An enhancer is a DNA sequence that can stimulate promoter activity, and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, and/or comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of some variation may have identical promoter activity. As is well-known in the art, promoters can be categorized according to their strength and/or the conditions under which they are active, e.g., constitutive promoters, strong promoters, weak promoters, inducible/repressible promoters, tissue-specific/developmentally regulated promoters, cell-cycle dependent promoters, etc.

(48) As used herein, the term genome editing is a type of genetic engineering in which DNA is inserted, replaced, or removed from a genome using artificially engineered nucleases, or molecular scissors. It is a useful tool to elucidate the function and effect of a gene in a sequence specific manner, and to make alterations within a genome that result in desirable phenotypic changes. Genome editing systems include, but are not limited to, meganucleases, zinc finger nucleases (ZFN), transcription activator-like effector-based nucleases (TALEN), and the clustered regularly interspaced short palindromic repeats (CRISPR).

(49) The term plant refers to any of various photosynthetic, eukaryotic multi-cellular organisms of the kingdom Plantae, characteristically producing embryos, containing chloroplasts, having cellulose cell walls and lacking locomotion. As used herein, a plant includes any plant or part of a plant at any stage of development, including seeds, suspension cultures, plant cells, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, microspores, and progeny thereof. Also included are cuttings, and cell or tissue cultures. As used in conjunction with the present disclosure, plant tissue includes, for example, whole plants, plant cells, plant organs, e.g., leafs, stems, roots, meristems, plant seeds, protoplasts, callus, cell cultures, and any groups of plant cells organized into structural and/or functional units.

(50) The term plant is used in its broadest sense. It includes, but is not limited to, any species of woody, ornamental or decorative, crop or cereal, fruit or vegetable plant, and algae (e.g., Chlamydomonas reinhardtii). It also refers to a plurality of plant cells that is largely differentiated into a structure that is present at any stage of a plant's development. Such structures include, but are not limited to, a fruit, shoot, stem, leaf, flower petal, etc.

(51) The term control plant or wild type as used herein refers to a plant cell, an explant, seed, plant component, plant tissue, plant organ, or whole plant used to compare against transgenic or genetically modified plant for the purpose of identifying an enhanced phenotype or a desirable trait in the transgenic or genetically modified plant. A control plant may in some cases be a transgenic plant line that comprises an empty vector or marker gene, but does not contain the recombinant polynucleotide of interest that is present in the transgenic or genetically modified plant being evaluated. A control plant may be a plant of the same line or variety as the transgenic or genetically modified plant being tested, or it may be another line or variety, such as a plant known to have a specific phenotype, characteristic, or known genotype. A suitable control plant would include a genetically unaltered or non-transgenic plant of the parental line used to generate a transgenic plant herein.

(52) The term plant tissue includes differentiated and undifferentiated tissues of plants including those present in roots, shoots, leaves, inflorescences, anthers, pollen, ovaries, seeds and tumors, as well as cells in culture (e.g., single cells, protoplasts, embryos, callus, etc.). Plant tissue may be in planta, in organ culture, tissue culture, or cell culture.

(53) The term plant part as used herein refers to a plant structure, a plant organ, or a plant tissue.

(54) A non-naturally occurring plant refers to a plant that does not occur in nature without human intervention. Non-naturally occurring plants include transgenic plants, plants created through genetic engineering and plants produced by non-transgenic means such as traditional or market assisted plant breeding.

(55) The term plant cell refers to a structural and physiological unit of a plant, comprising a protoplast and a cell wall. The plant cell may be in the form of an isolated single cell or a cultured cell, or as a part of a higher organized unit such as, for example, a plant tissue, a plant organ, or a whole plant. The term plant cell culture refers to cultures of plant units such as, for example, protoplasts, cells and cell clusters in a liquid medium or on a solid medium, cells in plant tissues and organs, microspores and pollen, pollen tubes, anthers, ovules, embryo sacs, zygotes and embryos at various stages of development.

(56) The term plant material refers to leaves, stems, roots, inflorescences and flowers or flower parts, fruits, pollen, anthers, egg cells, zygotes, seeds, cuttings, cell or tissue cultures, or any other part or product of a plant.

(57) A plant organ refers to a distinct and visibly structured and differentiated part of a plant, such as a root, stem, leaf, flower bud, inflorescence, spikelet, floret, seed or embryo.

(58) The term crop plant, means in particular monocotyledons such as cereals (wheat, millet, sorghum, rye, triticale, oats, barley, teff, spelt, buckwheat, fonio and quinoa), rice, maize (corn), and/or sugar cane; or dicotyledon crops such as beet (such as sugar beet or fodder beet); fruits (such as pomes, stone fruits or soft fruits, for example apples, pears, plums, peaches, almonds, cherries, strawberries, raspberries or blackberries); leguminous plants (such as beans, lentils, peas or soybeans); oil plants (such as rape, mustard, poppy, olives, sunflowers, coconut, castor oil plants, cocoa beans or groundnuts); cucumber plants (such as marrows, cucumbers or melons); fiber plants (such as cotton, flax, hemp or jute); citrus fruit (such as oranges, lemons, grapefruit or mandarins); vegetables (such as spinach, lettuce, cabbages, carrots, tomatoes, potatoes, cucurbits or paprika); lauraceae (such as avocados, cinnamon or camphor); tobacco; nuts; coffee; tea; vines; hops; durian; bananas; natural rubber plants; and ornamentals (such as flowers, shrubs, broad-leaved trees or evergreens, for example conifers). This list does not represent any limitation.

(59) The term woody crop or woody plant means a plant that produces wood as its structural tissue. Woody crops include trees, shrubs, or lianas. Examples of woody crops include, but are not limited to, thornless locust, hybrid chestnut, black walnut, Japanese maple, eucalyptus, casuarina, spruce, fir, pine (e.g. Pinus radiata and Pinus caribaea), and flowering dogwood.

(60) The term improved growth or increased growth is used herein in its broadest sense. It includes any improvement or enhancement in the process of plant growth and development. Examples of improved growth include, but are not limited to, increased photosynthetic efficiency, increased biomass, increased yield, increased seed number, increased seed weight, increased stem height, increased leaf area, and increased plant dry weight,

(61) By quantum yield it is meant the moles of CO.sub.2 fixed per mole of quanta (photons) absorbed, or else the efficiency with which light is converted into fixed carbon. The quantum yield of photosynthesis is derived from measurements of light intensity and rate of photosynthesis. As such, the quantum yield is a measure of the efficiency with which absorbed light produces a particular effect. The amount of photosynthesis performed in a plant cell or plant can be indirectly detected by measuring the amount of starch produced by the transgenic plant or plant cell. The amount of photosynthesis in a plant cell culture or a plant can also be detected using a CO.sub.2 detector (e.g., a decrease or consumption of CO.sub.2 indicates an increased level of photosynthesis) or a 02 detector (e.g., an increase in the levels of 02 indicates an increased level of photosynthesis (see, e.g., the methods described in Silva et al., Aquatic Biology 7:127-141, 2009; and Bai et al., Biotechnol. Lett. 33:1675-1681, 2011). Photosynthesis can also be measured using radioactively labeled CO.sub.2 (e.g., 14CO.sub.2 and H.sub.14CO.sub.3) (see, e.g., the methods described in Silva et al., Aquatic Biology 7:127-141, 2009, and the references cited therein). Photosynthesis can also be measured by detecting the chlorophyll fluorescence (e.g., Silva et al., Aquatic Biology 7:127-141, 2009, and the references cited therein). Additional methods for detecting photosynthesis in a plant are described in Zhang et al., Mol. Biol. Rep. 38:4369-4379, 2011.

(62) In the physical sciences, the term relaxation means the return of a perturbed system into equilibrium, usually from a high energy level to a low energy level. As used herein, the term non-photochemical quenching relaxation or NPQ relaxation refers to the process in which NPQ level decreases upon transition from high light intensity to low light intensity.

(63) Reference to about a value or parameter herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to about a value or parameter herein includes (and describes) aspects that are directed to that value or parameter per se. For example, description referring to about X includes description of X.

(64) Overview

(65) Faced with a fast growing world population, further increases in food production are imperative for global political and societal stability, and as such, a two-fold increase of crop production has been projected necessary to meet this demand by 2050. A better understanding of physiological processes underlying important crop traits such as photosynthesis is hence key to ameliorating world's food security crisis. Photosynthesis is a process used by plants and green algae to convert light energy into chemical energy that can be later released to fuel the organisms' activities, during which atmospheric carbon dioxide (CO.sub.2) is assimilated and oxygen is released. The ratio of the amount of CO.sub.2 being fixed or assimilated over the amount of photon (quantum) absorbed, also known as quantum yield, is commonly used as a measure of the photosynthetic efficiency of a plant.

(66) Although light is necessary for photosynthesis, damage can occur when leaves are exposed to high light intensity. To avoid this, plants have developed several photoprotective mechanisms. Non-photochemical quenching (NPQ) is one of those mechanisms, which allows excessive absorbed irradiance to be dissipated as heat. However, when a plant is transitioned from high to low light intensity, the quantum yield of photosynthesis is temporarily reduced, due to the fact that NPQ inhibits CO.sub.2 fixation. In addition, NPQ turns on (induces) rapidly at high light intensity, but turns off (relaxes) more slowly upon a return to limiting irradiance. As a result, the photosynthetic efficiency and growth of plants under fluctuating light, a common occurrence under natural field conditions, are compromised.

(67) The present disclosure provides a method to speed up the relaxation of NPQ after plants transition from high to low light intensity, thereby allowing a faster recovery of photosynthetic quantum yield of CO.sub.2 fixation. This method includes increasing expression of one or more nucleotide sequences encoding photosystem II subunit S (PsbS), zeaxanthin epoxidase (ZEP), and violaxanthin de-epoxidase (VDE). Since this is achieved without reducing the amplitude of NPQ, normal photoprotection under high light intensity is not affected. Under fluctuating light conditions, where plants frequently undergo transitions from high to low light intensity, this method results in improved photoprotection efficiency and in turn photosynthetic efficiency and growth of plants.

(68) The present disclosure further provides a method to genetically engineer plants for improved photosynthesis and growth. An expression vector comprising nucleotide sequences encoding PsbS, ZEP and VDE can be introduced into plants by currently available methods including, but not limited to, protoplast transformation, Agrobacterium-mediated transformation, electroporation, microprojectile bombardment. This method may be used to produce transgenic plants with improved photosynthesis and growth in plant species including, but not limited to, tobacco, wheat, maize, rice, soybean, sorghum, cassava, cowpea, poplar, and eucalyptus.

(69) It is well known in the art that mechanisms underlying NPQ response and the associated xanthophyll cycle are highly conserved across plants and green algae. See, e.g. Niyogi K K, Truong T B (2013). Evolution of flexible non-photochemical quenching mechanisms that regulate light harvesting in oxygenic photosynthesis. Curr Op Plant Biol 16: 307-314, Koziol A G, Borza T, Ishida K-I, Keeling P, Lee R W, Durnford D G (2007). Tracing the evolution of the light-harvesting antennae in chlorophyll a/b-containing organisms. Plant Physiol 143: 1802-1816, Engelken J, Brinkmann H, Adamska I (2010). Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily. BMC Evol Biol 10: 233, Brooks M D, Jansson S, Niyogi K K (2014). PsbS-dependent non-photochemical quenching. In: Non-photochemical quenching and energy dissipation in plants, algae and cyanobacteria. Demmig-Adams B, Garab G, Adams W W III, Govindjee eds. (Dordrecht: Springer), pp. 297-314, Kasajima I, Ebana K, Yamamoto T, Takahara K, Yano M, Kawai-Yamada M, Uchimiya H (2011). Molecular distinction in genetic regulation of nonphotochemical quenching in rice. Proc Natl Acad Sci USA 108:13835-13840, Alboresi A, Gerotto C, Giacometti G M, Bassi R, Morosinotto T (2010). Physcomitrella patens mutants affected on heat dissipation clarify the evolution of photoprotection mechanisms upon land colonization. Proc Natl Acad Sci USA 107:11128-11133, and Goss R, Lepetit B (2015). Biodiversity of NPQ. Journal of Plant Physiology, 172, 13-32. Therefore, methods disclosed in the present invention can be applied to all plants and green algae.

(70) Unless otherwise indicated, the disclosure encompasses all conventional techniques of plant transformation, plant breeding, microbiology, cell biology and recombinant DNA, which are within the skill of the art. See, e.g., Sambrook and Russell, Molecular Cloning: A Laboratory Manual, 3rd edition, 2001; Current Protocols in Molecular Biology, F. M. Ausubel et al. eds., 1987; Plant Breeding: Principles and Prospects, M. D. Hayward et al., 1993; Current Protocols in Protein Science, Coligan et al, eds., 1995, (John Wiley & Sons, Inc.); the series Methods in Enzymology (Academic Press, Inc.): PCR 2: A Practical Approach, M. J. MacPherson, B. D. Hames and G. R. Taylor eds., 1995.

(71) In one aspect, a transgenic plant, or a portion of a plant, or a plant material, or a plant seed, or a plant cell is provided, comprising one or more heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE operably linked to an expression control sequence. In one embodiment, the PsbS polypeptide is encoded by the nucleotide sequence of SEQ ID NO: 1, the ZEP polypeptide is encoded by the nucleotide sequence of SEQ ID NO:2, and the VDE polypeptide is encoded by the nucleotide sequence of SEQ ID NO: 3. In another embodiment, the transgenic plant comprises nucleotide sequences encoding PsbS, ZEP and VDE. The transgenic plant may comprise any combination of at least two of PsbS, ZEP and VDE, or comprise only one of PsbS, ZEP and VDE. The nucleotide sequences may have at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% sequence identity to SEQ ID NO: 1, SEQ ID NO:2, and/or SEQ ID NO:3. In another embodiment, the PsbS polypeptide has the amino acid sequence of SEQ ID NO: 4, the ZEP polypeptide has the amino acid sequence of SEQ ID NO:5, and the VDE polypeptide has the amino acid sequence of SEQ ID NO: 6. The polypeptides may be at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% amino acid sequence identity to SEQ ID NO: 4, SEQ ID NO:5, or SEQ ID NO:6. Homologues of Arabidopsis PsbS, Zep and VDE nucleotides and the polypeptides encoded by the nucleotide sequences exist in most species of plants, and the plants listed below, and may be used in place of the Arabidopsis genes.

(72) Enzymes having similar activity to PsbS, ZEP and VDE, or those having conserved domains could alternatively be used, including, but not limited to, homologues in switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, vegetable, forage, industrial, woody and biomass crops. PsbS has a conserved Chloroa_b-binding domain (SEQ ID NO: 7), ZEP comprises a NADB_Rossman and FHA superfamily domain (SEQ ID NO:8), and VDE has a Lipocalin domain (SEQ ID NO:9). Homologues having these domains could also be used.

(73) In another embodiment, the transgenic plant, or a portion of a plant, or a plant material, or a plant seed, or a plant cell is a crop plant, a model plant, a monocotyledonous plant, a dicotyledonous plant, a plant with Crassulacean acid metabolism (CAM) photosynthesis, a plant with C3 photosynthesis, a plant with C4 photosynthesis, an annual plant, a greenhouse plant, a horticultural flowering plant, a perennial plant, a switchgrass plant, a maize plant, a biomass plant, or a sugarcane plant. In another embodiment, the plant is selected from switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, vegetable, forage, industrial, woody and biomass crops. In a further embodiment, the transgenic plant is Nicotiana tabacum. In another embodiment, the plant has improved quantum yield and/or CO.sub.2 fixation under fluctuating light conditions, and/or improved growth. A balance of level of gene expression can play a role in plant improvements. In one embodiment, VDE and ZEP polypeptides are expressed at relatively similar levels.

(74) In another embodiment, the transgenic plant, or a portion of a plant, or a plant material, or a plant seed, or a plant cell has additional characteristics, for example, herbicide resistance, insect or pest resistance, disease resistance, modified fatty acid metabolism, and/or modified carbohydrate metabolism.

(75) In another aspect, an expression vector is provided, the expression vector comprising at least one expression control sequence operably linked to at least one nucleotide sequence encoding one or more polypeptides selected from PsbS, ZEP and VDE. In one embodiment, the vector comprises at least one expression control sequence comprising a promoter capable of driving expression of the nucleotide sequence encoding one or more polypeptides selected from PsbS, ZEP and VDE, in a plant, a portion of a plant, or a plant material, or a plant seed, or a plant cell. In another embodiment, the promoter is selected from Rbcs1A, GAPA-1 and FBA2. In a further embodiment, the vector comprises an Rbcs1A promoter drives expression of ZEP, a GAPA-1 promoter drives expression of PsbS, and an FBA2 promoter drives expression of VDE. In another embodiment, the vector is a T-DNA. In another embodiment, the vector comprises a vector as shown in FIG. 9. In another embodiment, the vector can express the nucleotide sequence encoding the PsbS, ZEP and VDE polypeptides in a plant, a portion of a plant, or a plant material, or a plant seed, or a plant cell of a crop plant, a model plant, a monocotyledonous plant, a dicotyledonous plant, a plant with Crassulacean acid metabolism (CAM) photosynthesis, a plant with C3 photosynthesis, a plant with C4 photosynthesis, an annual plant, a greenhouse plant, a horticultural flowering plant, a perennial plant, a switchgrass plant, a maize plant, a biomass plant, or a sugarcane plant. In another embodiment, the plant is selected from switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, vegetable, forage, industrial, woody and biomass crops.

(76) In another aspect, a transgenic plant, or a portion of a plant, or a plant material, or a plant seed is provided, comprising a recombinant vector as described herein.

(77) In another aspect, methods of increasing biomass production and/or carbon fixation and/or growth in a plant, or a portion of a plant, or a plant material, or a plant seed, or a plant cell are provided, the method comprising introducing into the genome of the plant, plant tissue, plant seed, or plant cell one or more nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE operably linked to one or more expression control sequences. It was found that incorporation of polypeptides encoded by the nucleotides SEQ ID NO: 1, SEQ ID NO: 2, and SEQ ID NO: 3 increased quantum yield, CO.sub.2 fixation under fluctuating light conditions, and improved plant growth. In one embodiment, the method comprises a recombinant vector as described herein.

(78) Transgenic Plants of the Disclosure

(79) In one aspect, provided herein is a transgenic plant having one or more heterologous nucleotide sequences encoding one or more polypeptides PsbS, ZEP, or VDE. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding PsbS. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding ZEP. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding VDE. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding PsbS and ZEP. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding PsbS and VDE. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding ZEP and VDE. In some embodiments, the transgenic plant has one or more heterologous nucleotide sequences encoding PsbS, ZEP and VDE.

(80) In some of the embodiments described above, the one or more heterologous nucleotide sequences are derived from a dicot. In some embodiments, the one or more heterologous nucleotide sequences are derived from a monocot. In some embodiments, the one or more heterologous nucleotide sequences are derived from Arabidopsis thaliana. In some embodiments, the one or more heterologous nucleotide sequences are derived from Zea mays. In some embodiments, the one or more heterologous nucleotide sequences are derived from Oryza sativa. In some embodiments, the one or more heterologous nucleotide sequences are derived from Sorghum bicolor. In some embodiments, the one or more heterologous nucleotide sequences are derived from Glycine max. In some embodiments, the one or more heterologous nucleotide sequences are derived from Vigna unguiculata. In some embodiments, the one or more heterologous nucleotide sequences are derived from Populus spp. In some embodiments, the one or more heterologous nucleotide sequences are derived from Eucalyptus spp. In some embodiments, the one or more heterologous nucleotide sequences are derived from Manihot esculenta. In some embodiments, the one or more heterologous nucleotide sequences are derived from Hordeum vulgare. In some embodiments, the one or more heterologous nucleotide sequences are derived from Solanum tuberosum. In some embodiments, the one or more heterologous nucleotide sequences are derived from Saccharum spp. In some embodiments, the one or more heterologous nucleotide sequences are derived from Medicago sativa. In some embodiments, the one or more heterologous nucleotide sequences are derived from switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(81) In some of the embodiments described above, the transcript level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, or at least about 30-fold, as compared to a control plant. In some embodiments, the protein level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold, as compared to a control plant.

(82) Photoprotection mechanism has a high degree of conservation among higher plants. The degree of conservation, or homology, can be analyzed through comparing sequences of nucleotides or amino acids of genes of interest. As used herein sequence identity refers to the percentage of residues that are identical in the same positions in the sequences being analyzed. Methods of alignment of sequences for comparison are well known to one of skill in the art, including, but not limited to, manual alignment and computer assisted sequence alignment and analysis. This latter approach is a preferred approach in the present disclosure, due to the increased throughput afforded by computer assisted methods. The determination of percent sequence identity between any two sequences can be accomplished using a mathematical algorithm. Examples of such mathematical algorithms are the algorithm of Myers and Miller, CABIOS 4:11-17 (1988); the local homology algorithm of Smith et al., Adv. Appl. Math. 2:482 (1981); the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443-453 (1970); the search-for-similarity-method of Pearson and Lipman, Proc. Natl. Acad. Sci. 85:2444-2448 (1988); the algorithm of Karlin and Altschul, Proc. Natl. Acad. Sci. USA 87:2264-2268 (1990), modified as in Karlin and Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5877 (1993). Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity and/or similarity. Such implementations include, for example: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the AlignX program, version10.3.0 (Invitrogen, Carlsbad, CA) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. Gene 73:237-244 (1988); Higgins et al. CABIOS 5:151-153 (1989); Corpet et al., Nucleic Acids Res. 16:10881-90 (1988); Huang et al. CABIOS 8:155-65 (1992); and Pearson et al., Meth. Mol. Biol. 24:307-331 (1994). The BLAST programs of Altschul et al. J. Mol. Biol. 215:403-410 (1990) are based on the algorithm of Karlin and Altschul (1990) supra.

(83) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identity to SEQ ID NO: 3. In some embodiments, PsbS has an amino acid sequence at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO: 8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(84) In some of the embodiments described above, the transgenic plant contains an expression vector, wherein the expression vector contains one or more nucleotide sequences described herein. In some embodiments, the transgenic plant produces a seed containing an expression vector that has one or more heterologous nucleotide sequences encoding any of PsbS, ZEP or VDE. In some embodiments, the seed that is derived from the transgenic plant further produces a progeny plant.

(85) In some of the embodiments described above, the transgenic plant has increased growth under fluctuating light conditions as compared to a control plant under fluctuating light conditions. In some embodiments, the transgenic plant has increased photosynthetic efficiency under fluctuating light conditions as compared to a control plant under fluctuating light conditions. In some embodiments, the transgenic plant has improved photoprotection efficiency under fluctuating light conditions as compared to a control plant under fluctuating light conditions. In some embodiments, the transgenic plant has improved quantum yield and CO.sub.2 fixation under fluctuating light conditions as compared to a control plant under fluctuating light conditions. In some embodiments, the transgenic plant is an elite line or elite strain. In some embodiments, the transgenic plant further includes expression of at least one additional polypeptide that provides herbicide resistance, insect or pest resistance, disease resistance, modified fatty acid metabolism, and/or modified carbohydrate metabolism.

(86) In some of the embodiments described above, the transcript level of VDE in the plant is increased 3-fold as compared to a control plant. In some of the embodiments described above, the transcript level of PsbS in the plant is increased 3-fold as compared to a control plant. In some of the embodiments described above, the transcript level of ZEP in the plant is increased 8-fold as compared to a control plant. In some of the embodiments described above, the transcript level of VDE in the plant is increased 10-fold as compared to a control plant. In some of the embodiments described above, the transcript level of PsbS in the plant is increased 3-fold as compared to a control plant. In some of the embodiments described above, the transcript level of ZEP in the plant is increased 6-fold as compared to a control plant. In some of the embodiments described above, the transcript level of VDE in the plant is increased 4-fold as compared to a control plant. In some of the embodiments described above, the transcript level of PsbS in the plant is increased 1.2-fold as compared to a control plant. In some of the embodiments described above, the transcript level of ZEP in the plant is increased 7-fold as compared to a control plant. In some of the embodiments described above, the protein level of VDE in the plant is increased 16-fold as compared to a control plant. In some of the embodiments described above, the protein level of PsbS in the plant is increased 2-fold as compared to a control plant. In some of the embodiments described above, the protein level of ZEP in the plant is increased 80-fold as compared to a control plant. In some of the embodiments described above, the protein level of VDE in the plant is increased 30-fold as compared to a control plant. In some of the embodiments described above, the protein level of PsbS in the plant is increased 4-fold as compared to a control plant. In some of the embodiments described above, the protein level of ZEP in the plant is increased 74-fold as compared to a control plant. In some of the embodiments described above, the protein level of VDE in the plant is increased 47-fold as compared to a control plant. In some of the embodiments described above, the protein level of PsbS in the plant is increased 3-fold as compared to a control plant. In some of the embodiments described above, the protein level of ZEP in the plant is increased 75-fold as compared to a control plant. In some of the embodiments described above, the increase of transcript level in the plant as compared to a control plant between VDE, PsbS and ZEP has a ratio of 3:3:8, 10:3:6, or 4:1.2:7. In some of the embodiments described above, the increase of protein level in the plant as compared to a control plant between VDE, PsbS and ZEP has a ratio of 16:2:80, 30:4:74, or 47:3:75. In some of the embodiments described above, the increase of transcript level of VDE in the plant as compared to a control plant is in the range of 3-fold to 10-fold. In some of the embodiments described above, the increase of transcript level of PsbS in the plant as compared to a control plant is from about 1.2-fold to about 3-fold. In some of the embodiments described above, the increase of transcript level of ZEP in the plant as compared to a control plant is from about 6-fold to about 8-fold. In some of the embodiments described above, the increase of protein level of VDE in the plant as compared to a control plant is in the range of 16-fold to 47-fold. In some of the embodiments described above, the increase of protein level of PsbS in the plant as compared to a control plant is from about 2-fold to about 4-fold. In some of the embodiments described above, the increase of protein level of ZEP in the plant as compared to a control plant is from about 74-fold to about 80-fold.

(87) Expression Vectors of the Disclosure

(88) In another aspect, the present disclosure relates to an expression vector having one or more nucleotide sequences encoding any of PsbS, ZEP, and VDE. In some embodiments, the expression vector has one or more nucleotide sequences encoding PsbS. In some embodiments, the expression vector has one or more nucleotide sequences encoding ZEP. In some embodiments, the expression vector has one or more nucleotide sequences encoding VDE. In some embodiments, the expression vector has one or more nucleotide sequences encoding PsbS and ZEP. In some embodiments, the expression vector has one or more nucleotide sequences encoding PsbS and VDE. In some embodiments, the expression vector has one or more nucleotide sequences encoding ZEP and VDE. In some embodiments, the expression vector has one or more nucleotide sequences encoding PsbS, ZEP and VDE.

(89) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identity to SEQ ID NO: 3. In some embodiments, PsbS has an amino acid sequence at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO: 8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(90) In some of the embodiments described above, the vector includes one or more expression control sequences having a promoter capable of driving expression of the nucleotide sequence of PsbS, ZEP, or VDE, in a plant. In some embodiments, the promoter is an inducible promoter. In some embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is a weak promoter. In some embodiments, the promoter is a tissue-specific promoter. In some embodiments, the promoter is a seed- and/or embryo-specific promoter. In some embodiments, the promoter is a leaf-specific promoter. In some embodiments, the promoter is a temporal-specific promoter. In some embodiments, the promoter is an anther- and/or pollen-specific promoter. In some embodiments, the promoter is a floral-specific promoter. In some embodiments, a combination of promoters is used in the expression vector.

(91) In some of the embodiments described above, the promoter is Rbcs1A, GAPA-1, or FBA2. In some embodiments, the Rbcs1A promoter drives expression of ZEP, a GAPA-1 promoter drives expression of PsbS, and an FBA2 promoter drives expression of VDE. In some embodiments, the vector is a T-DNA. In some embodiments, the expression vector further includes a nucleotide sequence encoding polypeptide that provides antibiotic resistance. In some embodiments, the expression vector further includes a left border (LB) and right border (RB) domain flanking the expression control sequences and the nucleotide sequence encoding the PsbS, ZEP and VDE polypeptides. In some embodiments, the expression vector is in a bacterial cell. In some embodiments, the expression vector is in an Agrobacterium cell.

(92) Methods of the Disclosure

(93) In certain other aspects, the present disclosure relates to methods of increasing photosynthesis and growth in a plant, including increasing expression in the plant of one or more polypeptides described herein.

(94) In some embodiments, the increased expression is achieved by introducing to a plant one or more heterologous nucleotide sequences encoding any of PsbS, ZEP and VDE. In some embodiments, the increased expression is achieved by modifying expression of the endogenous nucleotide sequences encoding any of PsbS, ZEP and VDE. In some embodiments, the increased expression is achieved by modifying the promoter of the endogenous nucleotide sequences encoding any of PsbS, ZEP and VDE. In some embodiments, the increased expression is achieved by modifying transcription factors that regulate the transcription efficiency of any of PsbS, ZEP and VDE. In some embodiments, the increased expression is achieved by increasing the stability of the mRNA of any of PsbS, ZEP and VDE. In some embodiments, the increased expression is achieved by optimizing codon usage of any of PsbS, ZEP and VDE in a target plant. In some embodiments, the increased expression is achieved by altering epigenetics in a plant. In some embodiments, the increased expression is achieved by altering DNA methylation in a plant. In some embodiments, the increased expression is achieved by altering histone modification in a plant. In some embodiments, the increased expression is achieved by altering small RNAs (sRNA) in a plant. In some embodiments, the increased expression is achieved by increasing the translation efficiency of any of PsbS, ZEP and VDE. In some embodiments, genome-editing techniques including, but not limited to, ZFN, TALEN and CRISPR are used to modify the nucleotide sequences regulating the expression of any of PsbS, ZEP and VDE.

(95) In some embodiments, the transcript level of VDE in the plant is increased 3-fold as compared to a control plant. In some embodiments, the transcript level of PsbS in the plant is increased 3-fold as compared to a control plant. In some embodiments, the transcript level of ZEP in the plant is increased 8-fold as compared to a control plant. In some embodiments, the transcript level of VDE in the plant is increased 10-fold as compared to a control plant. In some embodiments, the transcript level of PsbS in the plant is increased 3-fold as compared to a control plant. In some embodiments, the transcript level of ZEP in the plant is increased 6-fold as compared to a control plant. In some embodiments, the transcript level of VDE in the plant is increased 4-fold as compared to a control plant. In some embodiments, the transcript level of PsbS in the plant is increased 1.2-fold as compared to a control plant. In some embodiments, the transcript level of ZEP in the plant is increased 7-fold as compared to a control plant. In some embodiments, the protein level of VDE in the plant is increased 16-fold as compared to a control plant. In some embodiments, the protein level of PsbS in the plant is increased 2-fold as compared to a control plant. In some embodiments, the protein level of ZEP in the plant is increased 80-fold as compared to a control plant. In some embodiments, the protein level of VDE in the plant is increased 30-fold as compared to a control plant. In some embodiments, the protein level of PsbS in the plant is increased 4-fold as compared to a control plant. In some embodiments, the protein level of ZEP in the plant is increased 74-fold as compared to a control plant. In some embodiments, the protein level of VDE in the plant is increased 47-fold as compared to a control plant. In some embodiments, the protein level of PsbS in the plant is increased 3-fold as compared to a control plant. In some embodiments, the protein level of ZEP in the plant is increased 75-fold as compared to a control plant. In some embodiments, the increase of transcript level in the plant as compared to a control plant between VDE, PsbS and ZEP has a ratio of 3:3:8, 10:3:6, or 4:1.2:7. In some embodiments, the increase of protein level in the plant as compared to a control plant between VDE, PsbS and ZEP has a ratio of 16:2:80, 30:4:74, or 47:3:75. In some embodiments, the increase of transcript level of VDE in the plant as compared to a control plant is in the range of 3-fold to 10-fold. In some embodiments, the increase of transcript level of PsbS in the plant as compared to a control plant is from about 1.2-fold to about 3-fold. In some embodiments, the increase of transcript level of ZEP in the plant as compared to a control plant is from about 6-fold to about 8-fold. In some embodiments, the increase of protein level of VDE in the plant as compared to a control plant is in the range of 16-fold to 47-fold. In some embodiments, the increase of protein level of PsbS in the plant as compared to a control plant is from about 2-fold to about 4-fold. In some embodiments, the increase of protein level of ZEP in the plant as compared to a control plant is from about 74-fold to about 80-fold.

(96) Methods for Increasing Growth Under Fluctuating Light Conditions

(97) In one aspect, provided herein is a method for increasing growth in a plant under fluctuating light conditions, including increasing expression in the plant of PsbS, ZEP, and/or VDE, thereby producing a plant with increased expression of the one or more polypeptides as compared to a control plant. In some embodiments, the increased expression is in the form of increased transcript level. In some embodiments, the transcript level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, or at least about 30-fold, as compared to a control plant. In some embodiments, the increased expression is in the form of increased protein level. In some embodiments, the protein level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold, as compared to a control plant. In some embodiments, the method includes increasing expression of PsbS. In some embodiments, the method includes increasing expression of ZEP. In some embodiments, the method includes increasing expression of VDE. In some embodiments, the method includes increasing expression of PsbS and ZEP. In some embodiments, the method includes increasing expression of PsbS and VDE. In some embodiments, the method includes increasing expression of ZEP and VDE. In some embodiments, the method includes increasing expression of PsbS, ZEP and VDE.

(98) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(99) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(100) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(101) Methods for Increasing Photosynthetic Efficiency Under Fluctuating Light Conditions

(102) In another aspect, provided herein is a method for increasing photosynthetic efficiency in a plant under fluctuating light conditions, including increasing expression in the plant of any of PsbS, ZEP, or VDE, thereby producing a plant with increased expression of the one or more polypeptides as compared to a control plant. In some embodiments, the increased expression is in the form of increased transcript level. In some embodiments, the transcript level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, or at least about 30-fold, as compared to a control plant. In some embodiments, the increased expression is in the form of increased protein level. In some embodiments, the protein level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold, as compared to a control plant. In some embodiments, the method includes increasing expression of PsbS. In some embodiments, the method includes increasing expression of ZEP. In some embodiments, the method includes increasing expression of VDE. In some embodiments, the method includes increasing expression of PsbS and ZEP. In some embodiments, the method includes increasing expression of PsbS and VDE. In some embodiments, the method includes increasing expression of ZEP and VDE. In some embodiments, the method includes increasing expression of PsbS, ZEP and VDE.

(103) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(104) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(105) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(106) Methods for Increasing Photoprotection Efficiency Under Fluctuating Light Conditions

(107) In another aspect, provided herein is a method for increasing photoprotection efficiency in a plant under fluctuating light conditions, including increasing expression in the plant of PsbS, ZEP, and/or VDE, thereby producing a plant with increased expression of the one or more polypeptides as compared to a control plant. In some embodiments, the increased expression is in the form of increased transcript level. In some embodiments, the transcript level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, or at least about 30-fold, as compared to a control plant. In some embodiments, the increased expression is in the form of increased protein level. In some embodiments, the protein level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold, as compared to a control plant. In some embodiments, the method includes increasing expression of PsbS. In some embodiments, the method includes increasing expression of ZEP. In some embodiments, the method includes increasing expression of VDE. In some embodiments, the method includes increasing expression of PsbS and ZEP. In some embodiments, the method includes increasing expression of PsbS and VDE. In some embodiments, the method includes increasing expression of ZEP and VDE. In some embodiments, the method includes increasing expression of PsbS, ZEP and VDE.

(108) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(109) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(110) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(111) Methods for Increasing Quantum Yield and CO.sub.2 Fixation Under Fluctuating Light Conditions

(112) In another aspect, provided herein is a method for increasing quantum yield and CO.sub.2 fixation in a plant under fluctuating light conditions, including increasing expression in the plant of PsbS, ZEP, and/or VDE, thereby producing a plant with increased expression of the one or more polypeptides as compared to a control plant. In some embodiments, the increased expression is in the form of increased transcript level. In some embodiments, the transcript level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, or at least about 30-fold, as compared to a control plant. In some embodiments, the increased expression is in the form of increased protein level. In some embodiments, the protein level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold, as compared to a control plant. In some embodiments, the method includes increasing expression of PsbS. In some embodiments, the method includes increasing expression of ZEP. In some embodiments, the method includes increasing expression of VDE. In some embodiments, the method includes increasing expression of PsbS and ZEP. In some embodiments, the method includes increasing expression of PsbS and VDE. In some embodiments, the method includes increasing expression of ZEP and VDE. In some embodiments, the method includes increasing expression of PsbS, ZEP and VDE.

(113) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(114) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(115) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(116) Methods for Increasing the Rate of Relaxation of Non-Photochemical Quenching (NPQ) Under Fluctuating Light Conditions

(117) In another aspect, provided herein is a method for increasing the rate of relaxation of non-photochemical quenching (NPQ) in a plant, including increasing expression in the plant of PsbS, ZEP, and/or VDE, thereby producing a plant with increased expression of the one or more polypeptides as compared to a control plant. In some embodiments, the increased expression is in the form of increased transcript level. In some embodiments, the transcript level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 15-fold, at least about 20-fold, or at least about 30-fold, as compared to a control plant. In some embodiments, the increased expression is in the form of increased protein level. In some embodiments, the protein level of any of VDE, PsbS or ZEP is increased at least about 1-fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 20-fold, at least about 30-fold, at least about 40-fold, at least about 50-fold, at least about 60-fold, at least about 70-fold, at least about 80-fold, at least about 90-fold, or at least about 100-fold, as compared to a control plant. In some embodiments, the method includes increasing expression of PsbS. In some embodiments, the method includes increasing expression of ZEP. In some embodiments, the method includes increasing expression of VDE. In some embodiments, the method includes increasing expression of PsbS and ZEP. In some embodiments, the method includes increasing expression of PsbS and VDE. In some embodiments, the method includes increasing expression of ZEP and VDE. In some embodiments, the method includes increasing expression of PsbS, ZEP and VDE.

(118) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(119) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(120) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(121) Methods for Selecting a Plant for Improved Growth Characteristics Under Fluctuating Light Conditions

(122) In another aspect, provided herein are methods of selecting a plant for improved growth characteristics under fluctuating light conditions, including the steps of providing a population of plants; modifying the population of plants to increase the activity of any of PsbS, ZEP and VDE; detecting the level of non-photochemical quenching (NPQ) under fluctuating light conditions in a plant; comparing the level of NPQ under fluctuating light conditions in a plant with the control level of NPQ under fluctuating light conditions; and selecting a plant having increased rate of NPQ relaxation when the plant is transitioned from under high light intensity to low light intensity. In some embodiments, the control level of NPQ is the lowest level of NPQ in the population. In some embodiments, the control level of NPQ is the median level of NPQ in the population. In some embodiments, the control level of NPQ is the mean level of NPQ in the population. In some embodiments, the control level of NPQ is the level of NPQ in a control plant. In some embodiments, the population includes plants expressing heterologous sequences of PsbS, ZEP and/or VDE or in which the genome has been edited in order to increase expression of PsbS, ZEP, and/or VDE. In some embodiments, the genome editing technique is ZFN. In some embodiments, the genome editing technique is TALEN. In some embodiments, the genome editing technique is CRISPR. In some embodiments, the promoter of PsbS is modified. In some embodiments, the promoter of ZEP is modified. In some embodiments, the promoter of VDE is modified. In some embodiments, the population includes plants that have been treated to induce mutations in PsbS, ZEP and/or VDE. In some embodiments, the mutagen is EMS.

(123) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(124) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(125) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(126) Methods for Screening for a Polymorphism Associated with Improved Growth Characteristics Under Fluctuating Light Conditions

(127) In another aspect, provided herein are methods of screening for a nucleotide sequence polymorphism associated with improved growth characteristics under fluctuating light conditions, including the steps of providing a population of plants; obtaining the nucleotide sequences regulating and/or encoding any of PsbS, ZEP and VDE in the population of plants; obtaining one or more polymorphisms in the nucleotide sequences regulating and/or encoding any of PsbS, ZEP and VDE in the population of plants; detecting the rate of non-photochemical quenching (NPQ) relaxation upon transition from high light intensity to low light intensity in the population of plants; performing statistical analysis to determine association of the polymorphism with the rate of NPQ relaxation in the population of plants; and selecting the polymorphism having statistically significant association with the rate of NPQ relaxation. In some embodiments, the population is a collection of germplasm. In some embodiments, the population includes plants expressing heterologous sequences of PsbS, ZEP and/or VDE or in which the genome has been edited in order to increase expression of PsbS, ZEP, and/or VDE. In some embodiments, the population includes plants that have not been treated to induce mutations. In some embodiments, the population includes plants that have been treated to induce mutations in PsbS, ZEP and/or VDE. In some embodiments, the polymorphism is a single nucleotide polymorphism (SNP). In some embodiments, the polymorphism is an insertion/deletion (InDel). In some embodiments, the polymorphism is a simple sequence repeat (SSR). In some embodiments, the polymorphism is a presence/absence variation (PAV). In some embodiments, the polymorphism is a copy number variation (CNV). In some embodiments, the polymorphism is located in the promoter of PsbS. In some embodiments, the polymorphism is located in the promoter of ZEP. In some embodiments, the polymorphism is located in the promoter of VDE. In some embodiments, the polymorphism is detected by Sanger sequencing. In some embodiments, the polymorphism is detected by next-generation-sequencing. In some embodiments, the polymorphism is detected by agarose gel electrophoresis. In some embodiments, the polymorphism is detected by polyacrylamide gel electrophoresis. In some embodiments, the polymorphism is further used to screen a population different from the one from which the polymorphism is identified. In some embodiments, the polymorphism is further used as a target for genome editing in order to improve growth characteristics of a plant.

(128) In some of the embodiments described above, the improved growth characteristic is improved growth. In some embodiments, the improved growth characteristic is improved photosynthetic efficiency. In some embodiments, the improved growth characteristic is improved photoprotection efficiency. In some embodiments, the improved growth characteristic is improved quantum yield and CO.sub.2 fixation. In some embodiments, the improved growth characteristic is increased rate of relaxation of non-photochemical quenching (NPQ). In some embodiments, NPQ is detected using chlorophyll fluorescence imaging.

(129) In some of the embodiments described above, PsbS is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 1. In some embodiments, ZEP is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 2. In some embodiments, VDE is encoded by a nucleotide sequence having at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identity to SEQ ID NO: 3.

(130) In some of the embodiments described above, PsbS has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 4. In some embodiments, ZEP has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 5. In some embodiments, VDE has an amino acid sequence at least about 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99%, or 100% identical to SEQ ID NO: 6. In some embodiments, PsbS further includes a conserved domain of SEQ ID NO: 7. In some embodiments, ZEP further includes a conserved domain of SEQ ID NO:8. In some embodiments, VDE further includes a conserved domain of SEQ ID NO: 9.

(131) In some of the embodiments described above, the plant is Zea mays. In some embodiments, the plant is Oryza sativa. In some embodiments, the plant is Sorghum bicolor. In some embodiments, the plant is Glycine max. In some embodiments, the plant is Vigna unguiculata. In some embodiments, the plant is Populus spp. In some embodiments, the plant is Eucalyptus spp. In some embodiments, the plant is Manihot esculenta. In some embodiments, the plant is Hordeum vulgare. In some embodiments, the plant is Solanum tuberosum. In some embodiments, the plant is Saccharum spp. In some embodiments, the plant is Medicago sativa. In some embodiments, the plant is switchgrass, Miscanthus, Medicago, sweet sorghum, grain sorghum, sugarcane, energy cane, elephant grass, maize, cassava, cowpea, wheat, barley, oats, rice, soybean, oil palm, safflower, sesame, tobacco, flax, cotton, sunflower, Camelina, Brassica napus, Brassica carinata, Brassica juncea, pearl millet, foxtail millet, other grain, rice, oilseed, a vegetable crop, a forage crop, an industrial crop, a woody crop or a biomass crop.

(132) General Methods for Practice of the Embodiments Described Herein

(133) Transformation of Plants with Nucleotide Sequences of Interest

(134) Transgenic plants can be produced using conventional techniques to express any nucleotide sequence of interest in plants or plant cells (Methods in Molecular Biology, 2005, vol. 286, Transgenic Plants: Methods and Protocols, Pena L., ed., Humana Press, Inc. Totowa, NT). Typically, gene transfer, or transformation, is carried out using explants capable of regeneration to produce complete, fertile plants. Generally, a DNA or an RNA molecule to be introduced into the organism is part of a transformation vector. A large number of such vector systems known in the art may be used, such as plasmids. The components of the expression system can be modified, e.g., to increase expression of the introduced nucleic acids. For example, truncated sequences, nucleotide substitutions or other modifications may be employed. Expression systems known in the art may be used to transform virtually any plant cell under suitable conditions. A transgene comprising a DNA molecule encoding a gene of interest is preferably stably transformed and integrated into the genome of the host cells. Transformed cells are preferably regenerated into whole plants. Detailed description of transformation techniques are within the knowledge of those skilled in the art.

(135) Genetic Constructs for Transformation

(136) DNA constructs useful in the methods described herein include transformation vectors capable of introducing transgenes into plants. As used herein, transgenic refers to an organism in which a nucleic acid fragment containing a heterologous nucleotide sequence has been introduced. The transgenes in the transgenic organism are preferably stable and inheritable. The heterologous nucleic acid fragment may or may not be integrated into the host genome.

(137) Several plant transformation vector options are available, including those described in Gene Transfer to Plants, 1995, Potrykus et al, eds., Springer-Verlag Berlin Heidelberg New York, Transgenic Plants: A Production System for Industrial and Pharmaceutical Proteins, 1996, Owen et al, eds., John Wiley & Sons Ltd. England, and Methods in Plant Molecular Biology: A Laboratory Course Manual, 1995, Maliga et al., eds., Cold Spring Laboratory Press, New York. Plant transformation vectors generally include one or more coding sequences of interest under the transcriptional control of 5 and 3 regulatory sequences, including a promoter, a transcription termination and/or polyadenylation signal, and a selectable or screenable marker gene. For the expression of two or more polypeptides from a single transcript, additional RNA processing signals and ribozyme sequences can be engineered into the construct (U.S. Pat. No. 5,519,164). This approach has the advantage of locating multiple transgenes in a single locus, which is advantageous in subsequent plant breeding efforts. In one embodiment, the vector comprises at least one expression control sequence comprising a promoter capable of driving expression of the nucleotide sequence encoding one or more polypeptides selected from PsbS, ZEP and VDE, in a plant, a portion of a plant, or a plant material, or a plant seed, or a plant cell. In another embodiment, the promoter is selected from Rbcs1A, GAPA-1 and FBA2. In another embodiment, the RbcslA promoter drives expression of ZEP, a GAPA-1 promoter drives expression of PsbS, and an FBA2 promoter drives expression of VDE. In another embodiment, the vector is a T-DNA. In another embodiment, the vector is as shown in FIG. 9. Particular promoters and vectors that work in one plant type may not work in another, as known by one of skill in the art. Methods of making transgenic plants are well known in the art, as described herein.

(138) T-DNA

(139) Methods for introducing transgenes into plants by an Agrobacterium-mediated transformation method generally involve a T-DNA (transfer DNA) that incorporates the genetic elements of at least one transgene and transfers those genetic elements into the genome of a plant. The transgene(s) are typically constructed in a DNA plasmid vector and are usually flanked by an Agrobacterium Ti plasmid right border DNA region (RB) and a left border DNA region (LB). During the process of Agrobacterium-mediated transformation, the DNA plasmid is nicked by an endonuclease, VirD2, at the right and left border regions. A single strand of DNA from between the nicks, called the T-strand, is transferred from the Agrobacterium cell to the plant cell. The sequence corresponding to the T-DNA region is inserted into the plant genome.

(140) Integration of the T-DNA into the plant genome generally begins at the RB and continues to the end of the T-DNA, at the LB. However, endonucleases sometimes do not nick equally at both borders. When this happens, the T-DNA that is inserted into the plant genome often contains some or all of the plasmid vector DNA. This phenomenon is referred to as read-through. A desired approach is often that only the transgene(s) located between the right and left border regions (the T-DNA) is transferred into the plant genome without any of the adjacent plasmid vector DNA (the vector backbone). Vector backbone DNA contains various plasmid maintenance elements, including, for example, origin of replications, bacterial selectable marker genes, and other DNA fragments that are not required to express the desired trait(s) in plants.

(141) Engineered minichromosomes can also be used to express one or more genes in plant cells. Cloned telomeric repeats introduced into cells may truncate the distal portion of a chromosome by the formation of a new telomere at the integration site. Using this method, a vector for gene transfer can be prepared by trimming off the arms of a natural plant chromosome and adding an insertion site for large inserts (Yu et al., 2006, Proc. Natl. Acad. Sci. USA 103: 17331-17336; Yu et al., 2007, Proc. Natl. Acad. Sci. USA 104: 8924-8929).

(142) An alternative approach to chromosome engineering in plants involves in vivo assembly of autonomous plant minichromosomes (Carlson et al., 2007, PLoS Genet. 3: 1965-74). Plant cells can be transformed with centromeric sequences and screened for plants that have assembled autonomous chromosomes de novo. Useful constructs combine a selectable marker gene with genomic DNA fragments containing centromeric satellite and retroelement sequences and/or other repeats.

(143) Another approach useful to the described invention is Engineered Trait Loci (ETL) technology (U.S. Pat. No. 6,077,697; US 2006/0143732). This system targets DNA to a heterochromatic region of plant chromosomes, such as the pericentric heterochromatin, in the short arm of acrocentric chromosomes. Targeting sequences may include ribosomal DNA (rDNA) or lambda phage DNA. The pericentric rDNA region supports stable insertion, low recombination, and high levels of gene expression. This technology is also useful for stacking of multiple traits in a plant (US 2006/0246586).

(144) Zinc-finger nucleases (ZFN), TALEN and CRISPR-Cas9 are also useful for practicing the invention in that they allow double strand DNA cleavage at specific sites in plant chromosomes such that targeted gene insertion or deletion can be performed (Shukla et al., 2009, Nature 459: 437-441; Townsend et al, 2009, Nature 459: 442-445, WO 2015089427 A1).

(145) Tissue Culture-Based Methods for Nuclear Transformation

(146) Transformation protocols, as well as protocols for introducing nucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation.

(147) Suitable methods of introducing nucleotide sequences into plant cells and subsequent insertion into the plant genome are described in US 2010/0229256 A1 to Somleva & Ali and US 2012/0060413 to Somleva et al.

(148) The transformed cells are grown into plants in accordance with conventional techniques. See, for example, McCormick et al., 1986, Plant Cell Rep. 5: 81-84. These plants may then be grown, and either pollinated with the same transformed variety or different varieties, and the resulting hybrid having constitutive expression of the desired phenotypic characteristic identified. Two or more generations may be grown to ensure that constitutive expression of the desired phenotypic characteristic is stably maintained and inherited and then seeds harvested to ensure constitutive expression of the desired phenotypic characteristic has been achieved.

(149) In Planta Transformation Methods

(150) Procedures for in planta transformation are not complex. Tissue culture manipulations and possible somaclonal variations are avoided and only a short time is required to obtain transgenic plants. However, the frequency of transformants in the progeny of such inoculated plants is relatively low and variable. At present, there are very few species that can be routinely transformed in the absence of a tissue culture-based regeneration system. Stable Arabidopsis transformants can be obtained by several in planta methods including vacuum infiltration (Clough & Bent, 1998, The Plant J. 16: 735-743), transformation of germinating seeds (Feldmann & Marks, 1987, Mol. Gen. Genet. 208: 1-9), floral dip (Clough and Bent, 1998, Plant J. 16: 735-743), and floral spray (Chung et al., 2000, Transgenic Res. 9: 471-476). Other plants that have successfully been transformed by in planta methods include rapeseed and radish (vacuum infiltration, Ian and Hong, 2001, Transgenic Res., 10: 363-371; Desfeux et al., 2000, Plant Physiol. 123: 895-904), Medicago truncatula (vacuum infiltration, Trieu et al., 2000, Plant J. 22: 531-541), camelina (floral dip, WO/2009/1 17555 to Nguyen et al.), and wheat (floral dip, Zale et al., 2009, Plant Cell Rep. 28: 903-913). In planta methods have also been used for transformation of germ cells in maize (pollen, Wang et al. 2001, Acta Botanica Sin., 43, 275-279; Zhang et al, 2005, Euphytica, 144, 11-22; pistils, Chumakov et al. 2006, Russian J. Genetics, 42, 893-897; Mamontova et al. 2010, Russian J. Genetics, 46, 501-504) and Sorghum (pollen, Wang et al. 2007, Biotechnol. Appl. Biochem., 48, 79-83)

(151) Reporter Genes and Selectable Marker Genes

(152) Reporter genes and/or selectable marker genes may be included in an expression control sequence (expression cassette) as described in US Patent Applications 20100229256 and 20120060413, incorporated by reference herein. An expression cassette including a promoter sequence operably linked to a heterologous nucleotide sequence of interest can be used to transform any plant by any of the methods described above. Useful selectable marker genes and methods of selection transgenic lines for a range of different crop species are described in the examples herein.

(153) Nucleotide Sequence Expression in Plants

(154) Plant promoters can be selected to control the expression of the nucleotide sequence in different plant tissues or organelles for all of which methods are known to those skilled in the art (Gasser & Fraley, 1989, Science 244: 1293-1299).

(155) The choice of promoter(s) that can be used depends upon several factors, including, but not limited to, efficiency, selectability, inducibility, desired expression level, and/or preferential cell or tissue expression. It is a routine matter for one of skill in the art to modulate the expression of a nucleotide sequence by appropriately selecting and positioning promoters and other regulatory regions relative to that sequence. Examples of promoters that can be used are known in the art. Promoters that can be used include those present in plant genomes, as well as promoters from other sources. Some suitable promoters initiate transcription only, or predominantly, in certain cell types. Methods for identifying and characterizing promoter regions in plant genomic DNA include, for example, those described in Jordano, et al., Plant Cell 1:855-866, 1989; Bustos, et al., Plant Cell 1:839-854, 1989; Green, et al., EMBO J. 7:4035-4044, 1988; Meier et al., Plant Cell 3:309-316, 1991; and Zhang et al., Plant Physiology 110: 1069-1079, 1996.

(156) Additional examples of promoters that can be used include ribulose-1,5-bisphosphate carboxylase (RbcS) promoters, such as the RbcS promoter from Eastern larch (Larix laricina), the pine cab6 promoter (Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994), the Cab-1 gene promoter from wheat (Fejes et al., Plant Mol. Biol. 15:921-932, 1990), the CAB-1 promoter from spinach (Lubberstedt et al., Plant Physiol. 104:997-1006, 1994), the cab1R promoter from rice (Luan et al., Plant Cell 4:971-981, 1992), the GAPA-1 promoters from maize, the FBA2 promoter from Saccharomyces cerevisiae, the pyruvate orthophosphate dikinase (PPDK) promoter from maize (Matsuoka et al., Proc. Natl. Acad. Sci. U.S.A. 90:9586-9590, 1993), the tobacco Lhcb1*2 promoter (Cerdan et al., Plant Mol. Biol. 33:245-255, 1997), the Arabidopsis thaliana SUC2 sucrose-H.sup.+ symporter promoter (Truernit et al., Planta 196:564-570, 1995), and thylakoid membrane protein promoters from spinach (psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, and rbcS). Additional exemplary promoters that can be used to drive gene transcription in stems, leafs, and green tissue are described in U.S. Patent Application Publication No. 2007/0006346, herein incorporated by reference in its entirety. Additional promoters that result in preferential expression in plant green tissues include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al., Plant Mol. Biol. 20:81-93, 1992), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al., Plant Cell Physiol. 41(1):42-48, 2000).

(157) Inducible Promoters

(158) Chemical-regulated promoters can be used to modulate the expression of a nucleotide sequence in a plant through the application of an exogenous chemical regulator. Depending upon the objective, the promoter may be a chemical-inducible promoter, where application of the chemical induces gene expression, or a chemical-repressible promoter, where application of the chemical represses gene expression. Chemical-inducible promoters are known in the art and include, but are not limited to, the maize ln2-2 promoter, which is activated by benzenesulfonamide herbicide safeners, the maize GST promoter, which is activated by hydrophobic electrophlic compounds that are used as pre-emergent herbicides, and the tobacco PR-1 promoter which is activated by salicylic acid. Other chemical-regulated promoters include steroid-responsive promoters [see, for example, the glucocorticoid-inducible promoter (Schena et al, 1991, Proc. Natl. Acad. Sci. USA 88: 10421-10425; McNellis et al., 1998, Plant 14:247-257) and tetracycline-inducible and tetracycline-repressible promoters (see, for example, Gatz et al., 1991, Mol. Gen. Genet. 227: 229-237; U.S. Pat. Nos. 5,814,618 and 5,789,156, herein incorporated by reference in their entirety). A three-component osmotically inducible expression system suitable for plant metabolic engineering has recently been reported (Feng et al, 2011, PLoS ONE 6: 1-9).

(159) Constitutive Promoters

(160) Constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Pat. No. 6,072,050, the core CaMV 35S promoter (Odell et al., 1985, Nature 313: 810-812), rice actin (McElroy et al., 1990, Plant Cell 2: 163-171), ubiquitin (Christensen et al., 1989, Plant Mol. Biol. 12: 619-632; Christensen et al, 1992, Plant Mol. Biol. 18: 675-689), pEMU (Last et al, 1991, Theor. Appl. Genet. 81: 581-588), MAS (Velten et al., 1984, EMBO J. 3: 2723-2730), and ALS promoter (U.S. Pat. No. 5,659,026). Other constitutive promoters are described in U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5,608,142.

(161) Weak Promoters

(162) Where low level expression is desired, weak promoters may be used. Generally, the term weak promoter is intended to describe a promoter that drives expression of a nucleotide sequence at a low level. Where a promoter is expressed at unacceptably high levels, portions of the promoter sequence can be deleted or modified to decrease expression levels. Such weak constitutive promoters include, for example, the core promoter of the Rsyn7 promoter (WO 99/43838 and U.S. Pat. No. 6,072,050).

(163) Tissue Specific Promoters

(164) Tissue-preferred promoters can be used to target gene expression within a particular tissue. Compared to chemically inducible systems, developmentally and spatially regulated stimuli are less dependent on penetration of external factors into plant sells. Tissue-preferred promoters include those described by Van Ex et al., 2009, Plant Cell Rep. 28: 1509-1520; Yamamoto et al, 1997, Plant J. 12: 255-265; Kawamata et al., 1997, Plant Cell Physiol. 38: 792-803; Hansen et al., 1997, Mol. Gen. Genet. 254: 337-343; Russell et al., 199), Transgenic Res. 6: 157-168; Rinehart et al., 1996, Plant Physiol. 1 12: 1331-1341; Van Camp et al., 1996, Plant Physiol. 112: 525-535; Canevascini et al., 1996, Plant Physiol. 1 12: 513-524; Yamamoto et al., 1994, Plant Cell Physiol. 35: 773-778; Lam, 1994, Results Probl. Cell Differ. 20: 181-196, Orozco et al., 1993, Plant Mol. Biol. 23: 1 129-1 138; Matsuoka et al., 1993, Proc. Natl. Acad. Sci. USA 90: 9586-9590, and Guevara-Garcia et al, 1993, Plant J. 4: 495-505. Such promoters can be modified, if necessary, for weak expression.

(165) Seed/Embryo Specific Promoters

(166) Seed-preferred promoters include both seed-specific promoters (those promoters active during seed development such as promoters of seed storage proteins) as well as seed-germinating promoters (those promoters active during seed germination). See Thompson et al., 1989, BioEssays 10: 108-1 13, herein incorporated by reference. Such seed-preferred promoters include, but are not limited to, Cim1 (cytokinin-induced message), cZ19B1 (maize 19 kDa zein), milps (myo-inositol-1-phosphate synthase), and celA (cellulose synthase). Gamma-zein is a preferred endosperm-specific promoter. Glob-1 is a preferred embryo-specific promoter. For dicots, seed-specific promoters include, but are not limited to, bean -phaseolin, napin, -conglycinin, soybean lectin, cruciferin, and the like. For monocots, seed-specific promoters include, but are not limited to, maize 15 kDa zein, 22 kDa zein, 27 kDa zein, g-zein, waxy, shrunken 1, shrunken 2, and globulin 1. The stage specific developmental promoter of the late embryogenesis abundant protein gene LEA has successfully been used to drive a recombination system for excision-mediated expression of a lethal gene at late embryogenesis stages in the seed terminator technology (U.S. Pat. No. 5,723,765 to Oliver et al.).

(167) Leaf Specific Promoters

(168) Leaf-specific promoters are known in the art. See, for example, WO/2011/041499 and U.S. Patent No. 2011/0179511 A1 to Thilmony et al.; Yamamoto et al., 1997, Plant J. 12: 255-265; Kwon et al., 1994, Plant Physiol. 105: 357-367; Yamamoto et al, 1994, Plant Cell Physiol. 35: 773-778; Gotor et al, 1993, Plant J. 3: 509-518; Orozco et al., 1993, Plant Mol. Biol. 23: 1 129-1 138, and Matsuoka et al, 1993, Proc. Natl. Acad. Sci. USA 90: 9586-9590.

(169) Temporal Specific Promoters

(170) Also contemplated are temporal promoters that can be utilized during the developmental time frame, for example, switched on after plant reaches maturity in leaf to enhance carbon flow.

(171) Anther/Pollen Specific Promoters

(172) Numerous genes specifically expressed in anthers and/or pollen have been identified and their functions in pollen development and fertility have been characterized. The specificity of these genes has been found to be regulated mainly by their promoters at the transcription level (Ariizumi et al., 2002, Plant Cell Rep. 21: 90-96 and references therein). A large number of anther- and/or pollen-specific promoters and their key ds-elements from different plant species have been isolated and functionally analyzed.

(173) Floral Specific Promoters

(174) Floral-preferred promoters include, but are not limited to, CHS (Liu et al., 201 1, Plant Cell Rep. 30: 2187-2194), OsMADS45 (Bai et al., 2008, Transgenic Res. 17: 1035-1043), PSC (Liu et al, 2008, Plant Cell Rep. 27: 995-1004), LEAFY, AGAMOUS, and API (Van Ex et al., 2009, Plant Cell Rep. 28: 1509-1520), API (Verweire et al, 2007, Plant Physiol. 145: 1220-1231), PtAGIP (Yang et al, 201 1, Plant Mol. Biol. Rep. 29: 162-170), Leml (Somleva & Blechl, 2005, Cereal Res. Comm. 33: 665-671; Skadsen et al, 2002, Plant Mol. Biol. 45: 545-555), Lem2 (Abebe et al., 2005, Plant Biotechnol. J. 4: 35-44), AGL6 and AGL13 (Schauer et al., 2009, Plant J. 59: 987-1000).

(175) Combinations of Promoters

(176) Certain embodiments use transgenic plants or plant cells having multi-gene expression constructs harboring more than one promoter. The promoters can be the same or different.

(177) Any of the described promoters can be used to control the expression of one or more of the nucleotide sequences of the invention, their homologues and/or orthologues as well as any other genes of interest in a defined spatiotemporal manner.

(178) Maize Promoters

(179) Transgenic DNA constructs used for transforming plant cells will comprise the heterologous nucleotides which one desires to introduced into and a promoter to express the heterologous nucleotides in the host maize cells. As is well known in the art such constructs can further include elements such as regulatory elements, 3 untranslated regions (such as polyadenylation sites), transit or signal peptides and marker genes elements as desired. 1. Regulatory Elements A number of promoters that are active in plant cells have been described in the literature both constitutive and tissue specific promoters and inducible promoters. See the background section of U.S. Pat. No. 6,437,217 for a description of a wide variety of promoters that are functional in plants. Such promoters include the nopaline synthase (NOS) and octopine synthase (OCS) promoters that are carried on tumor-inducing plasmids of Agrobacterium tumefaciens, the caulimovirus promoters such as the cauliflower mosaic virus (CaMV) 19S and 35S promoters and the figwort mosaic virus (FMV) 35S promoter, the enhanced CaMV35S promoter (e35S), the light-inducible promoter from the small subunit of ribulose bisphosphate carboxylase (ssRUBISCO, a very abundant plant polypeptide). For instance, see U.S. Pat. No. 6,437,217 which discloses a maize RS81 promoter, 5,641,876 which discloses a rice actin promoter, 6,426,446 which discloses a maize RS324 promoter, 6,429,362 which discloses a maize PR-1 promoter, 6,232,526 which discloses a maize A3 promoter and 6,177,611 which discloses constitutive maize promoters, all of which are incorporated herein by reference.

(180) Requirements for Construction of Plant Expression Cassettes

(181) Nucleotide sequences intended for expression in transgenic plants are first assembled in expression cassettes behind a suitable promoter active in plants. The expression cassettes may also include any further sequences required or selected for the expression of the transgene. Such sequences include, but are not restricted to, transcription terminators, extraneous sequences to enhance expression such as introns, vital sequences, and sequences intended for the targeting of the gene product to specific organelles and cell compartments. These expression cassettes can then be transferred to the plant transformation vectors described herein. The following is a description of various components of typical expression cassettes.

(182) Transcriptional Terminators

(183) A variety of transcriptional terminators are available for use in expression cassettes. These are responsible for the termination of transcription beyond the transgene and the correct polyadenylation of the transcripts. Appropriate transcriptional terminators are those that are known to function in plants and include the CaMV 35S terminator, the tml terminator, the nopaline synthase terminator and the pea rbcS E9 terminator. These are used in both monocotyledonous and dicotyledonous plants.

(184) Sequences for the Enhancement or Regulation of Expression

(185) Numerous sequences have been found to enhance gene expression from within the transcriptional unit and these sequences can be used in conjunction with the genes to increase their expression in transgenic plants. For example, various intron sequences such as introns of the maize Adhl gene have been shown to enhance expression, particularly in monocotyledonous cells. In addition, a number of non-translated leader sequences derived from viruses are also known to enhance expression, and these are particularly effective in dicotyledonous cells.

(186) Coding Sequence Optimization

(187) The coding sequence of the selected gene may be genetically engineered by altering the coding sequence for optimal expression in the crop species of interest. Methods for modifying coding sequences to achieve optimal expression in a particular crop species are well known (Perlak et al, 1991, Proc. Natl. Acad. Sci. USA 88: 3324 and Koziel et al., 1993, Biotechnology 11: 194-200).

(188) Construction of Plant Transformation Vectors

(189) Numerous vectors available for plant transformation are known to those of ordinary skill in the plant transformation arts. The genes pertinent to this disclosure can be used in conjunction with any such vectors. The choice of vector depends upon the selected transformation technique and the target species.

(190) Many vectors are available for transformation using Agrobacterium tumefaciens. These typically carry at least one T-DNA sequence and include vectors such as pBIN19. Typical vectors suitable for Agrobacterium transformation include the binary vectors pCIB200 and pCIB2001, as well as the binary vector pCIB 10 and hygromycin selection derivatives thereof (See, for example, U.S. Pat. No. 5,639,949).

(191) Transformation without the use of Agrobacterium tumefaciens circumvents the requirement for T-DNA sequences in the chosen transformation vector and consequently vectors lacking these sequences are utilized in addition to vectors such as the ones described above which contain T-DNA sequences. The choice of vector for transformation techniques that do not rely on Agrobacterium depends largely on the preferred selection for the species being transformed. Typical vectors suitable for non-Agrobacterium transformation include pCIB3064, pSOG 19, and pSOG35. (See, for example, U.S. Pat. No. 5,639,949).

(192) Transformation and Selection of Cultures and Plants

(193) Plant cultures can be transformed and selected using one or more of the methods described above which are well known to those skilled in the art.

(194) Manipulation of Endogenous Promoters

(195) Zinc-finger nucleases (ZFN), TALEN, and CRISPR-Cas9 are also useful for practicing the invention in that they allow double strand DNA cleavage at specific sites in plant chromosomes such that targeted gene insertion or deletion can be performed (Shukla et al., 2009, Nature 459: 437-441; Townsend et al, 2009, Nature 459: 442-445). This approach may be particularly useful for the present invention to modify the promoter of endogenous genes to modify expression of genes homologous to PsbS, ZEP and VDE, which are present in the genome of the plant of interest. In this case the ZFN, TALEN or CRISPR/Cas9 can be used to change the sequences regulating the expression of the TF of interest to increase the expression or alter the timing of expression beyond that found in a non-engineered or wild type plant.

EXAMPLES

(196) The present disclosure will be more fully understood by reference to the following examples. It should not, however, be construed as limiting the scope of the present disclosure. It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims.

Example 1. Transgenic Nicotiana tabacum

(197) Nicotiana tabacum plants were transformed with a T-DNA cassette containing three Arabidopsis thaliana genes. Arabidopsis ZEP was overexpressed to increase the rate of xanthophyll epoxidation and corresponding NPQ relaxation, together with Arabidopsis PsbS overexpression to stimulate the amplitude of qE formation and Arabidopsis VDE to maintain critical levels of zeaxanthin for ROS scavenging. The resulting transgenic plants are shown to have modified NPQ kinetics leading to higher quantum yield and CO.sub.2 fixation without loss of photo-protective efficiency under fluctuating light intensity and increased growth in two independent greenhouse experiments. These results confirm that photosynthetic efficiency is transiently limited by NPQ under fluctuating light intensity and provide the first proof of principle for improvement of photosynthetic efficiency and crop yield via changes in NPQ kinetics.

Example 2. NPQ and PSII Operating Efficiency in Young Seedlings

(198) Transient NPQ was determined from chlorophyll fluorescence imaging on T.sub.1 progeny of 20 independent transformation events with the vde-psbs-zep (VPZ) construct during 10 minutes of illumination with 1000 mol quanta m.sup.2 s.sup.1, followed by 10 minutes of dark relaxation. Since the aim was to maintain similar non-photochemical quenching capacity, lines with maximum levels of NPQ similar to WT were selected for further investigation. This yielded eight lines from which two lines harboring a single T-DNA copy (VPZ-34 and 56) and one line with two T-DNA insertions (VPZ-23) were included in the present work. All results are reported for homozygous T.sub.2 progeny. NPQ kinetic behavior showed substantial differences between the three VPZ lines and WT (FIG. 1A). NPQ in the VPZ lines rapidly increased, reaching the maximum NPQ level between two to four minutes, after which the level of NPQ stabilized (VPZ-23) or even slightly decreased (VPZ-34 and VPZ-56). In contrast, NPQ in the WT control continued to increase for seven minutes, after which the maximum level was retained for the remaining three minutes. As a result of these contrasting induction patterns, NPQ was significantly higher in all three transgenic lines during the initial five minutes of induction, but not in the final five minutes (FIG. 1A). After turning the lights off, NPQ relaxation was very rapid and very similar in both WT and VPZ lines.

(199) Repetitive cycles of light intensity between 2000 (3 min) and 200 (2 min) mol m.sup.2 s.sup.1 resulted in even more pronounced differences in NPQ between the VPZ lines and WT (FIG. 1B). NPQ in the VPZ lines increased rapidly during the high light phase of the first two cycles, reaching maximum levels during the second minute of the second cycle. In contrast, NPQ increased more slowly in the WT seedlings, only reaching maximum levels in the third minute of the fourth cycle. Interestingly, NPQ during the low light phase of the cycles showed the opposite pattern. In the first cycle, NPQ levels during the low light phase were higher in the VPZ lines, however NPQ levels in the second cycle were equal between the VPZ lines and WT, and were significantly lower in the VPZ lines in the final three cycles.

(200) Photosystem II (PSII) operating efficiency, estimated in conjunction with NPQ, showed no differences between VPZ lines and WT in the first cycle (FIG. 1C). However, during the five following cycles, VPZ lines showed superior PSII operating efficiency during the low light phase of the cycles, whereas no differences were found during the high light phase. This pattern was established in the second cycle, and repeated throughout the remainder of the experiment.

Example 3. Transcription and Protein Expression

(201) All three VPZ-lines showed significant increases in combined transgenic (At) and native (Nt) transcript levels of VDE (3-fold), PsbS (3-fold) and ZEP (8-fold) relative to wild-type (FIGS. 2A, B and C). For PsbS the increase in transcript levels translated into approximately 2-fold higher PsbS protein level (FIG. 2E), as exemplified in two approximately equal density bands around 22 kDa (FIG. 2G, VPZ lanes), representing the native and transgenic protein. However, for VDE and ZEP the increase in transcript levels was amplified in the protein levels (FIG. 2G, labelled bands around 73 kDa for ZEP and 45 kDa for VDE), showing substantial increases of VDE (FIG. 2D) and ZEP (FIG. 2F) protein relative to WT (16 and 80-fold, respectively). Interaction between transgenic and native transcript and protein levels appeared to be negligible, since transcript and protein levels of the native proteins were similar in the VPZ lines and WT.

Example 4. Kinetics of NPQ in Young Seedlings Following Repeated Changes in Light Intensity

(202) To compare the kinetics of dynamic NPQ adjustment, time constants of a double exponential model were fitted to time-series of NPQ in young seedlings as a function of repeated changes in light intensity between 2000 and 200 mol m.sup.2 s.sup.1 (Table 1). During the first 2000/200 cycle no consistent differences between WT and VPZ overexpression lines were observed. The time constant of NPQ induction varied between 49.31.9 (VPZ-34) to 91.86.2 (VPZ-56), and time constants of readjustment from 2000 to 200 mol m.sup.2 s.sup.1 were also similar across WT and the three VPZ lines, averaging 10.2 s for .sub.1 and 669.9 s for .sub.2. During the second 2000/200 cycle, the effect of VPZ expression on NPQ kinetics became more apparent. The fast phase of NPQ increase in the WT was approximately 2.3 times faster than in the VPZ lines, with .sub.1 of 5.5 s in WT versus average .sub.1 of 12.6 s in the VPZ lines (Table 1). The second adjustment of NPQ to 200 mol m.sup.2 s.sup.1 showed a pronounced difference in the slow component of NPQ decline. Estimated .sub.2 in the VPZ lines, was found to be 1.9 times faster than WT (464.3 versus 886.4 s). Thus, repeated light intensity changes resulted in faster build-up and slower relaxation of NPQ in the WT, but the time constants in the VPZ lines were relatively unaffected. This same trend continued in the final 3 min at 2000 mol m.sup.2 s.sup.1 followed by 10 min of darkness. The fast phase of NPQ increase in the WT seedlings was approximately 2.4 times faster than the VPZ lines (.sub.1 of 4.3 versus 10.3 s) but final relaxation of NPQ during 10 min of darkness was 1.4 (.sub.1) and 3.5 times (.sub.2) faster in the VPZ lines relative to WT. In addition, .sub.1 and .sub.2 determined for recovery of PSII operating efficiency were 2.1 and 4.1 times faster in the VPZ lines, compared to WT.

(203) TABLE-US-00001 TABLE 1 Time constants of NPQ adjustment to repeated changes in light intensity (value se). Asterisks indicate significant differences between VPZ lines and wild-type (a = 0.05). Experiment phase (HL = 2000, LL = 200 mol Time m.sup.2 s.sup.1, D = dark) constant(s) WT VPZ-23 VPZ-34 VPZ-56 1.sup.st HL 1.sup.a 82.7 3.2 *63.4 2.8 *49.3 1.9 91.8 6.2 1.sup.st LL 1 10.4 2.9 5.6 1.9 14.6 5.4 n.d..sup.b 2 564.9 48.1 *1175.3 130.8 511.5 39.7 428.0 20.9 2.sup.nd HL 1 5.5 0.4 13.5 3.5 11.3 2.8 *12.9 3.2 2 115.3 24.4 127.5 150.1 111.2 71.2 389.3 1586.8 2.sup.nd LL 1 9.2 0.6 7.7 1.2 9.9 1.4 9.9 1.1 2 886.4 101.9 *470.1 45.0 *461.5 60.3 *461.4 64.6 3.sup.rd HL 1 4.3 0.3 *10.1 1.2 *10.2 1.4 *10.6 2.6 2 37.2 4.8 55.4 33.4 53.8 28.2 35.5 9.9 D 1 21.4 1.2 *13.3 1.3 19.4 1.4 *13.2 1.0 2 2641.1 821.2 792.6 131.7 *692.6 77.9 *774.9 94.5 D (PSII 1 29.2 2.0 *20.6 2.4 *14.2 1.0 *7.7 0.6 efficiency) 2 357.9 480.0 106.3 29.5 85.6 5.8 68.3 3.7 .sup.aData in 1.sup.st HL phase didn't constrain two time constants, so the model was reduced to a single exponential function and only one time constant was fitted. .sup.bData resolution was not sufficient to properly constrain fast phase, only slow phase was fitted.

Example 5. NPQ, Linear Electron Transport and CO.SUB.2 .Uptake in Steady State

(204) To measure steady state gas exchange and chlorophyll fluorescence in fully expanded leaves, light intensity was varied from low to high intensity, taking great care to allow gas exchange and fluorescence to fully stabilize at each intensity. NPQ was very similar between WT and VPZ lines, especially at light intensity below 400 mol m.sup.2 s.sup.1 (FIG. 3A). Corresponding response curves of linear electron transport and net assimilation rate as a function of absorbed light intensity did not show significant differences between WT and VPZ lines (FIG. 7). Additionally, fitted parameter values V.sub.cmax, J, TPU, and Rd derived from CO.sub.2 response curves were also similar between WT and the VPZ lines (Table 2.)

(205) Table 2. Parameter fits derived from CO.sub.2 response curves. Maximal carboxylation capacity (Vcmax), maximal rate of linear electron transport (Jmax), mitochondrial respiration rate not associated with photorespiration (R.sub.d) and maximal rate of triose phosphate utilization (TPU). Values se, n=10, no significant differences between wild-type and VPZ lines were found.

(206) TABLE-US-00002 WT VPZ-23 VPZ-34 VPZ-56 Vcmax 112.3 4.5 108.2 2.7 104.7 3.7 121.8 6.1 (mol m.sup.2 s.sup.1) Jmax 146.0 5.7 136.2 3.4 137.8 4.2 149.0 3.8 (mol m.sup.2 s.sup.1) TPU 11.1 0.4 10.1 0.3 10.5 0.3 10.9 0.3 (mol m.sup.2 s.sup.1) R.sub.d 2.1 0.3 1.8 0.3 2.2 0.2 2.3 0.3 (mol m.sup.2 s.sup.1)

Example 6. NPQ, Electron Transport and CO.SUB.2 .Fixation Under Fluctuating Light

(207) To evaluate the dynamic effect of VPZ overexpression on the shape of the light response curve, light intensity was varied in 4 min steps from high to low PFD with intermittent steps of 4 min of 2000 mol m.sup.2 s.sup.1 before each light transition. NPQ in the VPZ lines was similar to WT at high light intensity, but significantly lower than WT at low light intensity (FIG. 3B). The resulting response curves of linear electron transport rate and net assimilation rate were distinctly different between WT and VPZ lines (FIGS. 4A and B). Fitted convexity and asymptote parameters were similar between WT and VPZ lines (FIG. 8A-D), but initial slopes were distinctly different (FIGS. 4C and D). Fluctuating intensity reduced PSIImax to 0.5410.012 in the WT plants (FIG. 4C), but VPZ lines maintained a less reduced PSIImax of 0.6120.021 (VPZ-23), 0.5990.023 (VPZ-34) and 0.5950.023 (VPZ-56). Similarly CO.sub.2-max was reduced to 0.0580.001 in the WT plants (FIG. 4D), whereas CO.sub.2-max values in the VPZ lines were much less impacted by intermittent high light intensity, yielding 0.0690.003 for VPZ-23, 0.0660.003 for VPZ-34 and 0.0640.003 for VPZ-56. Thus, under these fluctuating conditions, average PSII-max and CO.sub.2-max of the VPZ lines were 11.3% and 14.0% higher than WT.

Example 7. Xanthophyll Cycle De-Epoxidation as a Function of Different Light Treatments

(208) To evaluate the effects of VPZ overexpression on the xanthophyll cycle, leaves were subjected to four different light treatments (Table 3). The combined pool size of violaxanthin, antheraxanthin, and zeaxanthin was similar between WT and VPZ lines. The xanthophyll pigment pool was completely epoxidated in dark-adapted leaves and no differences between WT and VPZ were observed. Exposure to PFD of 400 mol m.sup.2 s.sup.1 resulted in almost no change in the xanthophyll composition and DES remained close to zero, but illumination with PFD of 2000 mol m.sup.2 s.sup.1 led to considerable build-up of antheraxanthin and mainly zeaxanthin. VPZ lines retained significantly more violaxanthin and accumulated less zeaxanthin and antheraxanthin compared to WT, which led to xanthophyll DES in the VPZ lines to be almost two times lower than WT (25.5% versus 46.2%). The fluctuating light treatment showed the same trend as high light exposure, with even less xanthophyll de-epoxidation in the VPZ lines, relative to WT (17.8% versus 52.5%).

(209) Table 3 Xanthophyll cycle pigment concentrations and de-epoxidation state (DES) in fully expanded leaves in either dark-adapted state or after exposure to constant 400 or 2000 mol m.sup.2 s.sup.1 PFD or 3 cycles of 3 min 2000/3 min 200 mol m.sup.2 s.sup.1 PFD. Pigment concentration (valuese, n=3-5) has been normalized per unit leaf area (g m.sup.2). DES (%)=(Zea+0.5Ant)/(Zea+Ant+Viola), n.d.=not detected. Asterisks indicate significant differences between VPZ lines and wild-type (=0.05).

(210) TABLE-US-00003 Pigment Light treatment (g m.sup.2) WT VPZ-23 VPZ-34 VPZ-56 Dark-adapted Vio 7.72 0.37 6.64 0.45 6.94 0.64 6.70 0.40 Ant 0.01 0.00 0.00 0.00 0.00 0.00 0.01 0.00 Zea n.d. n.d. n.d. n.d. DES 0.0 0.0 0.0 0.0 Constant at 400 Vio 6.68 0.62 7.29 0.47 7.05 0.48 7.07 0.31 mol m.sup.2 s.sup.1 PFD Ant 0.03 0.01 0.01 0.00 0.02 0.01 0.01 0.00 Zea 0.20 0.10 0.00 0.00 0.05 0.05 0.00 0.00 DES 2.9 1.4 0.1 0.0 0.7 0.6 0.1 0.0 Constant at 2000 Vio 4.47 0.41 5.09 0.52 3.63 0.59 5.02 0.09 mol m.sup.2 s.sup.1 PFD Ant 0.07 0.00 0.08 0.01 0.06 0.00 0.09 0.01 Zea 3.81 3.81 *1.48 0.48 *1.23 0.24 *1.94 0.49 DES 46.2 2.8 *22.9 7.5 *26.2 5.3 *27.4 5.1 Fluctuating between Vio 4.20 0.16 *7.11 0.57 *5.72 0.15 *6.14 0.34 2000 and 200 Ant 0.16 0.02 *0.08 0.01 0.13 0.03 *0.08 0.01 mol m.sup.2 s.sup.1 PFD Zea 4.70 0.36 *0.88 0.08 *2.29 0.85 *1.20 0.21 DES 52.5 5.5 *11.4 0.9 *25.5 17.3 *16.4 4.2

Example 8. Efficiency of Photo-Protection by Non-Photochemical Quenching

(211) To evaluate the photo-protective efficiency in the VPZ lines relative to WT, seedlings were exposed to 2000 mol m.sup.2 s.sup.1 of blue light for one and two hours. The contrasting effects of photoinhibition and NPQ on Fo after the high light treatment were used to calculate a photo-protection index (FIG. 5), in which a value of 1 equals complete protection from photo-inhibitory damage. One hour of high light exposure resulted in significant induction of photo-inhibition, which was slightly higher in WT seedlings than in the VPZ lines (FIG. 5A). Photo-protective efficiency after two hours (FIG. 5B) was considerably less than after one hour, but VPZ seedlings were again found to be less photo-inhibited than WT. Residual NPQ after ten minutes of dark recovery tended to be lower in the VPZ seedlings (FIG. 5C). As a result of lower residual NPQ and higher photo-protection index, PSII efficiency in the VPZ seedlings also tended to be higher after 10 min of dark recovery (FIG. 5C).

Example 9. Plant Growth Under Greenhouse Conditions

(212) To investigate if the aforementioned differences in photosynthetic efficiency would affect growth, biomass accumulation was evaluated in two greenhouse experiments. Temperature was similar between both experiments and varied between 21 and 25 C. Peak light intensity exceeded 2000 mol m.sup.2 s.sup.1 in the first experiment and 1600 mol m.sup.2 s.sup.1 in the second experiment and daily light integrals averaged 21.3 and 19.3 mol m.sup.2 d.sup.1 in the first and second experiment, respectively. However, in the final week of the second experiment peak light intensity and daily light integral were decreasing substantially to 1037 mol m.sup.2 s.sup.1 and 8.9 mol m.sup.2 d.sup.1, due to seasonal decline in light intensity. As a result, average plant dry weight was substantially higher in the first experiment, 35.6 g versus 22.5 g respectively. Across both trials, plants from VPZ lines exhibited increased plant height (FIG. 6C) and leaf area (FIG. 6B), relative to WT. Additionally, total dry weight per plant was between 10 to 21% higher in VPZ lines (FIG. 6A), mainly due to substantial increases in stem dry weight (14 to 26%, FIG. 6E) as well as increases in leaf (7.5 to 16%, FIG. 6D) and root (12.5 to 38.3%, FIG. 6F) dry weight.

Example 10. Additional Data

(213) FIGS. 12 and 13 leaf, stem and root size, and growth, increase in transgenic plant lines N2-23 and N2-34 compared to wild type. FIG. 14 shows increased NPQ kinetics, quantum yield and CO.sub.2 fixation in transgenic lines VPZ-56, VPZ-23 and VPZ-34. These results show an increase in quantum yield and CO.sub.2 fixation at various light intensities, after prior exposure of the leaf to 2000 mol m.sup.2 s.sup.1 PFD. 1, 2 and 3 show the progression of this increase in time after exposure.

(214) FIG. 16 shows that the time constants of NPQ in the first induction/relaxation are similar, but subsequent light cycles lead to slower build up (independent of amplitude, these are time constants) and faster relaxation of NPQ in transgenic plants, and faster recovery of quantum yield in dark relaxation. These comparative results are entirely consistent with reduced build up of zeaxanthin in the transgenic lines. Levels of NPQ in VPZ lines at high light are similar or higher than WT. Levels of qE in VPZ lines estimated by dA532 nm are higher than WT, most likely associated with PsbS overexpression. Repeated high light exposure shows higher time constants of NPQ increase, and lower time constants of NPQ relaxation in VPZ lines. VPZ lines show 5-10% improved quantum yield at low PFD during rapid switches in PFD, due to faster rate of NPQ relaxation.

(215) Combined overexpression of VDE, ZEP and PsbS leads to modified kinetics of build-up and relaxation of NPQ in seedlings and fully grown plants, higher quantum yield under fluctuating light conditions in seedlings and fully grown plants, no significant differences in steady state gas exchange in fully grown plants, higher gross assimilation rate under fluctuating conditions in fully grown plants, and approximately 10% increase in growth in greenhouse.

Example 11. Materials and Methods

(216) Transformation

(217) N. tabacum cv. Petite Havana was transformed using the Agrobacterium-mediated leaf disc protocol according to Clemente, Agrobacterium Protocols (ed Wang K.), pp. 143-154. Humana Press Inc., Totowa. The binary plasmid contained coding sequences of three genes from A. thaliana: violaxanthin de-epoxidase (AtVDE), AtPsbS and zeaxanthin epoxidase (AtZEP) as well as the bar gene encoding resistance for bialaphos (Thompson et. al. Journal of Agricultural and Food Chemistry 35, 361-365, 1987). 20 independent T.sub.0 transformants were generated and T-DNA copy number was determined using digital droplet PCR (ddPCR) analysis of genomic DNA according to Glowacka et al Plant Cell and Environment doi: 10.1111/pce.12693, 2015. Two lines with a single copy (VPZ-34 and 56) and one line with two copies (VPZ-23) of the T-DNA were used to generate T.sub.1 progeny in which homozygous plants were identified by ddPCR according to Glowacka et al and self-pollinated to obtain homozygous T.sub.2 offspring for further analysis.

(218) Propagation of Plant Material

(219) T.sub.2 seeds of VPZ lines and WT seeds from the same harvest date were germinated on growing medium (LC1 Sunshine mix, Sun Gro Horticulture, Agawam, MA, USA) in a controlled environment walk-in growing chamber (Environmental Growth Chambers, Chagrin Falls, Ohio, USA) with 12 h day (23 C.)/12 h night (18 C.) cycle under 150 mol quanta m.sup.2 s.sup.1. Five days after germination, seedlings were transplanted to 812 potting trays (812 series, Hummert International, Earth City, MO, USA) for chlorophyll fluorescence imaging or 94 potting trays (3600 series, Hummert International) and grown until two true leaves had emerged. Seedlings to be used in gas exchange and biomass analyses were moved to the greenhouse after the first transplant.

(220) Transcription and Protein Expression

(221) Five leaf discs (total 2.9 cm2) were sampled from the youngest fully expanded leaves from five plants per line, from the position of the leaf where gas exchange was also performed. Protein and mRNA were extracted from the same leaf sample (NucleoSpin RNA/Protein kit, REF740933, Macherey-Nagel). Extracted mRNA was treated by DNase (Turbo DNA-free kit; AM1907, Thermo Fisher Scientific, Waltham, MA, USA) and transcribed to cDNA using Superscript III First-Strand Synthesis System for RT-PCR (18080-051; Thermo Fisher Scientific). RT-qPCR was used to quantify expression levels of the transgenes AtZEP, AtPsbS and AtVDE, and the native genes NtZEP, NtPsbS and NtVDE relative to NtActin and NtTubulin (primer sequences provided supplemental materials).

(222) After quantification of total protein concentration (protein quantification assay ref740967.50, Macherey-Nagel), 4 g protein was separated by SDS-PAGE electrophoresis, blotted to membrane (Immobilon-P, IPVH00010, Millipore, USA) using semi-dry blotting (Trans-Blot SD, Bio-Rad) and immuno-labelled with primary antibodies raised against AtPsbS (AS09533, Agrisera, Vnns, Sweden), AtZEP (AS08289, Agrisera) and AtVDE (AS153091, Agrisera) followed by incubation with secondary antibodies (Promega W401B). Chemiluminescence was detected using a scanner (ImageQuant LAS-4010, Fuji,) and densitometry was performed using ImageJ (version 1.47v, National Institute of Health, USA) to estimate protein concentrations Wild-type protein concentrations were used for normalization.

(223) NPQ and PSII Operating Efficiency in Young Seedlings

(224) Non-photochemical quenching (NPQ) was determined in 18 seedlings simultaneously, using a chlorophyll fluorescence imager (CF Imager, Technologica, Colchester, UK). Seedlings were first dark adapted for 20 minutes after which the dark-adapted minimal fluorescence (Fo) and maximal fluorescence (Fm) were imaged using a 800 ms pulse of saturating light intensity (6000 mol quanta m.sup.2 s.sup.1,max=470 nm). Subsequently, seedlings were subjected to either 10 minutes of 1000 mol quanta m.sup.2 s.sup.1 followed by 10 minutes of darkness or six cycles of three minutes 2000 mol quanta m.sup.2 s.sup.1 followed by two minutes of 200 mol quanta m.sup.2 s.sup.1. Saturating flashes were provided at regular intervals to image variable fluorescence (F) and the maximum fluorescence under illuminated conditions (Fm). Average NPQ per seedling was then calculated from these measurements according to Eq.1, assuming the Stern-Volmer quenching model:
NPQ=Fm/Fm1Eq.1

(225) Maximal or operating PSII efficiency were estimated from the fluorescence measurements according to equation 2 and 3, following Genty et al. Biochimica et Biophysica Acta 990, 87-921989, 1989.
Maximal PSII efficiency=(FmFo)/FmEq.2
PSII operating efficiency=(FmF)/FmEq.3
Time Constants of NPQ Adjustment to Changes in Light Intensity

(226) Seedlings were dark-adapted and chlorophyll fluorescence was determined using a chlorophyll fluorescence imager as described above. Maximal fluorescence was measured every 30 seconds while light intensity was changed every 3 min from 2000 to 200, 2000, 200, 2000 and finally 0 mol quanta m.sup.2 s.sup.1. The final relaxation in darkness lasted 10 minutes. Six sets of 18 seedlings of three VPZ transformed lines and wild-type were measured accordingly, whereby a 5 second frameshift was created between fluorescence measurements and light intensity changes between each set. NPQ was computed according to Eq. 1, normalized against the highest value within each set after which all six sets were compiled as a function of time to generate time-series of normalized NPQ with a resolution of 5 seconds. Time constants in a double exponential function for induction or relaxation of NPQ were fitted to the compiled time-series after each change in light intensity. For the final recovery in darkness, time constants were also fitted for PSII operating efficiency (estimated using equation 3).

(227) Photo Protection Efficiency

(228) Seedlings were dark-adapted for 20 min after which dark-adapted maximal PSII efficiency (Fv/Fm) was determined using the chlorophyll fluorescence imager as described above. Subsequently, seedlings were exposed to 2000 mol quanta m.sup.2 s.sup.1 for a duration of 60 min or 120 min. After the exposure, seedlings were allowed to recover in darkness for 10 min to allow relaxation of qE, after which minimal fluorescence (Fo) and maximal fluorescence (Fm) without full dark-adaptation were measured. The measurement of Fo was compared to a derived value which considers exclusively the effect of NPQ on Fo (Oxborough and Baker, Photosynthesis Research 54: 135-142, 1997). The difference between PSII efficiency using either measured or derived Fo was then used to determine the efficiency of photo-protection.

(229) Gas Exchange and Linear Electron Transport in Fully Expanded Leaves

(230) For gas exchange analyses, seedlings were transplanted from trays to 3.8 L pots (400C, Hummert International) filled with growing medium (LC1 Sunshine mix, supplemented with 10 g granulated fertilizer per pot (Osmocote Plus 15/9/12, The Scotts Company LLC, Marysville, Ohio, USA). Pots were randomized and spaced 30 cm apart on greenhouse tables. Plants were watered and plant positions were changed randomly every two days, until the fifth leaf was fully expanded. Gas exchange measurements were performed using an open gas exchange system (LI6400XT, LI-COR, Lincoln, Nebraska, USA) equipped with a 2 cm2 leaf chamber fluorometer. All gas exchange measurements were corrected for diffusive leaks between cuvette and surrounding atmosphere, using dark measurements at various CO.sub.2 concentrations according to Gong et al. Plant, Cell and Environment 38, 2417-24322015).

(231) To determine the light dose response curves of net assimilation rate and linear electron transport in fully expanded leaves, gas exchange and pulse amplitude modulated chlorophyll fluorescence were measured at a range of light intensities. All chlorophyll fluorescence measurements were performed using the multiphase flash routine (Loriaux et al. 2013). Youngest fully expanded leaves (n=6) were clamped in the cuvette with block temperature set at 25 C. and [CO.sub.2] in the airstream controlled at 1500 ppm. After 30 min of dark adaptation, minimal fluorescence (Fo) and maximal fluorescence (Fm) were determined. Subsequently, light intensity was varied in two different ways. The first experiment consisted of slowly increasing the light intensity from 0 to 50, 80, 110, 140, 170, 200, 400, 600, 800, 1000, 1200, 1500 and 2000 mol m.sup.2 s.sup.1, trying to keep induction of NPQ at each light intensity to an absolute minimum. When steady state was reached, gas exchange parameters were logged and baseline fluorescence (F) and light-adapted maximal fluorescence (Fm) were measured to estimate NPQ (Eq.1) and PSII operating efficiency (Eq.3). In the second experiment leaves were allowed to reach steady state gas exchange at 2000 mol m.sup.2 s.sup.1. Subsequently, light intensity was changed from 2000 to 1500, 1000, 800, 600, 400, 200, 170, 140, 110, 80 and 50, each step lasted 4 minutes and was preceded by 4 minutes of 2000 mol m.sup.2 s.sup.1. At each light intensity, F and Fm and gas exchange parameters were determined after 60 s, 140 s and 220 s. Average values of these three measurements were used for subsequent analysis to reconstruct light response curves with intermittent high PFD.

(232) Leaf absorptance of incident irradiance was measured on the same spot used for gas exchange analysis, using an integrating sphere (LI1800, LI-COR, USA) connected to a spectrometer (USB-2000, Ocean Optics Inc, Dunedin, Florida, USA). Rates of linear electron transport (J) were determined for both experiments according to:
J=Leaf absorptance*PSII operating efficiency*PFD*0.5Eq.4

(233) Light intensity dose response curves for linear electron transport and gas exchange from both experiments were adjusted to constant leaf temperature according to equations in Sharkey et al. (2007) and fitted to a descriptive non-rectangular hyperbola model (Von Caemmerer, Biochemical models of leaf photosynthesis. Collingwood, Australia: CSIRO Publishing 2000), yielding estimates for initial slope, convexity and asymptote.

(234) To analyze the CO.sub.2 dose response curve of net assimilation rate, leaves were clamped in the cuvette with block temperature controlled at 25 C. and light intensity set to 2000 mol m.sup.2 s.sup.1. CO.sub.2 concentration in the airstream was controlled at 400, 300, 200, 100, 75, 400, 400, 500, 600, 700, 800, 1200 and 1600 ppm and gas exchange parameters were logged when steady state was reached. The model for leaf photosynthesis by Farquhar et al. Planta 149, 78-90.1980 assuming infinite mesophyll conductance, with temperature corrections according to Sharkey et al. Plant Cell Environ. 30, 1035-1040, 2007 was fitted to derive the maximal carboxylation rate (Vcmax), electron transport rate at 2000 mol m.sup.2 s.sup.1 (J), triose phosphate utilization rate (TPU) and mitochondrial respiration rate not associated with photorespiration (Rd).

(235) Xanthophyll Cycle Pigment Concentrations

(236) Leaves were clamped in the leaf cuvette of an open gas exchange system and dark-adapted as described above. Subsequently, CO.sub.2 and H.sub.2O exchange were either allowed to reach steady state at 0, 400 and 2000 mol m.sup.2 s.sup.1 or subjected to a series of changes in light intensity (three cycles of 3 min 2000/3 min 200 mol m.sup.2 s.sup.1), immediately after which leaf discs (0.58 cm2) were sampled from the enclosed leaf spot, snap-frozen in liquid nitrogen and stored at 80 C. until extraction. Pigment analysis took place at the Horn Point Laboratory (University of Maryland Center for Environmental Science, Cambridge, MD, USA). Frozen samples were macerated in 90% acetone using an ultrasonic probe and the crude extract was filtered (0.45 m). Pigments were separated by HPLC using a Zorbax Eclipse XDB-C8 column (963967-906, Agilent Technologies, Santa Clara, CA, USA) and quantified according to the protocol by Van Heukelem and Thomas (2001).

(237) Growth and Final Biomass Accumulation

(238) To evaluate the effects of VPZ overexpression on growth, two independent greenhouse experiments were performed from May 25-Jun. 29, 2015 (using WT, VPZ-23 and VPZ-34) and from October 9-Nov. 13, 2015 (using WT, VPZ-23, VPZ-34 and VPZ-56). Seedlings were propagated as specified above (paragraph plant propagation) and transplanted from trays to 14.5 L pots (2000C, Hummert International) filled with growing medium (LC1 Sunshine mix, Sun Gro Horticulture) supplemented with 30 g slow release granulated fertilizer per pot (Osmocote Plus 15/9/12, The Scotts Company LLC). Pots were randomized and placed on greenhouse tables with 30 cm spacing. Plants were watered and plant positions were changed randomly every two days. Light intensity at leaf level was logged with a quantum sensor (LI-190R, LI-COR, USA) at the center of the greenhouse table, which was mounted on a tripod and adjusted daily to maintain a position of 10 cm above the youngest leaves. Air temperature, relative humidity and [CO.sub.2] were measured approximately 1 m above the plant canopy, using a combined temperature and humidity sensor (HMP60-L,Vaisala Oyj, Helsinki, Finland) and an infrared gas analyzer (SBA-5, PPsystems, Amesbury, MA, USA). All climate data was logged every 30 min using a datalogger (CR1000, Campbell Scientific Inc, Logan, UT, USA). Temperature in the greenhouse was generally kept between 28 C. (day) and 18 C. (night), using a combination of ventilation, evaporative cooling and gas heaters. Light intensity varied with incoming irradiance, with midday peaks reaching approximately 1800 mol m.sup.2 s.sup.1 in the first experiment and 1000-1500 mol m.sup.2 s.sup.1 in the second experiment. [CO.sub.2] was not controlled and varied between 360 ppm (day) and 430 ppm (night). After the first flower had opened, stem length and the number of leaves per plant were determined and total leaf area per plant was measured with a conveyor-belt scanner (LI-3100C Area Meter, LI-COR, USA). Plants were subsequently separated into leaf, stem and root fractions and dried to constant weight at 70 C.

(239) Statistical Analysis

(240) All statistical analyses were performed using SAS (version 9.3, SAS Institute Inc., Cary, NC, USA). Data was tested for homogeneity of variance using Brown-Forsythe's test and normality using Shapiro-Wilk's test. One-way analysis of variance was applied to fitted gas exchange parameters, transcription levels and protein expression. Datasets of chlorophyll fluorescence imaging of NPQ in young seedlings were analyzed by two-way (photo-protection), or repeated measures one-way (10 min on/off) or two-way (high/low light) analysis of variance. Analysis of the two replicated greenhouse trials was performed using a mixed model with two fully randomized blocks. In all cases, significant effects in ANOVA were followed by Dunnett's multiple comparison test of line means against WT control (=0.05). Fitted time constants of NPQ induction and relaxation were compared based on 95% confidence intervals.

Example 12. Transgenic Maize (Prophetic)

(241) This invention can also provide for a maize line with improved photosynthesis and growth as compared to a phenotype in parental units of said maize line. The maize line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic maize having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(242) An example of maize transformation protocol is described herein.

(243) Initiate Agrobacterium Culture

(244) 1. Streak AGL1 carrying a simple binary vector (e.g., pZY102) from 80 C. stock on ABC agar plates with appropriate antibiotics (for the vector and strain illustrated here, 100 mg/liter spectinomycin and 30 mg/liter rifampin), preparing a dilution series in order to obtain single colonies. Incubate the plates in the dark for 3 days at 28 C.

(245) 2. Select a single colony and streak it on YEP agar plates containing appropriate antibiotics (for the vector and strain illustrated here, 100 mg/liter spectinomycin and 30 mg/liter rifampin). Incubate the plates in the dark for 3 days at 20 C.

(246) 3. Add 5 ml of sterile PHI-A (inoculation medium) to a 15-ml conical centrifuge tube.

(247) 4. Transfer two full loops of AGL1 from the YEP plate to the tube prepared in step 3. After 2 to 3 min, shake the tube to thoroughly suspend bacterial cells.

(248) 5. Remove 1 ml of this suspension and place it in a spectrophotometer cuvette to check the optical density at 550 nm (OD550). Adjust the cell suspension to an OD550 of 0.35 (0.5109 cfu/ml) at room temperature (e.g., 24 C.) by either adding more Agrobacterium cells or diluting the culture with more PHI-A.

(249) 6. Shake the culture in a shaker at 100 rpm for 4 to 5 hr at room temperature (e.g., 24 C.).

(250) 7. Aliquot 1 ml of the suspension into 2-ml sterile microcentrifuge tube.

(251) Embryo Isolation, Inoculation, and Co-Cultivation

(252) 8. Remove the husks and silk from ears which were harvested 10 to 13 days post-pollination (with embryo size of 1.5 mm; see Support Protocol). Insert a pair of forceps into one end of the ear.

(253) 9. Completely submerge the fresh Hi-II ears in a solution containing 0.5 liters of 30% commercial bleach with a few drops of Tween 20 (in a sterile 1-liter wide-mouth bottle) for 20 min.

(254) 10. Wash ears three times with sterile water (making sure ears are completely submerged in the water each time), and let the ear stand upright on a sterile 15015-mm petri dish.

(255) 11. Remove top half of the kernels from each ear with a sterile #11 razor blade.

(256) 12. Isolate 1.5-mm immature embryos from the sterile ear with a sterile microspatula and transfer 50 to 100 embryos per 1.7- to 2.0-ml microcentrifuge tube. Wash the embryos with 1 ml PHI-A solution three times to remove debris and starch.

(257) 13. Immediately afterwards, add 1 ml of the Agrobacterium suspension to the tube containing the immature embryos, allow the tube to stand 5 min in the sterile hood, then pour the entire contents including all of the embryos onto PHI-B (co-cultivation medium) agar plate.

(258) 14. Draw off Agrobacterium suspension using a pipet with a fine tip, then spread the embryos evenly across the plate and place embryos with scutellum face up and flat side face down on the medium.

(259) 15. Seal the plate with parafilm and incubate in the dark at 20 C. for 3 days.

(260) Resting

(261) 16. Transfer the embryos with a spatula to a plate of PHI-C (resting medium). Avoid damaging the embryos.

(262) 17. Seal the plate with parafilm and incubate in the dark at 28 C. for 7 days.

(263) Selection

(264) 18. Transfer embryos with spatula or forceps to a plate of PHI-D1 (selection medium I). Place 25 embryos per plate and seal the plate. Incubate the embryos in the dark at 28 C. for the first 2-week selection.

(265) 19. Transfer calli with forceps from the PHI-D1 plate to a plate of PHI-D2 (selection medium II). Subculture the calli every 2 weeks onto fresh PHI-D2 medium for a total of 2 months using the incubation conditions in step 18.

(266) 20. Bulk up the herbicide-resistant calli by growing them on fresh PHI-D2 medium for another 2 weeks under the same conditions as in steps 18 and 19, until the diameter of the calli is about 1.0 cm.

(267) Maturation and Regeneration

(268) 21. Using forceps, transfer each entire callus mass containing opaque embryos onto PHI-E (maturation medium) in 20100 mm petri plates (wrapped with 3 M porous tape) and place culture plates in the dark at 28 C. for two 2 to 3 weeks to allow somatic embryos to mature.

(269) 22. Transfer ivory-white calli onto PHI-F (regeneration medium) and incubate at 25 C. under 16-hr photoperiod until shoots and roots develop.

(270) 23. Transfer each small plantlet to a 25150-mm tube containing PHI-F (regeneration medium), and grow at 25 C. under 16-hr photoperiod for 2 to 3 weeks.

(271) 24. Transfer the plants to small plastic pots with soil mixture, e.g., Promix BX soil, in a light incubator or culture room at 24 C. with an 18 hr/light, 6 hr/dark cycle.

Example 13. Transgenic Sorghum (Prophetic)

(272) This invention can also provide for a sorghum line with improved photosynthesis and growth as compared to a phenotype in parental units of said sorghum line. The sorghum line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic sorghum having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(273) Examples of sorghum transformation protocol are described in Guo et al., Methods Mol Biol 1223, 181-188, 2015, as well as Howe et al., Plant Cell Rep 25(8): 784-791, 2006.

Example 14. Transgenic Soybean (Prophetic)

(274) This invention can also provide for a soybean line with improved photosynthesis and growth as compared to a phenotype in parental units of said soybean line. The soybean line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic soybean having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(275) An example of soybean transformation protocol is described herein.

(276) Cotyledonary explants are prepared from the 5-day-old soybean seedlings by making a horizontal slice through the hypocotyl region, approximately 3-5 mm below the cotyledon. A subsequent vertical slice is made between the cotyledons, and the embryonic axis is removed. This manipulation generates 2 cotyledonary node explants. Approximately 7-12 vertical slices are made on the adaxial surface of the ex-plant about the area encompassing 3 mm above the cotyledon/hypocotyl junction and 1 mm below the cotyledon/hypocotyl junction. Explant manipulations are conducted with a No. 15 scalpel blade.

(277) Explants are immersed in the Agrobacterium inoculum for 30 min and then co-cultured on 10015 mm Petri plates containing the Agrobacterium resuspension medium solidified with 0.5% purified agar (BBL Cat #11853). The co-cultivation plates are overlaid with a piece of Whatman #1 filter paper (Mullins et al., 1990; Janssen and Gardner, 1993; Zhang et al., 1997). The explants (5 per plate) are cultured adaxial side down on the co-cultivation plates, that are overlaid with filter paper, for 3 days at 24 C., under an 18/6 hour light regime with an approximate light intensity of 80 mol s-1 m-2(F17T8/750 cool white bulbs, Litetronics). The co-cultivation plates are wrapped with Parafilm.

(278) Following the co-cultivation period explants are briefly washed in B5 medium supplemented with 1.67 mg 1-1 BAP, 3% sucrose, 500 mg 1-1 ticarcillin and 100 mg 1-1 cefotaxime. The medium is buffered with 3 mM MES, pH 5.6. Growth regulator, vitamins and antibiotics are filter sterilized post autoclaving. Following the washing step, explants are cultured (5 per plate) in 10020 mm Petri plates, adaxial side up with the hypocotyl imbedded in the medium, containing the washing medium solidified with 0.8% purified agar (BBL Cat #11853) amended with either 3.3 or 5.0 mg 1-1 glufosinate (AgrEvo USA). This medium is referred to as shoot initiation medium (SI). Plates are wrapped with 3M pressure sensitive tape (Scotch, 3M, USA) and cultured under the environmental conditions used during the seed germination step.

(279) After 2 weeks of culture, the hypocotyl region is excised from each of the explants, and the remaining explant, cotyledon with differentiating node, is subsequently sub-cultured onto fresh SI medium. Following an additional 2 weeks of culture on SI medium, the cotyledons are removed from the differentiating node. The differentiating node is sub-cultured to shoot elongation medium (SE) composed of Murashige and Skoog (MS) (1962) basal salts, B5 vitamins, 1 mgl-1 zeatin-riboside, 0.5 mg 1-1 GA3 and 0.1 mg 1-1 IAA, 50 mg 1-1 glutamine, 50 mg 1-1 asparagine, 3% sucrose and 3 mM MES, pH 5.6. The SE medium is amended with either 1.7 or 2.0 mg 1-1 glufosinate. The explants are sub-cultured biweekly to fresh SI medium until shoots reached a length greater than 3 cm. The elongated shoots are rooted on Murashige and Skoog salts with B5 vitamins, 1% sucrose, 0.5 mg 1-1 NAA without further selection in either Magenta boxes or Sundae cups (Industrial Soap Company, St. Louis MO).

Example 15. Transgenic Rice (Prophetic)

(280) This invention can also provide for a rice line with improved photosynthesis and growth as compared to a phenotype in parental units of said rice line. The rice line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic rice having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(281) An example of rice transformation protocol is described herein.

(282) Infection and Co-Cultivation

(283) Transfer the callus into sterile tea strainer and incubate the tea strainer in the agrobacterium suspension by very gently and intermittently shaking the strainer for 15 min, then blot dry strainer on top of stacked Whatmann 1 sterile filter paper in a sterile Petri dish to remove excess bacteria. Transfer the callus onto sterile filter paper placed on top of MSG4K medium, and culture in the dark at 25 C. for 48 h.

(284) Resting and Bialaphos (Basta) Selection

(285) Transfer the co-cultivated callus to a sterile 50 ml tube and wash them with sterile water for 5 times and once with liquid co-cultivation medium containing timentin 200 mg/l. Blot the callus dry in sterile Whatman filter paper and transfer them to MSG2K rest medium containing plates. Culture the callus plates in the dark at 25 C. for 7 days. Transfer the callus to MSG2K bialaphos selection medium. Culture the plates in the dark at 25 C. for 3 weeks. Repeat the process for additional 5 weeks subculturing into fresh medium in every 3 weeks.

(286) Callus Desiccation, Shoot Regeneration and Rooting

(287) After 8 weeks in selection medium with 3-4 rounds of selection, transfer the callus to sterile Petri dishes stacked with 2 layers of sterile Whatman #1 filter paper in sterile hood. Wrap it with 3M surgical tapes and leave in the hood as such undisturbed in dark for 24 h. The plates need to wrapped in aluminum foil to ensure the darkness for the callus. This partial desiccation of callus step is absolutely necessary to induce shoots in shoot regeneration medium. After 48 h, transfer the callus to MSG75K shoot regeneration medium and incubate in dark for 3 weeks. Transfer the proliferating callus with somatic embryos to same medium and incubate under low light, approximately 20 to 30 E m-2s-1 with 12 h/8 h dark cycle. Shoots will start appearing after 10 days in light and most of callus will become green. Continue to culture the green callus along embryos in MSG75K shoot regeneration medium under same light regime until satisfied amount of shoots were obtained. Meanwhile, when shoots reaches above 5 cm in length dissect them in the base and transfer to Greiner Bio-One plant culture containers (#968161-82051-508-container with lid, 330 ml, sterile, 68 Dia.110 H mm) with MSG100K rooting medium.

Example 16. Transgenic Wheat (Prophetic)

(288) This invention can also provide for a wheat line with improved photosynthesis and growth as compared to a phenotype in parental units of said wheat line. The wheat line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic wheat having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(289) An example of wheat transformation protocol is described in Medveck E, Harwood W A. Wheat (Triticum aestivum L.) Transformation Using Mature Embryos. Agrobacterium Protocols: Volume 1. 2015:199-209.

Example 17. Transgenic Cowpea

(290) Cowpea plants were transformed with a T-DNA construct containing nucleotide sequences encoding PsbS, ZEP and VDE, following the transformation protocol as described in Higgins et al., Innovative research along the cowpea value chain. Ibadan, Nigeria: International Institute of Tropical Agriculture, pp. 133-139, 2013. To compare the kinetics of dynamic NPQ adjustment, a double exponential model was fitted to dark relaxation of NPQ in T.sub.0 transgenic cowpea after exposure to fluctuating light. As shown in Table 4, the qE relaxation (1) was noticeably faster in the transformant line 164381A as compared to the control, with measurements of 20.5 s and 19.7 s versus 35.9 s and 29.7 s. The qZ phase of NPQ relaxation (2) was slower in the transformant line 1643B1 as compared to the control, likely caused by the limitation that the measurements were taken on T.sub.0 transgenic plants. As is known in the art, transgenic plants from T.sub.1 or T.sub.2 generations are usually preferred over T.sub.0 for phenotypic measurements. One reason is that in T.sub.0 transgenic plants, stress from the transformation and tissue culture processes can interfere with normal plant physiology and affect phenotypic measurements. Another reason is that molecular characterization of a transgene cannot be complete until in the T.sub.1 or T.sub.2 generation and transgenic characteristics such as copy number and insertion location in the genome can have significant effects on the transgene expression. As shown in FIG. 27, FIG. 28 and FIG. 29, NPQ relaxed faster in the transformant line 1643B1 than in the control plant. As shown in FIG. 30, NPQ relaxed slower in the transformant line CP472A (orange dots) than in the control plant (blue dots), which is likely caused by the limitation that measurements were taken on T.sub.0 transgenic plants as discussed above.

(291) TABLE-US-00004 TABLE 4 Time constants of NPQ relaxation in transgenic cowpea. 1643B1 Control Measurement 1 Measurement 2 Measurement 1 Measurement 2 Time constant 1 (s) 20.5 19.7 35.9 29.7 Time constant 2 (s) 1220.8 2272.0 1099.2 1043.0

Example 18. Transgenic Cassava (Prophetic)

(292) This invention can also provide for a cassava line with improved photosynthesis and growth as compared to a phenotype in parental units of said cassava line. The cassava line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic cassava having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(293) An example of cassava transformation protocol is described in Chetty et al., New Biotechnology 30.2: 136-143, 2013.

Example 19. Transgenic Poplar (Prophetic)

(294) This invention can also provide for a poplar line with improved photosynthesis and growth as compared to a phenotype in parental units of said poplar line. The poplar line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic poplar having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect, the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide construct where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(295) An example of poplar transformation protocol is described in Movahedi et al., International Journal of Molecular Science 15.6: 10780-10793, 2014.

Example 20. Transgenic Eucalyptus (Prophetic)

(296) This invention can also provide for a eucalyptus line with improved photosynthesis and growth as compared to a phenotype in parental units of said eucalyptus line. The eucalyptus line can be created by generating a population of transgenic plants comprising heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE as described herein. Each transgenic event comprises introducing into the genome of a parent plant at least one nucleotide construct comprising a promoter operably linked to heterologous nucleotide as described herein. The nucleotide construct is introduced into the parental genome in sufficient quantity to produce transgenic cells which can be cultured into plants of transgenic eucalyptus having said enhanced phenotype. The transgenic cells are cultured into transgenic plants producing progeny transgenic seed. The population of transgenic plants is screened for observable phenotypes. Seed is collected from transgenic plants which are selected as having an unexpected enhanced phenotype. Optionally, the method comprises repeating a cycle of germinating transgenic seed, growing subsequent generation plants from said transgenic seed, observing phenotypes of said subsequent generation plants and collecting seeds from subsequent generation plants having an enhanced phenotype. In another aspect of the method a large population is screened by employing at least one heterologous nucleotide sequences encoding polypeptides selected from PsbS, ZEP and VDE. Other preferred aspects of the method employ nucleotide constructs where the heterologous DNA is operably linked to a selected promoter, e.g. the 5 end of a promoter region. The DNA construct may be introduced into a random location in the genome or into a preselected site in the genome.

(297) An example of eucalyptus transformation protocol is described in Diwakar et al., Plant Tissue Culture: Propagation, Conservation and Crop Improvement, 219-244, 2016.

Example 21. Sequence Identity Analysis of NPQ Genes

(298) To identify amino acid sequences that are homologous to the Arabidopsis PsbS, ZEP and VDE, BLAST protein searches was performed with the BLASTX program. Percentage of sequence similarity by BLAST is presented in Table 5 for PsbS, Table 6 for ZEP, and Table 7 for VDE, where top 100 hits of sequences ordered by descending percentage of sequence identity to the Arabidopsis homologue are listed.

(299) To compare the sequence identity and/or similarity of the amino acid sequences that are homologous to the Arabidopsis PsbS, ZEP and VDE, alignment of sequences was performed with the CLUSTAL OMEGA program. FIG. 24 illustrates the amino acid sequence similarity through CLUSTAL O for (A) PsbS, (B) ZEP and (C) VDE, respectively.

(300) TABLE-US-00005 TABLE 5 Percentage of sequence identity for PsbS. Query E Description cover value Identity Accession Chlorophyll A-B binding family 100% 0 100% NP_175092.1 protein [Arabidopsis thaliana] unknown protein [Arabidopsis thaliana] 100% 0 99% AAK95290.1 hypothetical protein ARALYDRAFT_ 100% 0 98% XP_002891292.1 891398 [Arabidopsis lyrata subsp. lyrata] PREDICTED: photosystem II 22 kDa protein, 100% 2.00E178 97% XP_010500150.1 chloroplastic-like [Camelina sativa] PREDICTED: photosystem II 22 kDa protein, 100% 3.00E178 97% XP_010479050.1 chloroplastic isoform X1 [Camelina sativa] PREDICTED: photosystem II 22 kDa protein, 100% 2.00E177 97% XP_010461444.1 chloroplastic-like [Camelina sativa] hypothetical protein CARUB_v10010031 100% 8.00E176 96% XP_006304103.1 mg [Capsella rubella] Photosystem II 22 kDa protein, 100% 3.00E156 95% JAU12851.1 chloroplastic [Noccaea caerulescens] PREDICTED: photosystem II 22 kDa protein, 100% 8.00E151 95% XP_018447609.1 chloroplastic [Raphanus sativus] PREDICTED: photosystem II 22 kDa protein, 100% 1.00E149 95% XP_009107479.1 chloroplastic [Brassica rapa] hypothetical protein EUTSA_v10011718 99% 3.00E148 94% XP_006393723.1 mg [Eutrema salsugineum] PREDICTED: photosystem II 22 kDa protein, 100% 4.00E148 95% XP_013681211.1 chloroplastic-like [Brassica napus] PREDICTED: photosystem II 22 kDa protein, 100% 5.00E148 95% XP_018467982.1 chloroplastic [Raphanus sativus] PREDICTED: photosystem II 22 kDa protein, 100% 6.00E148 95% XP_013592876.1 chloroplastic [Brassica oleracea var. oleracea] PREDICTED: photosystem II 22 kDa protein, 100% 3.00E147 94% XP_013599587.1 chloroplastic-like [Brassica oleracea var. oleracea] PREDICTED: photosystem II 22 kDa protein, 99% 4.00E147 95% XP_009123055.1 chloroplastic [Brassica rapa] PREDICTED: photosystem II 22 kDa protein, 99% 6.00E125 78% XP_008466710.1 chloroplastic [Cucumis melo] Chlorophyll A-B binding family 96% 1.00E124 100% NP_973971.1 protein [Arabidopsis thaliana] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E122 76% XP_004150442.1 chloroplastic [Cucumis sativus] PREDICTED: photosystem II 22 kDa protein, 97% 2.00E121 77% XP_008783427.1 chloroplastic [Phoenix dactylifera] Photosystem II protein, 99% 5.00E121 76% JAT63827.1 chloroplastic [Anthurium amnicola] PREDICTED: photosystem II 22 kDa protein, 99% 2.00E120 77% XP_010692414.1 chloroplastic isoform X1 [Beta vulgaris subsp. vulgaris] hypothetical protein TSUD_ 99% 1.00E119 71% GAU40978.1 300570 [Trifolium subterraneum] Chloroa_b-bind domain-containing 100% 3.00E119 74% GAV71974.1 protein [Cephalotus follicularis] PsbS [Pisum sativum] 99% 5.00E119 71% AKG94171.1 PREDICTED: photosystem II 22 kDa protein, 88% 5.00E119 84% XP_010911871.1 chloroplastic [Elaeis guineensis] PREDICTED: photosystem II 22 kDa protein, 96% 2.00E118 96% XP_010479049.1 chloroplastic [Camelina sativa] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E118 76% XP_002285857.1 chloroplastic [Vitis vinifera] PREDICTED: photosystem II 22 kDa protein, 99% 2.00E117 82% XP_010544817.1 chloroplastic [Tarenaya hasleriana] RecName: Full = Photosystem II 22 kDa 82% 2.00E116 88% Q02060.1 protein, chloroplastic; AltName: Full = CP22; Flags: Precursor PREDICTED: photosystem II 22 kDa protein, 99% 7.00E116 78% XP_012447533.1 chloroplastic-like [Gossypium raimondii] PREDICTED: photosystem II 22 kDa protein, 99% 7.00E116 78% XP_016708802.1 chloroplastic-like [Gossypium hirsutum] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E115 78% XP_017604982.1 chloroplastic-like [Gossypium arboreum] PREDICTED: photosystem II 22 kDa protein, 99% 5.00E115 78% XP_016687044.1 chloroplastic-like [Gossypium hirsutum] Photosystem II 22 kDa, chloroplastic [Gossypium 99% 5.00E115 78% KHG12586.1 arboreum] PREDICTED: photosystem II 22 kDa protein, 99% 1.00E114 73% XP_006847012.1 chloroplastic [Amborella trichopoda] Chain A, Crystal Structure Of The Photoprotective 80% 1.00E114 88% 4RI2_A Protein Psbs From Spinach hypothetical protein PRUPE_ppa009763 100% 2.00E114 73% XP_007222356.1 mg [Prunus persica] PREDICTED: photosystem II 22 kDa protein, 93% 3.00E114 77% XP_019415222.1 chloroplastic-like [Lupinus angustifolius] light-harvesting complex I chlorophyll A/B-binding 99% 3.00E114 73% XP_003602031.1 protein [Medicago truncatula] unknown [Lotus japonicus] 99% 4.00E114 75% AFK43146.1 PREDICTED: photosystem II 22 kDa protein, 99% 6.00E114 75% XP_002513761.1 chloroplastic [Ricinus communis] PREDICTED: photosystem II 22 kDa protein, 99% 8.00E114 73% XP_004290871.1 chloroplastic [Fragaria vesca subsp. vesca] PREDICTED: photosystem II 22 kDa protein, 100% 1.00E113 73% XP_008219642.1 chloroplastic [Prunus mume] Chlorophyll A-B binding protein [Corchorus 99% 2.00E113 73% OMO59479.1 capsularis] Chlorophyll A-B binding protein [Corchorus 99% 8.00E113 73% OMP06543.1 olitorius] PREDICTED: photosystem II 22 kDa protein, 99% 2.00E112 76% XP_007019073.2 chloroplastic [Theobroma cacao] PREDICTED: photosystem II 22 kDa protein, 100% 2.00E112 74% XP_008375547.1 chloroplastic-like [Malus domestica] photosystem 11 22 kDa protein [Pyrus x 100% 7.00E112 73% AHM26637.1 bretschneideri] Photosystem II 22 kDa family protein [Populus 99% 3.00E111 74% XP_002300987.1 trichocarpa] hypothetical protein L484_004387 [Morus 100% 8.00E111 72% XP_010106359.1 notabilis] PREDICTED: photosystem II 22 kDa protein, 99% 1.00E110 73% XP_015621169.1 chloroplastic [Oryza sativa Japonica Group] PREDICTED: photosystem II 22 kDa protein, 100% 2.00E110 75% XP_010242794.1 chloroplastic [Nelumbo nucifera] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E110 76% XP_017247379.1 chloroplastic [Daucus carota subsp. sativus] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E110 74% XP_011027529.1 chloroplastic [Populus euphratica] PREDICTED: photosystem II 22 kDa protein, 79% 3.00E110 87% XP_008352659.1 chloroplastic-like [Malus domestica] PREDICTED: photosystem II 22 kDa protein, 100% 5.00E110 75% XP_017613374.1 chloroplastic-like [Gossypium arboreum] PREDICTED: photosystem II 22 kDa protein, 99% 2.00E109 70% XP_004502468.1 chloroplastic [Cicer arietinum] hypothetical protein B456_009G245800 [Gossypium 99% 4.00E109 76% KJB59229.1 raimondii] unknown [Picea sitchensis] 80% 6.00E109 83% ABK20973.1 PREDICTED: photosystem II 22 kDa protein, 99% 1.00E108 76% XP_012078240.1 chloroplastic [Jatropha curcas] photosystem II 22 kDa protein, 99% 4.00E108 74% KZV16554.1 chloroplastic [Dorcoceras hygrometricum] PREDICTED: photosystem II 22 kDa protein, 100% 5.00E108 74% XP_008378474.1 chloroplastic [Malus domestica] chloroplast photosystem II subunit [Sedum alfredii] 74% 7.00E108 88% AEK26371.1 predicted protein [Hordeum vulgare subsp. vulgare] 99% 2.00E107 70% BAJ90394.1 PREDICTED: photosystem II 22 kDa protein, 98% 2.00E107 74% XP_018817122.1 chloroplastic [Juglans regia] unknown [Medicago truncatula] 95% 2.00E107 73% ACJ84782.1 putative photosystem II protein [Gossypioides 99% 3.00E107 76% ACD56611.1 kirkii] Photosystem II, 22 kDa Protein [Plantago major] 99% 3.00E107 72% CAJ38395.1 PREDICTED: photosystem II 22 kDa protein, 100% 6.00E107 72% XP_018501271.1 chloroplastic [Pyrus x bretschneideri] PREDICTED: photosystem II 22 kDa protein, 99% 9.00E107 75% XP_009399195.1 chloroplastic-like [Musa acuminata subsp. malaccensis] Photosystem II 22 kDa protein, 100% 4.00E106 71% KHN09207.1 chloroplastic [Glycine soja] hypothetical protein CICLE_v10002099 99% 2.00E105 72% XP_006434195.1 mg [Citrus Clementina] putative photosystem II protein [Gossypium 100% 2.00E105 75% ABO41853.1 hirsutum] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E105 72% XP_016163508.1 chloroplastic [Arachis ipaensis] PREDICTED: photosystem II 22 kDa protein, 99% 4.00E105 72% XP_006472781.1 chloroplastic [Citrus sinensis] photosystem II 22 kDa protein, 98% 5.00E105 70% XP_020228501.1 chloroplastic [Cajanus cajan] Chlorophyll A-B binding family 99% 2.00E104 74% EOY16298.1 protein [Theobroma cacao] PREDICTED: photosystem II 22 kDa protein, 100% 3.00E104 69% XP_003523444.1 chloroplastic [Glycine max] PREDICTED: photosystem II 22 kDa protein, 100% 3.00E104 73% XP_010065001.1 chloroplastic [Eucalyptus grandis] unnamed protein product [Coffea canephora] 98% 5.00E104 71% CDP10910.1 unknown [Picea sitchensis] 80% 6.00E104 80% ABK25763.1 photosystem II 22 kDa protein, chloroplastic- 100% 1.00E103 70% NP_001276237.1 like [Glycine max] PREDICTED: photosystem II 22 kDa protein, 100% 2.00E103 71% XP_015885664.1 chloroplastic [Ziziphus jujuba] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E103 73% XP_011074844.1 chloroplastic [Sesamum indicum] PREDICTED: photosystem II 22 kDa protein, 90% 4.00E103 82% XP_012467939.1 chloroplastic-like [Gossypium raimondii] unknown [Glycine max] 100% 5.00E103 69% ACU23291.1 PREDICTED: photosystem II 22 kDa protein, 86% 7.00E103 80% XP_015633953.1 chloroplastic [Oryza sativa Japonica Group] PREDICTED: photosystem II 22 kDa protein, 83% 8.00E103 80% XP_006653075.1 chloroplastic like [Oryza brachyantha] PREDICTED: photosystem II 22 kDa protein, 90% 8.00E103 82% XP_016727785.1 chloroplastic-like [Gossypium hirsutum] PREDICTED: photosystem II 22 kDa protein, 90% 1.00E102 82% XP_016732479.1 chloroplastic-like [Gossypium hirsutum] B0518A01.1 [Oryza sativa Indica Group] 100% 1.00E102 72% CAH68096.1 PsbS protein [Phyllostachys edulis] 74% 1.00E102 86% ACU33835.1 PREDICTED: photosystem II 22 kDa protein, 99% 1.00E102 72% XP_009623344.1 chloroplastic [Nicotiana tomentosiformis] PREDICTED: photosystem II 22 kDa protein, 74% 2.00E102 86% XP_006645083.2 chloroplastic [Oryza brachyantha] OSJNBa0039K24.28 [Oryza sativa Japonica Group] 86% 2.00E102 80% CAE01809.2 chloroplast photosystem II 22 kDa 99% 3.00E102 71% ABC59515.1 component [Nicotiana benthamiana] PREDICTED: photosystem II 22 kDa protein, 99% 3.00E102 71% XP_009771859.1 chloroplastic [Nicotiana sylvestris] Photosystem II subunit S [Zostera marina] 99% 5.00E102 70% KMZ60119.1 hypothetical protein M569_10990 [Genlisea aurea] 80% 1.00E101 84% EPS63793.1

(301) TABLE-US-00006 TABLE 6 Percentage of sequence identity for ZEP. Query E Description cover value Identity Accession zeaxanthin epoxidase (ZEP) (ABA1) 100% 0 100% NP_851285.1 [Arabidopsis thaliana] AtABAI [Arabidopsis thaliana] 100% 0 99% BAB11935.1 zeaxanthin epoxidase [Arabidopsis thaliana] 100% 0 99% AAF82390.1 zeaxanthin epoxidase [Arabidopsis thaliana] 100% 0 99% AAG17703.1 hypothetical protein CARDB_v10026026 100% 0 93% XP_006280131.1 mg [Capsella rubella] PREDICTED: zeaxanthin epoxidase, 100% 0 94% XP_010444704.1 chloroplastic [Camelina sativa] hypothetical protein ARALYDRAFT_ 100% 0 95% XP_002865032.1 496897 [Arabidopsis lyrata subsp. lyrata] PREDICTED: zeaxanthin epoxidase, 100% 0 93% XP_010484561.1 chloroplastic [Camelina sativa] hypothetical protein EUTSA_v10003769 99% 0 91% XP_006393901.1 mg [Eutrema salsugineum] zeaxanthin epoxidase [Eutrema halophilum] 99% 0 91% AAV85824.1 hypothetical protein EUTSA_v10003769 99% 0 91% XP_006393902.1 mg [Eutrema salsugineum] hypothetical protein AALP_ 100% 0 90% KFK28343.1 AA8G503900 [Arabis alpina] Zeaxanthin epoxidase, chloroplastic 100% 0 90% JAU06164.1 [Noccaea caerulescens] Zeaxanthin epoxidase, chloroplastic 100% 0 90% JAU34415.1 [Noccaea caerulescens] Zeaxanthin epoxidase, chloroplastic 100% 0 90% JAU86000.1 [Noccaea caerulescens] BnaA07g12170D [Brassica napus] 99% 0 90% CDY01444.1 zeaxanthin epoxidase, chloroplastic 99% 0 90% NP_001302817.1 [Brassica napus] PREDICTED: zeaxanthin epoxidase, 99% 0 90% XP_009103460.1 chloroplastic [Brassica rapa] zeaxanthin epoxidase [Brassica rapa 99% 0 90% ACM68704.1 subsp. pekinensis] PREDICTED: zeaxanthin epoxidase, 99% 0 89% XP_018441511.1 chloroplastic [Raphanus sativus] zeaxanthin epoxidase [Brassica napus] 100% 0 90% ADC29517.1 PREDICTED: zeaxanthin epoxidase, 100% 0 89% XP_013686243.1 chloroplastic-like isoform X2 [Brassica napus] PREDICTED: zeaxanthin epoxidase, 100% 0 89% XP_013597987.1 chloroplastic isoform X2 [Brassica oleracea var. oleracea] PREDICTED: zeaxanthin epoxidase, 100% 0 89% XP_013686242.1 chloroplastic-like isoform X1 [Brassica napus] PREDICTED: zeaxanthin epoxidase, 100% 0 89% XP_013597986.1 chloroplastic isoform X1[Brassica oleracea var. oleracea] zeaxanthin epoxidase (ZEP) (ABA1) 91% 0 96% NP_201504.2 [Arabidopsis thaliana] PREDICTED: zeaxanthin epoxidase, 100% 0 85% XP_013613157.1 chloroplastic [Brassica oleracea var. oleracea] PREDICTED: zeaxanthin epoxidase, 100% 0 86% XP_018457364.1 chloroplastic-like isoform X3 [Raphanus sativus] BnaC09g07550D [Brassica napus] 100% 0 85% CDX81344.1 PREDICTED: zeaxanthin epoxidase, 100% 0 84% XP_009112352.1 chloroplastic-like [Brassica rapa] BnaA09g07610D [Brassica napus] 100% 0 84% CDY18634.1 PREDICTED: zeaxanthin epoxidase, 95% 0 86% XP_018457365.1 chloroplastic-like isoform X4 [Raphanus sativus] PREDICTED: zeaxanthin epoxidase, 95% 0 86% XP_018457362.1 chloroplastic-like isoform X1 [Raphanus sativus] PREDICTED: zeaxanthin epoxidase, 95% 0 86% XP_018457363.1 chloroplastic-like isoform X2 [Raphanus sativus] PREDICTED: zeaxanthin epoxidase, 100% 0 80% XP_010547517.1 chloroplastic-like [Tarenaya hasleriana] PREDICTED: zeaxanthin epoxidase, 100% 0 79% XP_010558547.1 chloroplastic [Tarenaya hasleriana] PREDICTED: zeaxanthin epoxidase, 86% 0 90% XP_013597988.1 chloroplastic isoform X3 [Brassica oleracea var. oleracea] zeaxanthin epoxidase precursor [Arabidopsis 74% 0 100% AAL91193.1 thaliana] PREDICTED: zeaxanthin epoxidase, 99% 0 72% XP_002523587.1 chloroplastic [Ricinus communis] PREDICTED: zeaxanthin epoxidase, 99% 0 72% XP_012079233.1 chloroplastic [Jatropha curcas] hypothetical protein COLO4_11419 92% 0 75% OMP01999.1 [Corchorus olitorius] zeaxanthin epoxidase [Vitis vinifera] 99% 0 71% NP_001268202.1 PREDICTED: zeaxanthin epoxidase, 95% 0 73% XP_011043539.1 chloroplastic-like [Populus euphratica] unnamed protein product [Vitis vinifera] 99% 0 71% CBI21425.3 zeaxanthin epoxidase [Vitis vinifera] 99% 0 71% AAR11195.1 hypothetical protein JCGZ_12396 92% 0 74% KDP31935.1 [Jatropha curcas] hypothetical protein Csa_2G277050 98% 0 70% KGN61963.1 [Cucumis sativus] hypothetical protein CCACVL1_26372 92% 0 75% OMO56663.1 [Corchorus capsularis] RecName: Full = Zeaxanthin epoxidase, 98% 0 72% 081360.1 chloroplastic; AltName: Full = PA-ZE; Flags: Precursor PREDICTED: zeaxanthin epoxidase, 100% 0 70% XP_014509031.1 chloroplastic-like [Vigna radiata var. radiata] zeaxanthin epoxidase, chloroplastic 98% 0 70% NP_001292713.1 [Cucumis sativus] PREDICTED: zeaxanthin epoxidase, 97% 0 73% XP_018844974.1 chloroplastic [Juglans regia] zeaxanthin epoxidase family protein 94% 0 73% APR63737.1 [Populus tomentosa] hypothetical protein PRUPE_ppa002248 98% 0 72% XP_007204247.1 mg [Prunus persica] hypothetical protein PRUPE_7G133100 98% 0 72% ONH96498.1 [Prunus persica] FHA domain-containing protein/FAD_ 99% 0 70% GAV73676.1 binding_3 domain-containing protein [Cephalotus follicularis] zeaxanthin epoxidase 1 [Bixa orellana] 97% 0 73% AMJ39488.1 PREDICTED: zeaxanthin epoxidase, 96% 0 73% XP_007047261.2 chloroplastic isoform X2 [Theobroma cacao] zeaxanthin epoxidase [Camellia sinensis] 98% 0 71% AJB84624.1 Zeaxanthin epoxidase (ZEP) (ABA1) isoform 96% 0 73% EOX91418.1 2 [Theobroma cacao] zeaxanthin epoxidase, chloroplastic 98% 0 70% NP_001315402.1 [Cucumis melo] PREDICTED: zeaxanthin epoxidase, 97% 0 71% XP_017411486.1 chloroplastic-like [Vigna angularis] zeaxanthin epoxidase family protein 93% 0 71% XP_002307265.1 [Populus trichocarpa] PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_010028248.1 chloroplastic [Eucalyptus grandis] zeaxanthin epoxidase, chloroplastic-like 98% 0 71% XP_020238178.1 isoform X1 [Cajanus cajan] PREDICTED: zeaxanthin epoxidase, 98% 0 72% XP_008241462.1 chloroplastic [Prunus mume] hypothetical protein PHAVU_003G243800 98% 0 71% XP_007155924.1 g [Phaseolus vulgaris] Zeaxanthin epoxidase (ZEP) (ABA1) isoform 96% 0 72% EOX91419.1 3 [Theobroma cacao] PREDICTED: zeaxanthin epoxidase, 96% 0 72% XP_007047260.2 chloroplastic isoform X1 [Theobroma cacao] PREDICTED: zeaxanthin epoxidase, 100% 0 70% XP_015890147.1 chloroplastic [Ziziphus jujuba] PREDICTED: zeaxanthin epoxidase, 90% 0 75% XP_011005864.1 chloroplastic-like [Populus euphratica] Zeaxanthin epoxidase (ZEP) (ABA1) isoform 96% 0 72% EOX91417.1 1 [Theobroma cacao] PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_015955494.1 chloroplastic-like [Arachis duranensis] hypothetical protein MANES_13G124100 98% 0 72% OAY33781.1 [Manihot esculenta] zeaxanthin epoxidase [Citrus unshiu] 99% 0 70% BAB78733.1 zeaxanthin epoxidase [Citrus unshiu] 99% 0 70% BAI79257.1 hypothetical protein GLYMA_11G055700 99% 0 70% KRH28470.1 [Glycine max] PREDICTED: zeaxanthin epoxidase, 99% 0 70% XP_006466600.1 chloroplastic [Citrus sinensis] hypothetical protein CISIN_1g005770 99% 0 69% KDO79210.1 mg [Citrus sinensis] PREDICTED: zeaxanthin epoxidase, 99% 0 69% XP_006494451.1 chloroplastic-like [Citrus sinensis] hypothetical protein CICLE_v10025089 99% 0 69% XP_006425899.1 mg [Citrus Clementina] zeaxanthin epoxidase, chloroplastic-like 97% 0 71% NP_001241348.1 [Glycine max] Zeaxanthin epoxidase, chloroplastic 98% 0 70% KHN26473.1 [Glycine soja] PREDICTED: zeaxanthin epoxidase, 97% 0 71% XP_009343160.1 chloroplastic-like [Pyrus x bretschneideri] PREDICTED: zeaxanthin epoxidase, 100% 0 69% XP_008340140.1 chloroplastic-like [Malus domestica] zeaxanthin epoxidase [Citruilus lanatus] 98% 0 69% ADI56522.1 PREDICTED: zeaxanthin epoxidase, 98% 0 69% XP_016185162.1 chloroplastic [Arachis ipaensis] zeaxanthin epoxidase [Malus domestica] 98% 0 69% AHA61555.1 PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_009767383.1 chloroplastic [Nicotiana sylvestris] zeaxanthin epoxidase [Chrysanthemum x 91% 0 74% BAE79556.1 morifolium] PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_004511928.1 chloroplastic-like [Cicer arietinum] PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_018505293.1 chloroplastic-like [Pyrus x bretschneideri] RecName: Full = Zeaxanthin epoxidase, 98% 0 71% Q40412.1 chloroplastic; Flags: Precursor zeaxanthin epoxidase [Chrysanthemum boreale] 91% 0 74% AGU91434.1 zeaxanthin epoxidase 1 isoform [Bixa orellana] 93% 0 74% AMJ39489.1 PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_016476042.1 chloroplastic [Nicotiana tabacum] PREDICTED: zeaxanthin epoxidase, 98% 0 70% XP_009345968.1 chloroplastic [Pyrus x bretschneideri] PREDICTED: zeaxanthin epoxidase, 99% 0 67% XP_010666612.1 chloroplastic [Beta vulgaris subsp. vulgaris] hypothetical protein CISIN_1g005770 99% 0 68% KDO79209.1 mg [Citrus sinensis] PREDICTED: zeaxanthin epoxidase, chloroplastic 98% 0 69% XP_010269709.1 isoform X1 [Nelumbo nucifera]

(302) TABLE-US-00007 TABLE 7 Percentage of sequence identity for VDE. Query E Description cover value Identity Accession non-photochemical quenching 1 [Arabidopsis 100% 0 100% NP_172331.1 thaliana] non-photochemical quenching 1 [Arabidopsis 100% 0 96% XP_002889702.1 lyrata subsp. lyrata] hypothetical protein CARDB_v10009082 100% 0 95% XP_006307456.1 mg [Capsella rubella] PREDICTED: violaxanthin de-epoxidase, 100% 0 93% XP_010475655.1 chloroplastic [Camelina sativa] PREDICTED: violaxanthin de-epoxidase, 100% 0 94% XP_010458094.1 chloroplastic [Camelina sativa] PREDICTED: violaxanthin de-epoxidase, 100% 0 94% XP_010488996.1 chloroplastic [Camelina sativa] PREDICTED: violaxanthin de-epoxidase, 100% 0 88% XP_013641072.1 chloroplastic [Brassica napus] PREDICTED: violaxanthin de-epoxidase, 100% 0 87% XP_009148110.2 chloroplastic [Brassica rapa] BnaA06g04940D [Brassica napus] 100% 0 87% CDX93554.1 Violaxanthin de-epoxidase, chloroplastic 100% 0 87% JAU20005.1 [Noccaea caerulescens] Violaxanthin de-epoxidase, chloroplastic 100% 0 87% JAU75731.1 [Noccaea caerulescens] Violaxanthin de-epoxidase, chloroplastic 100% 0 87% JAU51142.1 [Noccaea caerulescens] violaxanthin de-epoxidase, chloroplastic- 100% 0 87% NP_001302836.1 like [Brassica napus] BnaC05g06200D [Brassica napus] 100% 0 87% CDX95051.1 hypothetical protein EUTSA_v10007587 100% 0 88% XP_006417674.1 mg [Eutrema salsugineum] Violaxanthin de-epoxidase, chloroplastic 100% 0 87% JAU77894.1 [Noccaea caerulescens] PREDICTED: violaxanthin de-epoxidase, 100% 0 74% XP_010528777.1 chloroplastic [Tarenaya hasleriana] NPQ1 [Arabidopsis thaliana] 72% 0 100% OAP18415.1 PREDICTED: violaxanthin de-epoxidase, 88% 0 76% XP_010043341.1 chloroplastic [Eucalyptus grandis] PREDICTED: violaxanthin de-epoxidase, 89% 0 74% XP_017627747.1 chloroplastic isoform X2 [Gossypium arboreum] hypothetical protein MANES_09G144600 91% 0 73% OAY41983.1 [Manihot esculenta] Non-photochemical quenching 1 isoform 1 91% 0 73% EOY10737.1 [Theobroma cacao] PREDICTED: violaxanthin de-epoxidase, 82% 0 79% XP_017627745.1 chloroplastic isoform X1 [Gossypium arboreum] PREDICTED: violaxanthin de-epoxidase, 82% 0 79% XP_016673034.1 chloroplastic-like [Gossypium hirsutum] PREDICTED: violaxanthin de-epoxidase, 91% 0 72% XP_007030235.2 chloroplastic [Theobroma cacao] hypothetical protein PQPTR_0013s05000 83% 0 78% XP_002319136.2 g [Populus trichocarpa] PREDICTED: violaxanthin de-epoxidase, 83% 0 78% XP_017627748.1 chloroplastic isoform X3 [Gossypium arboreum] PREDICTED: violaxanthin de-epoxidase, 84% 0 78% XP_012092715.1 chloroplastic [Jatropha curcas] chloroplast violaxanthin de-epoxidase 81% 0 79% AIZ75647.1 [Prunus humilis] PREDICTED: violaxanthin de-epoxidase, 81% 0 79% XP_009379699.1 chloroplastic isoform X1 [Pyrus x bretschneideri] PREDICTED: violaxanthin de-epoxidase, 81% 0 79% XP_009379700.1 chloroplastic isoform X2 [Pyrus x bretschneideri] violaxanthin de-epoxidase 1 [Bixa orellana] 94% 0 68% AMJ39491.1 hypothetical protein PRUPE_ppa005029 81% 0 79% XP_007207430.1 mg [Prunus persica] PREDICTED: violaxanthin de-epoxidase, 82% 0 78% XP_002267152.1 chloroplastic [Vitis vinifera] PREDICTED: violaxanthin de-epoxidase, 81% 0 79% XP_016651828.1 chloroplastic [Prunus mume] hypothetical protein CICLE_v10019925 82% 0 77% XP_006443345.1 mg [Citrus Clementina] hypothetical protein PRUPE_6G356100 81% 0 79% ONI05101.1 [Prunus persica] hypothetical protein PRUPE_6G356100 81% 0 79% ONI05102.1 [Prunus persica] unnamed protein product [Vitis vinifera] 82% 0 78% CBI28686.3 hypothetical protein CISIN_1g011550 82% 0 77% KDO45543.1 mg [Citrus sinensis] PREDICTED: violaxanthin de-epoxidase, 81% 0 79% XP_008388766.1 chloroplastic [Malus domestica] violaxanthin de-epoxidase [Citrus sinensis] 84% 0 74% NP_001275810.1 violaxanthin de-epoxidase 1 [Vitis vinifera] 82% 0 78% AFP28802.1 PREDICTED: violaxanthin de-epoxidase, 89% 0 75% XP_012492660.1 chloroplastic isoform X2 [Gossypium raimondii] hypothetical protein B456_007G268500 89% 0 75% KJB44721.1 [Gossypium raimondii] PREDICTED: LOW QUALITY PROTEIN: 81% 0 78% XP_008350656.1 violaxanthin de-epoxidase, chloroplastic-like [Malus domestica] PREDICTED: violaxanthin de- 100% 0 67% XP_011034433.1 epoxidase, chloroplastic [Populus euphratica] VDE domain-containing protein [Cephalotus 81% 0 82% GAV86158.1 follicularis] PREDICTED: violaxanthin de-epoxidase, 82% 0 79% XP_012492659.1 chloroplastic isoform X1 [Gossypium raimondii] PREDICTED: violaxanthin de-epoxidase, 82% 0 79% XP_012492661.1 chloroplastic isoform X3 [Gossypium raimondii] PREDICTED: violaxanthin de-epoxidase, 84% 0 73% XP_004302125.1 chloroplastic [Fragaria vesca subsp. vesca] PREDICTED: violaxanthin de-epoxidase, 90% 0 76% XP_015901670.1 chloroplastic [Ziziphus jujuba] violaxanthin de-epoxidase [Fragaria x ananassa] 84% 0 72% AFR11775.2 hypothetical protein B456_007G268500 82% 0 79% KJB44724.1 [Gossypium raimondii] Violaxanthin de-epoxidase, chloroplastic 89% 0 72% KHG25773.1 [Gossypium arboreum] RecName: Full = Violaxanthin de-epoxidase, 82% 0 75% Q9SM43.2 chloroplastic; Flags: Precursor PREDICTED: violaxanthin de-epoxidase, 82% 0 75% XP_008810272.1 chloroplastic [Phoenix dactylifera] Violaxanthin de-epoxidase [Corchorus capsularis] 83% 0 78% OMO84679.1 violaxanthin de-epoxidase [Coffea arabica] 79% 0 82% ABB70816.1 PREDICTED: violaxanthin de-epoxidase, 82% 0 75% XP_010913044.1 chloroplastic isoform X2 [Elaeis guineensis] PREDICTED: violaxanthin de-epoxidase, 82% 0 75% XP_010913041.1 chloroplastic isoform X1 [Elaeis guineensis] Violaxanthin de-epoxidase [Morus notabilis] 85% 0 72% XP_010109315.1 PREDICTED: violaxanthin de-epoxidase, 83% 0 78% XP_002525473.1 chloroplastic [Ricinus communis] violaxanthin de-epoxidase [Coffea canephora] 79% 0 82% ABB70514.1 PREDICTED: violaxanthin de-epoxidase, 82% 0 78% XP_010247237.1 chloroplastic isoform X1 [Nelumbo nucifera] PREDICTED: violaxanthin de-epoxidase, 82% 0 78% XP_010247238.1 chloroplastic isoform X2 [Nelumbo nucifera] violaxanthin de-epoxidase [Camellia sinensis] 84% 0 77% AJB84625.1 PREDICTED: violaxanthin de-epoxidase, 84% 0 76% XP_018826961.1 chloroplastic [Jugians regia] PREDICTED: violaxanthin de-epoxidase, 81% 0 76% XP_006652202.2 chloroplastic [Oryza brachyantha] violaxanthin deepoxidase [Chrysanthemum x 83% 0 78% BAE79554.1 morifolium] violaxanthin de-epoxidase [Medicago truncatula] 79% 0 79% XP_003626506.2 RecName: Full = Violaxanthin de-epoxidase, 79% 0 81% Q40251.1 chloroplastic; Flags: Precursor violaxanthin deepoxidase [Chrysanthemum boreale] 83% 0 79% AGU91436.1 violaxanthin de-epoxidase [Camellia sinensis] 84% 0 77% AAL67858.2 violaxanthin de-epoxidase [Citrus limon] 81% 0 75% BAO18773.1 violaxanthin de-epoxidase, chloroplastic 83% 0 76% XP_020111643.1 [Ananas comosus] violaxanthin de-epoxidase [Citrus sinensis] 81% 0 75% BAO18772.1 PREDICTED: violaxanthin de-epoxidase, 81% 0 78% XP_006576259.1 chloroplastic-like isoform X5 [Glycine max] PREDICTED: violaxanthin de-epoxidase, 79% 0 79% XP_006830529.1 chloroplastic [Amborella trichopoda] PREDICTED: violaxanthin de-epoxidase, 81% 0 77% XP_004975369.1 chloroplastic [Setaria italica] PREDICTED: violaxanthin de-epoxidase, 65% 0 96% XP_010462602.2 chloroplastic-like [Camelina sativa] violaxanthin de-epoxidase [Citrus unshiu] 81% 0 74% BAN91498.1 violaxanthin de-epoxidase, chloroplastic 97% 0 68% XP_020213947.1 isoform X2 [Cajanus cajan] PREDICTED: violaxanthin de-epoxidase, 82% 0 75% XP_015636342.1 chloroplastic [Oryza sativa Japonica Group] violaxanthin de-epoxidase, chloroplastic 97% 0 68% XP_020213942.1 isoform X1 [Cajanus cajan] PREDICTED: violaxanthin de-epoxidase, 81% 0 78% XP_014628869.1 chloroplastic-like isoform X3 [Glycine max] PREDICTED: violaxanthin de-epoxidase, 81% 0 78% XP_014628868.1 chloroplastic-like isoform X1 [Glycine max] Violaxanthin de-epoxidase, chloroplastic 81% 0 78% KHN35342.1 [Glycine soja] PREDICTED: violaxanthin de-epoxidase, 84% 0 75% XP_010674199.1 chloroplastic [Beta vulgaris subsp. vulgaris] PREDICTED: violaxanthin de-epoxidase, 81% 0 78% XP_006576257.1 chloroplastic-like isoform X2 [Glycine max] violaxanthin de-epoxidase, chloroplastic-like 81% 0 78% NP_001241404.1 precursor [Glycine max] PREDICTED: violaxanthin de-epoxidase, 81% 0 79% XP_004494767.1 chloroplastic isoform X1 [Cicer arietinum] violaxanthin de-epoxidase precursor [Oryza 82% 0 75% AAL09678.1 sativa Japonica Group] OSJNBb0089B03.4 [Oryza sativa Japonica 82% 0 75% CAE03990.1 Group] violaxanthin de-epoxidase precursor [Oryza 81% 0 76% AAF97601.3 sativa Indica Group] PREDICTED: violaxanthin de-epoxidase, 81% 0 79% XP_004494768.1 chloroplastic isoform X2 [Cicer arietinum] hypothetical protein TSUD_347010 81% 0 78% GAU13597.1 [Trifolium subterraneum] hypothetical protein LR48_Vigan10g159600 79% 0 79% KOM55704.1 [Vigna angularis] violaxanthin de-epoxidase, chloroplastic-like 81% 0 77% NP_001240949.1 [Glycine max] PREDICTED: violaxanthin de-epoxidase, 79% 0 78% XP_017437597.1 chloroplastic [Vigna angularis]

Example 22. Greenhouse NPQ Expression Experiment

(303) Nicotiana tabacum was transformed with the coding sequences of Arabidopsis VDE, ZEP, and PsbS under the control of different promoters for expression in leaves. Two transformants with a single transfer DNA (T-DNA) integration (VPZ-34 and -56) and one transformant with two T-DNA insertions (VPZ-23) were selected based on a seedling NPQ screen and self-pollinated to obtain homozygous T.sub.2 progeny for further investigation. These plants were then grown in a greenhouse. Levels of mRNA and protein of VDE, PsbS, and ZEP were measured (FIG. 25).

(304) All three VPZ lines showed increases in total (transgenic plus native) transcript levels of VDE (10-fold), PsbS (threefold), and ZEP (sixfold) relative to those of WT (A, C, and E). For PsbS, the increase in transcript levels translated into an approximately fourfold-higher PsbS protein level (D), as exemplified in bands at 21 kDa (AtPsbS) and 24 kDa (NtPsbS) (G). For VDE and ZEP, the increase in transcript levels corresponded to 30-fold for VDE (45 kDa) (B and G) and 74-fold for ZEP (73 kDa) (F and G) increases over WT protein levels.

Example 23. Field NPQ Expression Experiment

(305) Nicotiana tabacum was transformed with the coding sequences of Arabidopsis VDE, ZEP, and PsbS under the control of different promoters for expression in leaves. Two transformants with a single transfer DNA (T-DNA) integration (VPZ-34 and -56) and one transformant with two T-DNA insertions (VPZ-23) were selected based on a seedling NPQ screen and self-pollinated to obtain homozygous T.sub.2 progeny for further investigation. These plants were then grown in a field. Levels of mRNA and protein of VDE, PsbS, and ZEP were measured (FIG. 26).

(306) All three VPZ lines showed increases in total (transgenic plus native) transcript levels of VDE (4-fold), PsbS (1.2-fold), and ZEP (7-fold) relative to those of WT. All three VPZ lines also showed increases in total (transgenic plus native) protein levels of VDE (47-fold), PsbS (3-fold), and ZEP (75-fold) relative to those of the WT.

Example 24. Transgenic Rice Experiment

(307) Rice plants were transformed with a T-DNA construct containing nucleotide sequences encoding PsbS, ZEP and VDE, following the transformation protocol described in Example 15. The same expression construct used in the transgenic tobacco experiment was used in this experiment. Leaves of nine independent T.sub.0 transformants and two GUS controls were dark adapted. Subsequently, NPQ was measured during 10 min of 1000 mol m-2 s-1 light followed by 3 min of darkness. FIG. 31 shows the NPQ of the nine rice transformants (dots) and the control (line) over the course of 10 min of 1000 mol m-2 s-1 light followed by 3 min of darkness. FIG. 32 shows the average of NPQ of the nine rice transformants (blue dot) and the control (orange dot) over the course of 10 min of 1000 mol m-2 s-1 light followed by 3 min of darkness.

(308) As shown in FIG. 31 and FIG. 32, NPQ amplitudes of these nine transformants were lower than the control during the 10 min of 1000 mol m-2 s-1 light. This result is consistent with increased expression of ZEP in these transformants, which prevents zeaxanthin formation and thus reduces NPQ amplitude. An alternative explanation is that PsbS overexpression interferes with expression of native PsbS and thus reduces the NPQ amplitude. Results also showed that there was no significant difference in NPQ between the transformants and the control during the 3-min relaxation in the dark, due to the possible lack of zeaxanthin built up in this experiment.

(309) The lack of change in NPQ kinetics in these transgenic rice plants is most plausibly ascribed to a limitation of the experimental design: in this experiment, the rice plants were transformed with an expression cassette constructed for tobacco transformation, which contains promoters designed for optimal gene expression in dicot plants. It is known in the art that dicot promoters do not work well in monocot plants. Therefore, expression of PsbS, ZEP and VDE in these transgenic rice plants was likely not optimally increased to the level that would be conducive to increase of NPQ relaxation rate.

Example 25. Additional Experiments

(310) Transient overexpression of NPQ-related genes was conducted in Nicotiana benthamiana. Measurements of NPQ were taken on leaf spots overexpressing FLAG-tagged PsbS, VDE, ZEP, and GUS as a negative control, during 13 min illumination at 600 mol photons m-2 s-1, followed by 10 min of dark. As shown in FIG. 18, results showed that overexpression of PsbS increased NPQ capacity relative to the GUS control. Overexpression of VDE sped up NPQ induction. Overexpression of ZEP sped up NPQ relaxation but negatively impacted NPQ induction and capacity.

(311) Transient co-overexpression of VDE and ZEP was conducted in Nicotiana benthamiana. Results showed an increased rate of NPQ induction and relaxation as seen in FIG. 19. Co-overexpression of VDE was shown necessary to balance overexpression of ZEP and prevent negative impact of ZEP overexpression on NPQ induction and capacity.

(312) FIG. 20 shows the NPQ kinetics of stable transgenic T.sub.1 plants of Nicotiana tabacum cv. Petite Havana. NPQ measurements with DUAL PAM were taken on the youngest fully developed leaf of T.sub.1 adult plants for three different lines: one wild-type segregant (Null), one overexpressing ZEP (ZEP) and one overexpressing ZEP and VDE (ZEP-VDE), during 10 min illumination at 600 mol photons m-2 s-1, followed by 10 min of dark. Results showed that the ZEP-VDE line showed faster NPQ induction and relaxation.

(313) FIG. 21 shows the photosystem II quantum yield (YII) of stable transgenic T.sub.1 plants of Nicotiana tabacum cv. Petite Havana. Measurements of YII performed simultaneously with NPQ measurements described in FIG. 20, were taken on the same plants and in the same conditions. During the dark recovery period, YII was higher for the line overexpressing ZEP-VDE compared to the one overexpressing ZEP or the Null.

(314) FIG. 22 shows the growth experiment in the greenhouse. Results demonstrated the increased size and biomass of stable transgenic T.sub.1 plants of Nicotiana tabacum cv. Petite Havana that overexpress ZEP and VDE (ZEP-VDE), compared to wild type (Null). Lines overexpressing PsbS (PsbS) or ZEP and PSBS (ZEP-PsbS) showed a similar biomass to wild type. Four sets of plants are shown in the figure, one per transgenic line. Each set contains 36 plants. The above-ground biomass for each set was determined by the total wet weight and total dry weight of the harvest of the 36 plants, after 19 days of growth. The data represent the results of a single experiment.