Method for obtaining glyphosate-resistant rice by site-directed nucleotide substitution

Abstract

The present invention discloses a method for obtaining glyphosate-resistant rice by a site-directed nucleotide substitution, and also relates to a method capable of generating a site-directed nucleotide substitution and a fragment substitution. The method for obtaining a glyphosate-resistant plant provided by the present invention comprises the following steps: only substituting threonine (T) at position 8 of the amino acid sequence of a conserved region of endogenous EPSPS protein of a target plant with isoleucine (I), and substituting proline (P) at position 12 with serine (S) to obtain a plant, i.e., a glyphosate-resistant plant. The method provided by the present invention is of great significance in breeding new herbicide-resistant plant varieties. The present invention also discloses a method for utilizing a CRISPR-mediated NHEJ pathway to substitute a region between two gRNA sites by designing the two gRNA sites, thereby realizing a site-directed mutation of a target nucleotide and site-directed substitution of a fragment.

Claims

1. A method for substituting a target nucleotide for a desired nucleotide in a target gene of a target plant's genome, comprising the step of introducing the following into a cell or tissue of the target plant via gene gun transformation: a first genetic material, a second genetic material and a donor vector: the first genetic material is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a first CRISPR/Cas9 nuclease; the second genetic material is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a second CRISPR/Cas9 nuclease; wherein the first CRISPR/Cas9 nuclease is able to specifically cleave a first target fragment in the genome of the target plant and the donor vector; and wherein the second CRISPR/Cas9 nuclease is able to specifically cleave a second target fragment in the genome of the target plant and the donor vector, wherein the donor vector additionally comprises a mutation target sequence released by the cleavage of the donor vector by the first and second CRISPR/Cas9 nucleases; the mutation target sequence contains a DNA fragment sequence corresponding to a sequence in the genome of the target plant from the 5′ end of a first target fragment to the 3′ end of a second target fragment, which contains the desired nucleotide substitution; wherein the first target fragment is positioned in an intron region or a promoter region in the genome of the target plant upstream of the target nucleotide of the target gene in the genome of the target plant; wherein the second target fragment is positioned in an intron region or a 3′-UTR region in the genome of the target plant downstream of the target nucleotide of the target gene in the genome of the target plant, wherein the target nucleotide is located in an exon of the target gene, wherein the first genetic material, the second genetic material, and the donor vector are delivered simultaneously in a molar ratio of 1:1:2.

2. The method according to claim 1, wherein the cell is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture; or the tissue is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture.

3. The method according to claim 2, wherein said plant is Arabidopsis; said target gene is Atsnc1(At4g16890) of SEQ ID NO: 9; said first sequence specific nuclease comprises a sgDNA corresponding to SEQ ID NO: 12; said second sequence specific nuclease comprises a sgDNA corresponding to SEQ ID NO: 13; said mutation target sequence is set forth in SEQ ID NO.14; substitution of the target nucleotide results in the replacement of Exon 3 of Atsnc1 of SEQ ID NO: 10 with SEQ ID NO: 11, and thus conferring on the plant the resistance against Pseudomonas syringae pv maculicola ES4326 and Peronospora parasitica Noco2.

4. The method according to claim 1, wherein said target plant is rice or Arabidopsis.

5. A method for obtaining a glyphosate-resistant plant, the method comprising: substituting threonine (T) at position 8 of the amino acid sequence of a conserved region of endogenous EPSPS protein of a target plant with isoleucine (I), and substituting proline (P) at position 12 with serine (S) to obtain a glyphosate-resistant plant, wherein the conserved region of the endogenous EPSPS protein of the target plant comprises the amino acid sequence of SEQ ID NO: 2, wherein the substituting step comprises introducing the following into a cell or tissue of the target plant via gene gun transformation: a first genetic material, a second genetic material and a donor vector: the first genetic material is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a first CRISPR/Cas9 nuclease; the second genetic material is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a second CRISPR/Cas9 nuclease; wherein the first CRISPR/Cas9 nuclease is able to specifically cleave a first target fragment in the genome of the target plant and the donor vector; and wherein the second CRISPR/Cas9 nuclease is able to specifically cleave a second target fragment in the genome of the target plant and the donor vector, wherein the donor vector additionally comprises a mutation target sequence released by the cleavage of the donor vector by the first and second CRISPR/Cas9 nucleases; the mutation target sequence contains a DNA fragment sequence corresponding to a sequence in the genome of the target plant from the 5′ end of a first target fragment to the 3′ end of a second target fragment, which contains the desired nucleotide substitution; wherein the first target fragment is positioned in an intron region or a promoter region in the genome of the target plant upstream of the nucleotide sequence encoding the amino acid sequence of the conserved region of the endogenous EPSPS protein, wherein the second target fragment is positioned in an intron region or a 3′-UTR region in the genome of the target plant downstream of a nucleotide sequence encoding the amino acid sequence of the conserved region of the endogenous EPSPS protein, wherein the nucleotide substitution is a mutation by which threonine (T) at position 8 of the amino acid sequence of the conserved region of endogenous EPSPS protein of a target plant is substituted with isoleucine (I), and proline (P) at position 12 is substituted with serine (S), and wherein the first genetic material, the second genetic material, and the donor vector are delivered simultaneously in a molar ratio of 1:1:2.

6. The method according to claim 5, wherein (a) the first target fragment is positioned in an intron region in the genome of the target plant upstream of the first intron region comprising a nucleotide sequence encoding the amino acid sequence of the conserved region of the endogenous EPSPS protein; wherein the nucleotide sequence of the first intron region comprises the nucleotides from position 1 to 704 of SEQ ID NO: 3; wherein both the first sequence specific nuclease and the second sequence specific nuclease are CRISPR/Cas9 nucleases, and wherein the first target fragment is a fragment complying with the formula of 5′-N.sub.X-NGG-3′ or 5′-CCN-N.sub.X-3′ within the nucleotide sequence corresponds to position 1-704 of SEQ ID NO: 3; wherein N represents any one of A, G, C, and T; 14≤X≤30 and X is an integer; and wherein N.sub.X represents X consecutive nucleotides; and/or (b) the second target fragment is positioned in an intron region in the genome of the target plant downstream of the second intron region comprising a nucleotide sequence encoding the amino acid sequence of the conserved region of the endogenous EPSPS protein, wherein the nucleotide sequence of the second intron region comprises the nucleotides from position 950 to 1030 of SEQ ID No. 3, and wherein both the first and second sequence specific nucleases are CRISPR/Cas9 nucleases, and wherein the second target fragment is a fragment comprising a sequence of the formula of 5′-N.sub.X-NGG-3′ or 5′-CCN-N.sub.X-3′ within a nucleotide sequence comprised of the nucleotides from position 950 to 1030 of SEQ ID NO: 3, wherein N represents any one of A, G, C, and T; 14≤X≤30 and X is an integer; and N.sub.X represents X consecutive nucleotides.

7. The method according to claim 6, wherein the nucleotide sequence of the first target fragment is SEQ ID NO: 4; and wherein the nucleotide sequence of the second target fragment is SEQ ID NO: 5.

8. The method according to claim 7, wherein the first genetic material is a recombinant plasmid obtained by substituting the fragment between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID NO: 4, wherein the second genetic material is a recombinant plasmid obtained by substituting the fragment between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID NO: 5, or wherein the nucleotide sequence of the mutation target sequence carried by the donor vector is set forth in SEQ ID NO: 6.

9. The method according to claim 5, wherein the cell is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture, and wherein the tissue is any tissue that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 is a schematic diagram showing the structure of OsEPSPS gene and sequences of two target sites (C3 and C4) for the CRISPR/Cas9 technology. The sequence of TACTAAATATACAATCCCTTGGG is SEQ ID NO: 4 and the sequence of AAAATATGTATGGAATTCATGGG is SEQ ID NO: 5.

(2) FIGS. 2A-2D show the detection of activity of C3 and C4 targeting OsEPSPS in rice protoplasts and corresponding sequencing results. FIG. 2A shows the PCR/RE detection results of the target site C3 in the protoplast. FIG. 2A shows the corresponding sequencing results of the target site C3. FIG. 2B discloses SEQ ID NOS: 27-31, respectively, in order of appearance. FIG. 2C shows the PCR/RE detection results of the target site C4 in the protoplast. FIG. 2D shows the corresponding sequencing results of the target site C4. FIG. 2D discloses SEQ ID NOS: 32-36, respectively, in order of appearance. WT represents a genomic sequence of wild-type rice (Oryza sativa L. japonica. cv. Nipponbare), “−” represents a deletion mutation, “+” represents an insertion mutation, the number after “−/+” represents the number of deleted or inserted nucleotides (lowercase letters represent inserted nucleotides), and M1 to M4 represent four mutation types.

(3) FIGS. 3A and 3B are schematic diagrams showing the structure of a donor vector (pEPSPS—donor) containing substitutions. FIG. 3A shows a DNA sequence in a conserved region of EPSPS in a genome of rice (SEQ ID NO: 1) and the coded amino acid sequence of the conserved region (SEQ ID NO: 2). FIG. 3B shows the DNA sequence (SEQ ID NO: 37) and the coded amino acid sequence of the conserved region of EPSPS (SEQ ID NO: 38) in the donor vector, and the amino acid in bold is a substitution amino acid. To facilitate the later detection, an enzyme site PvuI is obtained by a synonymous mutation.

(4) FIGS. 4A and 4B show the detection of T0-generation mutants of CRISPR-mediated site-directed mutation rice OsEPSPS gene by using PCR/RE and the sequencing results. FIG. 4A shows the PCR/RE detection results of the T0-generation mutants, wherein 1 to 16 are different regeneration lines, PCR product is cleaved by using PvuI restriction enzymes, ck is a control of wild type rice (Oryza sativa L. japonica. cv. Nipponbare) FIG. 4B shows sequencing results of mutants 1, 5 and 7, wherein G represents a partial sequence of an EPSPS gene of the wild type rice (Oryza sativa L. japonica. cv. Nipponbare): the left sequence is a C3 site sequence, the middle is a DNA sequence in the conserved region of EPSPS, and the right is a C4 site sequence; D represents a partial sequence of an EPSPS gene of the donor vector: the left sequence is a C3 site sequence, the middle sequence is a DNA sequence in the conserved region of EPSPS with site-directed mutations, and the right sequence is a C4 site sequence. FIG. 4B discloses SEQ ID NOS: 39-46, respectively, in order of appearance. “−” represents a deletion mutation, “+” represents an insertion mutation, the number after “−/+” represents the number of deleted or inserted nucleotides (lowercase letters represent inserted nucleotides).

(5) FIG. 5 shows the growth of a rice plant in N6 culture medium containing 1 mg/L glyphosate. After cultivation for 10 days, a) represents a mutant TO-1 obtained by making TIPS site-directed mutation in OsEPSPS gene; b) is a control of wild type rice (Oryza sativa L. japonica. cv. Nipponbare).

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

(6) Unless otherwise specified, experimental methods used in the following examples are all conventional methods.

(7) Unless otherwise specified, materials, reagents, etc. used in the following examples are commercially available.

(8) pHUN411 vector: disclosed in a literature “Hui-Li Xing, Li Dong, Zhi-Ping, Wang Hai-Yan Zhang, Chun-Yan Han, Bing, Liu Xue-Chen Wang, Qi-Jun Chen. A CRISPR/Cas9 toolkit for multiplex genome editing in the plants. The BMC plant biology. 14: 327-338 (2014)”, and can be obtained by the public from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. The plasmid can be used for transcribing a guide RNA and expressing a Cas9 protein at the same time.

Example 1. Selection of OsEPSPS Target Sites of Rice and Construction of a CRISPR Vector

(9) I. Selection of an OsEPSPS Target Site

(10) The locus number of an OsEPSPS gene is 06g04280, and the OsEPSPS gene is positioned on chromosome No. 6 of rice, contains 8 exons and 7 introns, and encodes 515 amino acids. The conserved region of the OsEPSPS gene is positioned in the second exon, and the target sites selected for construction of knockout vectors are respectively positioned in the first intron and the second intron (FIG. 1). The sequence of the first intron, a second exon containing the conserved region and the second intron of the OsEPSPS gene in a genome of rice is shown in SEQ ID No. 3, wherein position 1-704 of SEQ ID No. 3 is the first intron, position 705-949 is the second exon, and position 950-1030 is the second intron.

(11) One strand of a target double-strand for CRISPR knockout technology has the following structure: 5-Nx-NGG-3, the N in PAM (NGG) represents any one of A, T, C and G, N in Nx represents any one of A, T, C and G, and x is equal to 20. The target sequence of the OsEPSPS gene is as follows, and the underlined is PAM (Protospacer adjacent motif). Target C3 is positioned in the first intron, and target C4 is positioned in the second intron.

(12) TABLE-US-00001 (SEQ ID No. 4) C3: 5′-TACTAAATATACAATCCCTTGGG-3′; (SEQ ID No. 5) C4: 5′-AAAATATGTATGGAATTCATGGG-3′.

(13) After the rice was transformed by the knockout vector, Cas9 protein cleaved the target sequence region under the mediation of gRNA to form DNA double-strand breaks, the self-damage repair mechanism in the organism was triggered, and mutations (the ‘mutation’ referred to any mutation, including an insertion mutation, a deletion mutation, a substitution mutation and other forms, and the vast majority of these mutations were gene function inactivation mutations) would be introduced during the process that the cell repairs the gap spontaneously.

(14) The above-mentioned target sequence C3 contains a BsaJI enzyme digestion recognition sequence (sequence in bold italic), and can be cleaved by a BsaJI restriction enzyme; the above-mentioned target sequence C4 contains an EcoRI enzyme digestion recognition sequence (sequence in bold italic), and can be cleaved by an EcoRI restriction enzyme. After the C3 target sequence region was cleaved, if the mutation occurred, the BsaJI enzyme digestion recognition sequence would be destroyed and can not be cleaved by the restriction enzyme BsaJI; if no mutation occurred, the BsaJI enzyme digestion recognition sequence can be cleaved by the restriction enzyme BsaJI. Similarly, after the C4 target sequence region was cleaved, if the mutation occurred, the EcoRI enzyme digestion recognition sequence would be destroyed and can not be cleaved by the restriction enzyme EcoRI; if no mutation occurred, the EcoRI enzyme digestion recognition sequence can be cleaved by the restriction enzyme EcoRI.

(15) II. Construction of Recombinant Vectors

(16) 1. The pHUN411 plasmid (the plasmid contains two BsaI restriction enzyme recognition sites) was digested by the restriction enzyme BsaI, and a vector backbone of about 12.5 kb was recovered, and named HUN411.

(17) 2. According to C3 and C4 target site sequences designed by step I, primers with cohesive ends (underlined) were synthesized as follows:

(18) TABLE-US-00002 (SEQ ID NO. 15) C3-F: 5′-GGCGTACTAAATATACAATCCCTT-3′; (SEQ ID NO. 16) C3-R: 5′-AAACAAGGGATTGTATATTTAGTA-3′. (SEQ ID NO. 17) C4-F: 5′-GGCGAAAATATGTATGGAATTCAT-3′; (SEQ ID NO 18) C4-R: 5′-AAACATGAATTCCATACATATTTT-3′.

(19) 3. C3-F and C3-R as well as C4-F and C4-R were annealed respectively to form double-stranded DNAs with cohesive ends named C3 and C4, which were ligated to a gel recovery product HUN411 in the step 1 to obtain recombinant plasmids pHUN411-C3 and pHUN411-C4.

(20) The structure of the recombinant plasmid pHUN411-C3 was described as follows: the recombinant plasmid was obtained by substituting the small fragment (about 1.2 kb) between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID No. 4, and the plasmid can be used for transcribing a guide RNA containing SEQ ID No. 4 and expressing a Cas9 protein.

(21) The structure of the recombinant plasmid pHUN411-C4 was described as follows: the recombinant plasmid was obtained by substituting the small fragment (about 1.2 kb) between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID No. 5, and can be used for transcribing a guide RNA containing SEQ ID No. 5 and expressing a Cas9 protein.

Example 2. Transformation of Rice Protoplasts and Detection of Activity of Recombinant Vectors in Protoplasts

(22) The recombinant plasmids pHUN411-C3 and pHUN411-C4 constructed in Example 1 were respectively delivered into the protoplasts of rice (Oryza sativa L. japonica. cv. Nipponbare) through a PEG-mediated approach. The genomic DNAs of the protoplasts were extracted, and OsEPSPS gene containing target sites C3 and C4 was amplified by PCR using specific primers. Then PCR amplification products containing the target sites C3 and C4 were respectively digested with restriction enzymes BsaJI and EcoRI (if some bands of the PCR amplification products can not be cleaved, it indicates that the target sites designed in the Example 1 are effective). The PCR amplification products which could not be digested by the restriction enzymes were subjected to gel recovery, and inserted to a pEASY-Blunt vector (TransGen Biotech Co., Ltd., catalogue number: CB101), and individual colonies were selected for sequencing.

(23) The primers for respectively amplifying the gene containing the target sites C3 and C4 had sequences as follows:

(24) TABLE-US-00003 Upstream primer OsEC3-F: (SEQ ID NO. 19) 5′-CTAGGAATTATCTCTCAAGTCAATC-3′; Downstream primer OsEC3-R: (SEQ ID NO. 20) 5′-CTCACTGTTCAGCAAGTTGTCC-3′. Upstream primer OsEC4-F: (SEQ ID NO. 21) 5′-TTCTTAATAGCTTTGATCGCG-3′; Downstream primers OsEC4-R: (SEQ ID NO 22) 5′-TAACCTTGCCACCAGGAAGTC-3′.

(25) During the experiment, an undigested PCR product control of wild type rice (Oryza sativa L. japonica. cv. Nipponbare) and a wild type PCR product control digested by BsaJI or EcoRI were set. The experiment was repeated three times.

(26) The enzyme digestion results for detecting the activity of the C3 recombinant vectors in the protoplasts were shown in FIG. 2a, lanes 1 and 2 were transformed protoplasts, which contain PCR bands that could not be cleaved by BsaJI (the size was about 640 bp, as expected), indicating that the target site C3 is effective; lane 3 was an undigested wild type PCR product control; lane 4 was a digested wild type PCR product control that could be completely digested by BsaJI. The sequencing results (FIG. 2b) indicated that an insertion or a deletion of a small number of nucleotides occurred at the target sites, and confirmed that the recombinant vector pHUN411-C3 performed site-directed gene editing at the target site C3.

(27) The enzyme digestion results for detecting the activity of the C4 recombinant vectors in the protoplasts through were shown in FIG. 2 c, lanes 1 and 2 were transformed protoplasts, which contain PCR bands that could not be cleaved by EcoRI (the size was about 730 bp, as expected), indicating that the target site C4 is effective; lane 3 was an undigested wild type PCR product control; lane 4 was a digested wild type PCR product control that could be completely cleaved by EcoRI. The sequencing results (FIG. 2b) indicated that an insertion or a deletion of a small number of nucleotides occurred at the target sites, and confirmed that the recombinant vector pHUN411-C4 performed site-directed gene editing at the target site C4.

Example 3. Construction of Donor Vector

(28) This example was intended to construct a donor vector containing a mutation target sequence so that the donor vector can be used together with CRISPR/Cas9 nucleases to achieve substituting threonine (T) at position 8 of the conserved region polypeptide (the coding gene of the conserved region polypeptide is SEQ ID No. 1 in the sequence listing) as shown in SEQ ID No. 2 in rice endogenous EPSPS protein with isoleucine (I), and substituting proline (P) at position 12 with serine (S). Namely, the sequence of the mutated conserved region polypeptide was SEQ ID No. 7 in the sequence listing, and the mutation was called TIPS mutation for short hereinafter. The specific construction method of the donor vector was as follows:

(29) the genomic DNA of the wild type rice (Oryza sativa L. japonica. cv. Nipponbare) was used as a template, and a primer pair OsEPSPS-DF/OsEPSPS-DR was used for PCR amplification. Amplification product was subjected to electrophoresis detection. A target band of 1.2 Kb was obtained, and the PCR product was purified and ligated to pEASY-Blunt vector (TransGen Biotech Co., Ltd., catalogue number: CB101). A clone containing the EPSPS fragment was obtained after PCR verification, and the plasmid was extracted. The sequencing results indicated that the plasmid as obtained contains a DNA fragment shown in SEQ ID No. 8 inserted into the T-Blunt vector, which was named TB-EPSPS-D. Positions 12 to 1041 of SEQ ID No. 8 were completely identical to SEQ ID No. 3.

(30) TABLE-US-00004 (SEQ ID NO. 23) OsEPSPS-DF: 3′5′-CCCTCTCCGAGGTGAGACG- (position 1-19 of SEQ ID No. 8); (SEQ ID NO. 22) OsEPSPS-DR: 5′-TAACCTTGCCACCAGGAAGTC-3′ (a reverse complementary sequence of position 1179-1199 of SEQ ID No. 8).

(31) The plasmid TB-EPSPS-D was used as a template, and amplified with the primers OsEPSPS-TIPSF/OsEPSPS-TIPSR (to facilitate the later detection, PvuI restriction enzyme digestion sites were designed by synonymous mutation in both primers). PCR product was treated by DpnI, and transformed into E. coli. A clone was selected and sent for sequencing. After sequencing, the recombinant plasmid obtained be inserting a DNA fragment shown in SEQ ID No. 6 to the T-Blunt vector was named pEPSPS-donor. The difference between the SEQ ID No. 6 and SEQ ID No. 8 was only a mutation site introduced into the OsEPSPS-TIPSF/OsEPSPS-TIPSR primer, and the mutated amino acid sequence in the conserved region was shown in SEQ ID No. 7 in the sequence listing.

(32) A schematic diagram showing the structure of PEPSPS-donor was shown in FIG. 3.

(33) TABLE-US-00005 (SEQ ID NO. 24) (SEQ ID NO. 25) OsEPSPS - TIPSR: 5 ′- TGCTGTCAAcGATCGCATTGCAATTCCAGCGTTCCCCAAG - 3′.

(34) Mutation nucleotides were shown in frames, and enzyme digestion sites PvuI resulted from mutations was shown in bold.

Example 4. Transformation of Rice and Detection of TIPS EPSPS Mutants

(35) The recombinant plasmids pHUN411-C3 and pHUN411-C4 constructed in Example 1 and the recombinant plasmid pEPSPS-donor constructed in Example 3 were co-introduced into rice (Oryza sativa L. japonica. cv. Nipponbare) through a gene gun transformation method at the same time. The callus of the rice (Oryza sativa L. japonica. cv. Nipponbare) was used as transformation recipient; the molar ratio of the recombinant plasmids pHUN411-C3 to pHUN411-C4 to pEPSPS-donor during co-transformation was 1:1:2. Complete plants (namely, T0 generation) were regenerated by tissue culture after transformation.

(36) The genomic DNA of T0-generation transgenic plant was extracted, and the specific primers OsEF1 and OsER containing the target sites C3 and C4 and a TIPS mutation site were used for PCR amplification on the genomic DNA.

(37) TABLE-US-00006 (SEQ ID NO. 26) OsEF1: 5′-CAACAGGATCCTCCTCCTCTC-3′ (positioned at 30 bp upstream SEQ ID No. 8/6 in a rice genome); (SEQ ID NO. 22) OsER: 5′-TAACCTTGCCACCAGGAAGTC-3′ (a sequence reverse complementary to position 1179 to 1199 of SEQ ID No. 6).

(38) PCR product was digested with a single enzyme PvuI, and the enzyme digestion result was shown in FIG. 4a. After PCR and enzyme digestion detection, three lines of plants with mutations at the TIPS site were obtained, such as T0-1, T0-5, T0-7 (respectively corresponding to lanes 1, 5 and 7 in FIG. 4a, which also contain target bands (with the size of about 950 bp and 270 bp) from digestion of PvuI in addition to a PCR product band (with the size of about 1.2 kb)), the remaining numbered plants (respectively corresponding to lanes 2, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15 and 16 in FIG. 4) belonged to the wild type.

(39) Furthermore, the sequencing results of mutants were shown in FIG. 4b. The three lines (T0-1, T0-5, and T0-7) contain target nucleotide mutations at the designed target sites, and the insertion and deletion of a small number of nucleotides were generated at the target sites C3 and C4 at the same time. Because C3 and C4 were positioned in the introns, the open reading frame of OsEPSPS gene was not affected by the deletion and insertion of a small number of nucleotides. An the protein generated from translation was affected by the target nucleotide mutations, indicating that mutants containing mutations at TIPS EPSPS site were successfully obtained.

Example 5. Verification of Glyphosate Resistance of TIPS EPSPS Site Mutants

(40) The three TIPS EPSPS site mutation lines (T0-1, T0-5 and T0-7) obtained from Example 4 and wild type rice (Oryza sativa L. japonica. cv. Nipponbare) plants were placed into an N6 culture medium containing 1 mg/L glyphosate, and cultured under the routine culture conditions. The resistance results were recorded after 10 days. Verification was carried out in more than 3 plants for each TIPS EPSPS site mutation line.

(41) The results showed that the wild type rice (Oryza sativa L. japonica. cv. Nipponbare) plants had become chlorotic and wilting to die, and all the TIPS EPSPS site mutation plants survived normally (leaves thereof were green). FIG. 5a shows TIPS EPSPS site mutated T0-1, and FIG. 5b shows a wild type rice (Oryza sativa L. japonica. cv. Nipponbare) control plant.

Example 6. Intron-Mediated Site-Specific Gene Replacement in Arabidopsis thaliana

(42) Generation of precise modifications of genome such as point mutations and gene replacements have been of great value for functional genomic studies in Arabidopsis thaliana, which is a model plant of dicotyledon. We report here an intron-mediated site-specific gene replacement approach via the non-homologous end joining (NHEJ) pathway using the CRISPR/Cas9 system in Arabidopsis thaliana.

(43) A point mutation (G1654-A) in Atsnc1 (At4g16890) leading to the Glu552-to-Lys-552 substitution, was identified previously that constitutively expresses pathogenesis-related (PR) genes and could confer the plant with resistance against both Pseudomonas syringae pv maculicola ES4326 and Peronospora parasitica Noco2. Hence we set out to obtain an amino acid substitution of the endogenous Atsnc1 gene. The genomic sequence of Atsnc1 is SEQ ID No. 9.

(44) The point mutation occurs in Exon 3 of Atsnc1 and the coding sequence of Exon 3 is SEQ ID No. 10. To replace the endogenous exon 3 with a new exon containing the point mutation (G1654-A) (SEQ ID No. 11), we designed dual sgRNAs targeting introns 2 and 3 of Atsnc1, respectively. The sgRNA targeting the intron 2 of Atsnc1 is SEQ ID No. 12 (S1) and the sgRNA targeting the intron 3 of Atsnc1 is the SEQ ID No. 13 (S2).

(45) We integrated S1 sgRNA (driven by the AtU626 promoter), S2 sgRNA (driven by the AtU629 promoter) and donor sequence containing one nucleotide substitution (G1654-A) into the pHEE401 vector carrying hygromycin B phosphotransferase (hpt) and Cas9 expression cassettes, resulting in the construct pHEE411-S1S2Donor. The donor sequence containing the nucleotide substitution is SEQ ID No. 14.

(46) The final vector pHEE411-S1S2Donor is transformed into Agrobacterium strain GV3101 using freeze-thaw method. Arabidopsis Col-0 wild-type plants were used for transformation via the floral dip method. The collected seeds were screened on MS plates containing 25 mg/L hygromycin. Genomic DNA was extracted from T1 transgenic plants grown in soil. Fragments surrounding the target sites were amplified by PCR using gene-specific primer and sequenced. Finally the gene replacement plants were obtained.