RICE PAL1 GENE, AND ENCODING PROTEIN AND USE THEREOF

Abstract

The present disclosure relates to a rice PAL1 gene, an encoding protein and use thereof. The rice PAL1 gene has the nucleotide sequence shown in SEQ ID NO. 1, and the rice PAL1 protein has the amino acid sequence shown in SEQ ID NO. 4. Mutation of the gene leads to reduction of rice plant height and panicle length, while decreasing the number of primary branches, secondary branches and grains per panicle. It is found that the PAL1 gene can restore a mutant panicle type to a normal phenotype. The present disclosure provides a PAL1 gene functioning as a regulator of the rice panicle length and an encoding protein thereof. A rice panicle type is an important trait influencing rice yield. Therefore, it will be desired to directionally design a plant type and improve the rice yield by regulating panicle traits of rice with the PAL1 gene.

Claims

1. A method for regulating rice panicle length, number of branches, or number of grains per panicle, wherein the method comprises using a rice PAL1 protein, an encoding gene of the rice PAL1 protein, or a biomaterial comprising the encoding gene of the rice PAL1 protein; wherein the rice PAL1 protein has the amino acid sequence shown in SEQ ID NO. 4; the encoding gene of the rice PAL1 protein has the nucleotide sequence shown in SEQ ID NO. 1; the biomaterial is an expression cassette, a vector, a host bacterium, or a host cell that cannot be reproduced as a plant individual.

2. The method according to claim 1, wherein the regulating rice panicle length, number of branches, or number of grains per panicle comprising increasing rice panicle length, number of branches, or number of grains per panicle.

3. A method for preparing transgenic rice with high number of grains per panicle or high yield, wherein the method comprises using a rice PAL1 protein, an encoding gene of the rice PAL1 protein, or a biomaterial comprising the encoding gene of the rice PAL1 protein; wherein the rice PAL1 protein has the amino acid sequence shown in SEQ ID NO. 4; the encoding gene of the rice PAL1 protein has the nucleotide sequence shown in SEQ ID NO. 1; the biomaterial is an expression cassette, a vector, a host bacterium, or a host cell that cannot be reproduced as a plant individual.

4. A mutant gene of a rice PAL1 gene, wherein the mutant gene is a sequence of 6 bases deleted from positions 256 to 261 of a CDS sequence of the rice PAL1 gene shown in SEQ ID NO. 3, and a deleted sequence is “gaccag”.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0032] FIGS. 1A-1I illustrate phenotypes of wild-type Huaidao No. 5 and pal1 mutant provided by the present disclosure, in which FIG. 1A illustrates the plant phenotype, FIG. 1B illustrates closed panicle types, FIG. 1C illustrates patulous panicle types, and FIG. 1D illustrates patulous branches, FIG. 1E to 1I illustrate the statistical analysis of plant height, panicle length, number of primary branches, number of secondary branches, and number of grains per panicle.

[0033] FIGS. 2A-2D illustrate the mapping and structure of the PAL1 gene of the present disclosure.

[0034] FIG. 3 is a schematic diagram of the structure of the vector pCAMBIA 1305.1::PAL1 of the present disclosure.

[0035] FIGS. 4A-4F illustrate a comparison of panicle types of wild-type, pal1 mutant, and PAL1 transgenic complementary plants. Herein, FIG. 4A illustrates closed panicle types, and FIG. 4B illustrates patulous panicle types. FIGS. 4C to 4F illustrate the statistical analysis of panicle length, number of primary branches, number of secondary branches, and number of grains per panicle. In T.sub.0 transgenic plants, a total of 15 independent transformed lines are obtained, 10 of which are restored to wild-type phenotypes, named B590-1, B590-2, . . . B590-10, respectively; investigation and statistics are made on panicle traits of transgenic plants B590-1 and B590-2, and results show that the panicle length, the number of primary branches, the number of secondary branches, and the number of grains per panicle are significantly greater in the transgenic plants than in the pal1 mutant, and reach the wild-type levels. All of the other 8 transgenic plants, B590-3 to B590-10, have similar phenotypes.

[0036] FIG. 5 illustrates an expression pattern analysis of the PLA1 gene of the present disclosure in various tissues of rice.

[0037] FIGS. 6A-6G illustrate changes in the apical meristem and young panicle primordium of the rice pal1 mutant of the present disclosure. Herein, FIG. 6A and FIG. 6BB are the longitudinal section of the apical meristem; FIG. 6C illustrates a statistical analysis of the longitudinal section area of the apical meristem; FIG. 6D and FIG. 6E illustrate scanning electron microscopic observations of the apical meristem and young panicle primordia; FIG. 6F and FIG. 6G illustrate statistical analyses of the longitudinal area of the apical meristem and the number of primary rachis branch primordia, respectively.

DETAILED DESCRIPTION OF THE EMBODIMENTS

[0038] The preferred implementation of the present disclosure will be described in detail below in conjunction with examples.

[0039] All experimental methods used in the following examples are conventional methods, unless otherwise specified. All materials and reagents used in the following examples can be commercially available, unless otherwise specified.

Example 1 Acquisition and Phenotypic Analysis of pal1 Mutant

[0040] A mutant pal1 (panicle length 1) with lower plant height and shorter panicle length was obtained by radiation mutagenesis of a japonica rice cultivar Huaidao No. 5 by .sup.60Co-γ irradiation (Yuan C Y, Yuan S T, Wen Z H, et al. Characteristics and high-yielding cultivation technique of Huaidao No. 5[J]. China Rice, 2002, (4): 14). Twenty samples of wild type and pal1 mutants were selected, respectively; statistical analyses were conducted on their plant height, panicle length, number of primary branches, number of secondary branches, and number of grains per panicle. The analysis results showed that the plant height of the rice pal1 mutant was significantly lowered by 15.2% compared with the wild type (A and E in FIG. 1). Compared with the wild type, the panicle length of the pal1 mutant was significantly shortened by 25.6%, and the number of primary branches and the number of secondary branches were also significantly reduced by 22.0% and 45.9%, respectively (B, C, D, F, G and H in FIG. 1); eventually, the number of grains per panicle was significantly reduced by 40.2% (I in FIG. 1).

Example 2 Acquisition of Rice PAL1 Gene

[0041] The pal1 mutant was crossed with the indica rice cultivar Dular with normal phenotype and high nucleotide acid polymorphism to obtain F.sub.1, F.sub.1 was selfed to obtain F.sub.2 segregation population, and the F.sub.2 population was used for genetic analysis and gene mapping. The analysis of the lines with trait segregation in the F.sub.2 showed that the normal plant and the mutant plant met a segregation ratio of 3:1, which indicated that the mutant trait was controlled by a pair of recessive genes.

[0042] With 30 F.sub.2 mutants as materials, primary mapping was conducted by using a plurality of InDel markers developed by the alignment of the whole genome sequence of the indica rice cultivar Dular sequenced in this experiment to the genome sequence of a japonica rice cultivar Nipponbare provided on NCBI (http://www.ncbi.nlm.nih.gov/) and uniformly distributed on 12 chromosomes of rice; candidate genes were mapped between R3-17 and R3-20 markers on chromosome 3 (A in FIG. 2). In order to further finely map the candidate genes, the F.sub.2 mapping population continued to be expanded to 299 plants, while developing new markers X1, X2, X3, X4, X5, and X6 for linkage analysis (see Table 1 for the primers used); it was found that recombination events occurred at these markers were 5, 32, 2, 22, 0, and 1, respectively, indicating that the candidate genes were mapped between X3 and X6 (B in FIG. 2).

[0043] The physical distance between the two markers X3 and X6 is 86 kb (C in FIG. 2). According to the gene annotation information provided by the Rice Genome Annotation Project (rice.uga.edu/), there are 10 genes between the markers X3 and X6 (C in FIG. 2). Herein, the function of the gene numbered LOC_Os03g50860 is inferred to be related to the phenotype. For this reason, the full-length genomic DNA of this gene is subjected to segmental PCR amplification. Each segment is about 1.5 kb in size, with a total of 6 fragments (see Table 2 for the primers used). DNAStar software is used to analyze the sequencing results of the wild type and mutants. The analysis results show that in the pal1 mutant, a total of 6 bases from positions 256 to 261 after the initiation codon of the gene are deleted (D in FIG. 2), resulting in the deletion of one aspartic acid and one glutamine. The full length of PAL1 genomic DNA is 6249 bp (including 5′UTR and 3′UTR) (as shown in SEQ ID NO. 1), which contains 11 exons; the CDS has a full length of 3018 bp (as shown in SEQ ID NO. 3), encoding a protein consisting of 1013 amino acids (as shown in SEQ ID NO. 4). The primer sequences of the molecular markers involve in Example 2 are shown in Table 1.

TABLE-US-00001 TABLE 1 The primer sequences of the molecular markers Molec- Sequence of SEQ Sequence of SEQ ular forward primer ID reverse primer ID marker (5′-3′) NO. (5′-3′) NO. R3-16 AAGGTTAGGCGTGG  5 GAGATGAAGGAATG  6 ATTCCTC TTCAGTCC R3-17 TGGGCTATTATTGG  7 CGTGGGATAAAACC  8 GCTTTG ACCAAG R3-20 CAACTGCCCAGCTA  9 TTTGGGACGGAGGA 10 TATTGC AGTAGT X1 TGCTGCCGGCGATT 11 TTCGAGACGGGGAT 12 AACAACT TTGATG X2 GATGGGTTCGCATC 13 CTTACCCAGTCTCG 14 GTCAC AGGTAG X3 GACTCAGAGACGGG 15 CGTGGCGACTGATC 16 GACTAG AGCG X4 TGGAGAGAGTACAG 17 GAAGCATTGTACTT 18 TACTAC CTAGTC X5 AGGCGCGTAGAATT 19 AAAGCTGCCCAAAC 20 CCTAGT TATGCG X6 GCTTATGCGTCACA 21 AAAGGTTTGCGTAC 22 TCACTAC AGCGAG

[0044] The sequencing primer sequences involved in Example 2 were shown in Table 2.

TABLE-US-00002 TABLE 2 The sequencing primer sequences Name Forward SEQ Reverse SEQ of sequence ID sequence ID primer (5′-3′) NO. (5′-3′) NO. Frag_1 AAGTCAACGGT 23 CATGGTCTTG 24 GTCATACGA ATGATCCACC Frag_2 GTGTGGCTGAT 25 GGTGTTCTGA 26 GAATCTTCT TCTCATGAGA Frag_3 CTTGGAGTCGC 27 CTGGACGGTA 28 TACGATAATG ATGGGTGCAA Frag_4 CAAGCTGACAG 29 GATAGTCAAC 30 CTCAACTTC GAGGTGGCAC Frag_5 CAAGGTAAACC 31 CCAGCAACAC 32 TCAGAGTGGC ACCTGTGGCT Frag_6 TTGTTGCTCTT 33 CATGTTAGCC 34 CAACAGAGG ACGATGCCTC

Example 3 pCAMBIA1305.1::PAL1 Vector Transformed Rice pal1 Mutant

[0045] In order to carry out a functional complementation assay, a functional complementary vector driven by the PAL1 gene promoter was constructed. A fragment of 2525 bp upstream of the translation initiation site ATG was selected as the promoter of the gene, and the promoter region and the genomic DNA (without 3′UTR) were amplified simultaneously. One EcoRI site was introduced into the 5′-end of the amplified fragment and one PmlI site was introduced into the 3′-end. The PCR product was 8836 bp in length (including the homologous sequence on the vector). Finally, the PAL1 gene promoter and the entire genome of 8802 bp (shown in SEQ ID NO. 2) were ligated between the EcoRI and PmlI sites of the pCAMBIA1305.1 vector to form a complementary vector driven by its own promoter (FIG. 3).

[0046] The constructed complementary vector was transformed into Agrobacterium EHA105 and infected the callus induced from the pal1 mutant seeds. In the T.sub.0 transgenic plants, a total of 15 independent transformed lines were obtained, 10 of which were restored to the wild-type phenotypes. Investigation and statistics were made on panicle traits of transgenic plants, and results showed that the panicle length, the number of primary branches, the number of secondary branches, and the number of grains per panicle were significantly greater in the transgenic plant (B590) than in the pal1 mutant, and reached the wild-type levels (A-F in FIG. 4). These results indicated that the reduced panicle type of the pal1 mutant was indeed caused by PAL1 gene mutation. The primer sequences involved in Example 3 were shown in Table 3.

TABLE-US-00003 TABLE 3 The sequences of primers for PAL1 gene amplification Forward sequence Reverse sequence Name of (5′-3′) (5′-3′) primer (SEQ ID NO. 35) (SEQ ID NO. 36) promPAL1 CCATGATTACGAATTC GTCACCAATTCACACG CGTGAACAATGTCTAC TGCTACCAGCCTACAG GTAGGAGG CATAGTACTC

Example 4 Expression Pattern of Rice PAL1 Gene

[0047] In order to clarify the tissue expression pattern of the PAL1 gene, real-time qPCR was used to detect the expression levels of the gene in various tissues of rice, including root, stem, leaf blade, shoot base, leaf sheath, and young panicles of different lengths. The results showed that the PAL1 gene was expressed in all tissues of rice, with higher expression in the stem and panicles, and the highest expression in the shoot base (FIG. 5). The expression intensity of the PAL1 gene in different organs and parts was consistent with the functional role of the gene. The primer sequences involved in Example 4 were shown in Table 4.

TABLE-US-00004 TABLE 4 The sequences of primers used in real-time qPCR Forward SEQ Reverse SEQ Name of sequence ID sequence ID primer (5′-3′) NO. (5′-3′) NO. Ubiquitin AACCAGCTGA 37 ACGATTGATTTA 38 GGCCCAAGA ACCAGTCCATGA qPAL1 CAAGATTCCA 39 GCCTGTCGCTTC 40 ATAGCCCAGC ATCGTC

Example 5 the Effects of pal1 on Apical Meristem and Panicle Primordia

[0048] In order to clarify how the pal1 shortened the panicle length and reduced the yield, the meristem development was observed in the vegetative and reproductive growth phases. In the vegetative growth phase, the longitudinal sections of the shoot apical meristems (SAMs) of the wild type and the pal1 mutant were observed under a laser scanning confocal microscope. The results showed that compared with the wild type, the apical meristem of the pal1 mutant became smaller significantly (A and B in FIG. 6). Statistical analysis showed that the longitudinal section area of the apical meristem of the pal1 mutant was significantly reduced (C in FIG. 6). At the same time, using scanning electron microscopy, observations were conducted on the apical meristems in the critical period of vegetative growth and reproductive growth phases, as well as the formation of primary rachis branch primordia in the reproductive growth phase. The results showed that the apical meristem of the pal1 mutant in the vegetative growth phase was significantly smaller than that of the wild type (D in FIG. 6). At the same time, the number of primary primordia were reduced by 2-4 (E in FIG. 6). Statistical analysis showed that both the longitudinal area of the apical meristem and the number of primary rachis branch primordia of the pal1 mutant were significantly reduced (F and G FIG. 6). Therefore, pal1 may influence the activity of the meristem, making the apical meristem smaller and reducing the number of rachis branch primordial. Ultimately, the panicle length was shortened, the number of branches and the number of grains per panicle were reduced, and the yield was lowered.

[0049] Although the general description and specific embodiments have been used to describe the present disclosure in detail above, it is apparent to those skilled in the art that some modifications or improvements can be made on the basis of the present disclosure. Therefore, these modifications or improvements made without departing from the spirit of the present disclosure fall within the protection scope of the present disclosure.