WO2017028768A1 - Method for obtaining glyphosate-resistant rice by site-directed nucleotide substitution - Google Patents

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

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WO2017028768A1
WO2017028768A1 PCT/CN2016/095307 CN2016095307W WO2017028768A1 WO 2017028768 A1 WO2017028768 A1 WO 2017028768A1 CN 2016095307 W CN2016095307 W CN 2016095307W WO 2017028768 A1 WO2017028768 A1 WO 2017028768A1
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target
sequence
genetic material
specific nuclease
plant
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PCT/CN2016/095307
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French (fr)
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Caixia Gao
Jun Li
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Institute Of Genetics And Developmental Biology, Chinese Academy Of Sciences
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Priority to BR112018002026-5A priority Critical patent/BR112018002026A2/en
Priority to KR1020207018034A priority patent/KR20200078685A/en
Priority to EA201890492A priority patent/EA201890492A1/en
Priority to CA2994883A priority patent/CA2994883A1/en
Priority to US15/752,514 priority patent/US11767536B2/en
Priority to AU2016309392A priority patent/AU2016309392A1/en
Priority to JP2018507556A priority patent/JP2018527920A/en
Priority to EP16836632.6A priority patent/EP3334832A4/en
Priority to KR1020187005411A priority patent/KR102127418B1/en
Publication of WO2017028768A1 publication Critical patent/WO2017028768A1/en

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    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8201—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation
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    • C12N9/10—Transferases (2.)
    • C12N9/1085—Transferases (2.) transferring alkyl or aryl groups other than methyl groups (2.5)
    • C12N9/1092—3-Phosphoshikimate 1-carboxyvinyltransferase (2.5.1.19), i.e. 5-enolpyruvylshikimate-3-phosphate synthase
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    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/66—General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8274—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for herbicide resistance
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    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
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    • C12Y205/00—Transferases transferring alkyl or aryl groups, other than methyl groups (2.5)
    • C12Y205/01—Transferases transferring alkyl or aryl groups, other than methyl groups (2.5) transferring alkyl or aryl groups, other than methyl groups (2.5.1)
    • C12Y205/01019—3-Phosphoshikimate 1-carboxyvinyltransferase (2.5.1.19), i.e. 5-enolpyruvylshikimate-3-phosphate synthase
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]

Definitions

  • the present invention belongs to the field of biotechnological breeding, relates to a method for obtaining glyphosate-resistant rice by site-directed nucleotide substitution, and also relates to a method for generating site-directed nucleotide substitution and fragment substitution.
  • Rice is the main food crop in China and even the world. In our country, the total area, total yield and yield per unit area of rice top the list, and the planting area is about 500 million mu. In China, the paddy weeds occurrence area accounts for about 45%of the rice planting area. The yield of the rice is generally reduced by 5%to 15%in the absence of weed control, resulting in a loss about 10 million tons every year. In some severe situation, the yield may be reduced by 15%to 30%. In order to control paddy weeds, a lot of manpower and material resources and financial resources were input, and also a large amount of herbicide was applied. Therefore, it is of vital importance to develop herbicide-resistant rice. Traditional breeding is time-consuming, and the available germplasm resources are deficient. With the development of transgenic technology and genome editing technology, an effective way is provided for the breeding of glyphosate resistance rice.
  • the genome editing technology is a rising new technology in recent years, and mainly includes three types of sequence specific nucleases: zinc finger nuclease (ZFN) , transcription activator -like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas9) system.
  • ZFN zinc finger nuclease
  • TALEN transcription activator -like effector nuclease
  • CRISPR/Cas9 clustered regularly interspaced short palindromic repeats/CRISPR associated
  • DSBs DNA double-strand breaks
  • HR homologous recombination
  • Glyphosate is a nonselective herbicide with the advantages of broad spectrum, high efficiency, low toxicity and low residue, nonselective for the majority of plants, and is the herbicide mostly used in the world currently. Its mechanism of action mainly lies in competitively inhibiting the activity of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the shikimic acid pathway, resulting in the block of aromatic amino acid synthesis, and eventually killing the plants.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • the present invention discloses a method for obtaining a glyphosate-resistant plant.
  • the method for obtaining the glyphosate-resistant plants 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 amino acid sequence of the conserved region of the endogenous EPSPS protein of the target plant is set forth in SEQ ID No. 2.
  • amino acid sequence of the conserved region obtained after the substitution is set forth in SEQ ID No. 7.
  • the steps of “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) ” are realized by introducing the following a) , b) , c) , d) , e) or f) into a cell or tissue of the target plant, and then culturing the cell or tissue as obtained into complete plants;
  • the genetic material 1 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 1
  • the genetic material 2 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 2;
  • the genetic material 12 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing the sequence specific nuclease 1 and also expressing the sequence specific nuclease 2;
  • the non-genetic material 1 is an mRNA capable of expressing the sequence specific nuclease 1
  • the non-genetic material 2 is an mRNA capable of expressing the sequence specific nuclease 2;
  • the non-genetic material 1 is the protein of the sequence specific nuclease 1 expressed in vitro
  • the non-genetic material 2 is the protein of the sequence specific nuclease 2 expressed in vitro
  • a donor vector capable of expressing the sequence specific nuclease 1 and also capable of expressing the sequence specific nuclease 2;
  • the donor vector is a vector carrying a mutation target sequence
  • 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 target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide mutation
  • the target fragment 1 is positioned in an intron region (denoted as intron region 1) 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
  • the target fragment 2 is positioned in an intron region (denoted as intron region 2) 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
  • the nucleotide mutation 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
  • the mutation target sequence may be a DNA fragment sequence corresponding to a sequence in the genome of the target plant from the 5’end of a target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide mutation; and may further contains an upstream and/or downstream homologous sequence, wherein the upstream homologous sequence is a segment of sequence positioned in the upstream of the target fragment 1 in the genome of the target plant, the downstream homologous sequence is a segment of sequence positioned in the downstream of the target fragment 2 in the genome of the target plant.
  • the sequence specific nuclease 1 is able to specifically cleave the target fragments 1 in the genome of the target plant and the donor vector;
  • the sequence specific nuclease 2 is able to specifically cleave the target fragments 2 in the genome of the target plant and the donor vector; when the sequence specific nuclease 1 and the sequence specific nuclease 2 cleave the target fragments 1 and the target fragments 2 in the genome of the target plant and the donor vector at the same time, the fragment containing the substituted nucleotide between two target sites of the donor vector can be inserted between the two target sites of the genome of the target plant, thus obtaining a genome sequence with a site-directed nucleotide substitution.
  • sequence specific nuclease (such as the sequence specific nuclease 1 or the sequence specific nuclease 2) specifically cleaves the target fragments in the genome of the target plant and the donor vector at the same time, which possibly results in an insertion mutation, and /or a deletion mutation of several nucleotides, but such mutation is positioned in the prompter region, and/or intron region, and/or UTR region (Untranslated Region) , and thus generally the function of the protein will not be affected; when the two sequence specific nucleases (such as the sequence specific nuclease 1 or the sequence specific nuclease 2) cleave the target fragments 1 and the target fragments 2 in the genome of the target plant and the donor vector at the same time, a nucleotide substitution mutation of the sequence between two target sites can be generated.
  • Both the sequence specific nuclease 1 and the sequence specific nuclease 2 may be a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any sequence specific nuclease capable of realizing genome editing; the sequence specific nuclease 1 and the sequence specific nuclease 2 may be of the same type or may be of different type.
  • the plant may be a monocotyledon or dicotyledon.
  • the monocotyledon may be a gramineous plant.
  • the gramineous plant may be rice.
  • the plant is rice (Oryza sativa L.japonica. cv. Nipponbare) .
  • the residues to be mutated (position 8 and position 12) in the amino acid sequence of the conserved region of the endogenous EPSPS protein of the target plant are positioned in the second exon of the endogenous EPSPS protein of the target plant;
  • the intron region 1 is the first intron, the nucleotide sequence of which corresponds to position 1-704 of SEQ ID No. 3 in the sequence listing;
  • the intron region 2 is the second intron, the nucleotide sequence of which corresponds to position 950-1030 of SEQ ID No. 3 in the sequence listing.
  • Both the sequence specific nuclease 1 and the sequence specific nuclease 2 are CRISPR/Cas9 nucleases, and the target fragment 1 is a fragment complying with the formula 5 '-N X -NGG -3'or 5 '-CCN -N X -3'within the nucleotide sequence corresponds to position 1-704 of SEQ ID No. 3 in the sequence listing; N represents any one of A, G, C, and T; 14 ⁇ X ⁇ 30 and X is an integer (e.g., X is 20) ; and N X represents X consecutive nucleotides.
  • the target fragment 2 is a fragment complying with the formula 5 '-N X -NGG -3'or 5 '-CCN -N X -3'within the nucleotide sequence corresponds to position 950-1030 of SEQ ID No. 3 in the sequence listing; N represents any one of A, G, C, and T; 14 ⁇ X ⁇ 30 and X is an integer (e.g., X is 20) ; and N X represents X consecutive nucleotides.
  • nucleotide sequence of the target fragment 1 is set forth in SEQ ID No. 4 in the sequence listing; the nucleotide sequence of the target fragment 2 is set forth in SEQ ID No. 5 in the sequence listing.
  • the genetic material 1 is a recombinant plasmid (pHUN411-C3) obtained by substituting the small fragment between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID No. 4 in the sequence listing;
  • the genetic material 2 is a recombinant plasmid (pHUN411-C4) obtained by substituting the small fragment between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID No. 5 in the sequence listing.
  • the nucleotide sequence of the mutation target sequence carried by the donor vector is SEQ ID No. 6 in the sequence listing.
  • the donor vector is a recombinant plasmid (pEPSPS-donor) obtained by inserting a DNA fragment shown in SEQ ID No. 6 No. 6 in the sequence listing into a pEASY -Blunt vector (TransGen Biotech Co., Ltd, catalogue number: CB101)
  • the pHUN411-C3, the pHUN411-C4 and the pEPSPS-donor are introduced into rice calluses (Oryza sativa L. japonica. cv. Nipponbare) , at a molar ratio of 1: 1: 2.
  • the cell may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture;
  • the tissue may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture.
  • the cell may be a protoplast cell or suspension cell; for example, the tissue may be callus, immature embryo or mature embryo.
  • the approach for introducing a) , b) , c) , d) or e) into the cell or tissue of the target plant may be a gene gun approach, an Agrobacterium infection approach, a PEG-mediated protoplast transformation approach or any other introduction approach.
  • the amino acid sequence of the conserved region of the rice endogenous EPSPS protein is SEQ ID No. 2 in the sequence listing;
  • Said transgenic cell line is a non-propagating material.
  • the present invention also provide a method for substituting a target nucleotide in a target gene, wherein the target nucleotide may be one or more non-consecutive nucleotides, and may also be a fragment formed by a plurality of consecutive nucleotides.
  • the step of substituting the target nucleotide in the target gene of a target organism is realized by introducing the following a) , b) , c) , d) or e) into a cell or tissue of the target organism:
  • the genetic material 1 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 1
  • the genetic material 2 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 2;
  • the genetic material 12 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing the sequence specific nuclease 1 and also expressing the sequence specific nuclease 2;
  • the non-genetic material 1 is an mRNA capable of expressing the sequence specific nuclease 1
  • the non-genetic material 2 is an mRNA capable of expressing the sequence specific nuclease 2;
  • the non-genetic material 1 is a protein of the sequence specific nuclease 1 expressed in vitro
  • the non-genetic material 2 is a protein of the sequence specific nuclease 2 expressed in vitro
  • a donor vector capable of expressing the sequence specific nuclease 1 and also expressing the sequence specific nuclease 2;
  • the donor vector is a vector carrying a mutation target sequence
  • the mutation target sequence contains a DNA fragment sequence corresponding to a sequence in the genome of the target organism from the 5’end of a target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide substitution
  • the target fragment 1 is positioned in an intron region or a promoter region upstream the target nucleotide of the target gene in the genome of the target organism
  • the target fragment 2 is positioned in an intron region or a 3’-UTR region downstream the target nucleotide of the target gene in the genome of the target organism.
  • the target sites of the two sequence specific nucleases are positioned in the prompter region, and/or the intron region, and/or a UTR region (Untraslated Region) , and the expression of the target genet generally will not be affected by an insertion and a deletion of a small number of nucleotides in such regions.
  • the mutation target sequence may be a DNA fragment sequence corresponding to a sequence in the genome of the target organism from the 5’end of a target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide substitution; and may further contains an upstream and/or downstream homologous sequence, wherein the upstream homologous sequence is a segment of sequence positioned in the upstream of the target fragment 1 in the genome of the target organism, the downstream homologous sequence is a segment of sequence positioned in the downstream of the target fragment 2 in the genome of the target organism.
  • the sequence specific nuclease 1 is able to specifically cleave the target fragments 1 in the genome of the target organism and the donor vector; the sequence specific nuclease 2 is able to specifically cleave the target fragments 2 in the genome of the target organism and the donor vector.
  • the donor vector is directed to the target gene in the genome of the target organism by the upstream and downstream homologous sequences in the donor vector.
  • sequence specific nuclease 1 and the sequence specific nuclease 2 cleave the target fragments 1 and the target fragments 2 in the genome of the target organism and the donor vector at the same time, a fragment containing the nucleotide to be substituted between two target sites of the donor vector can be inserted between the two target sites of the genome of the target organism, thus obtaining a genome sequence with a site-directed nucleotide substitution.
  • the target organism may be a target plant, target animal or target microorganism.
  • Both the sequence specific nuclease 1 and the sequence specific nuclease 2 may be a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any sequence specific nuclease capable of realizing genome editing.
  • the sequence specific nuclease 1 and the sequence specific nuclease 2 may be of the same type and may also be of different types.
  • said target organism is a plant, including monocotyledon or dicotyledon, such as rice or Arabidopsis.
  • the cell may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture; the tissue may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture.
  • the cell may be a protoplast cell or suspension cell; for example, the tissue may be callus, immature embryo or mature embryo.
  • the approach for introducing a) , b) , c) , d) or e) into the cell or tissue of the target plant may be a gene gun approach, an Agrobacterium infection approach, a PEG-mediated protoplast transformation approach or any other introduction approach.
  • said plant is Arabidopsis; said target gene is Atsnc1 (At4g16890) of SEQ ID NO. 9; said sequence specific nuclease 1 comprises a sgDNA corresponding to SEQ ID NO. 12; said sequence specific nuclease 2 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 the plant the resistance against Pseudomonas syringae pv maculicola ES4326 and Peronospora parasitica Noco2.
  • two gRNA sites respectively positioned in the first intron and the second intron of EPSPS gene are designed, the two gRNAs cleave the target fragments 1 and 2 in the genome and the donor vector at the same time through CRISPR/Cas9 technology, a fragment corresponding to the sequence between the target sites in which the nucleotide (s) is substituted has a chance to be inserted between the target sites in the genome to substitute the second exon of rice, so that the site-directed mutation of two amino acids in the conserved region is realized, and thus rice with glyphosate resistance is produced. It is of great significance in breeding new herbicide-resistant plant varieties.
  • the present invention also provides a method for site-directed substitution of a target nucleotide in a target gene.
  • Figure 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.
  • Figure 2 shows the detection of activity of C3 and C4 targeting OsEPSPS in rice protoplasts and corresponding sequencing results.
  • a) shows the PCR/RE detection results of the target site C3 in the protoplast
  • b) shows the corresponding sequencing results of the target site C3
  • c) shows the PCR/RE detection results of the target site C4 in the protoplast
  • d) shows the corresponding sequencing results of the target site C4.
  • WT represents a genomic sequence of wild-type rice (Oryza sativa L. japonica. cv.
  • FIG. 3 is a schematic diagram showing the structure of a donor vector (pEPSPS -donor) containing substitutions.
  • a) shows a DNA sequence in a conserved region of EPSPS in a genome of rice and the coded amino acid sequence of the conserved region
  • b) shows the DNA sequence and the coded amino acid sequence of the conserved region of EPSPS in the donor vector, and the amino acid in bold is a substitution amino acid.
  • an enzyme site PvuI is obtained by a synonymous mutation.
  • FIG. 4 shows the detection of T0-generation mutants of CRISPR-mediated site-directed mutation rice OsEPSPS gene by using PCR/RE and the sequencing results.
  • a) 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) ;
  • b) 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.
  • the left sequence is a C3 site sequence
  • the middle is a DNA sequence in the conserved region of EPSPS
  • 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.
  • "-" represents a deletion mutation
  • "+” represents an insertion mutation
  • the number after "-/+” represents the number of deleted or inserted nucleotides (lowercase letters represent inserted nucleotides) .
  • Figure 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 T0-1 obtained by making TIPS site-directed mutation in OsEPSPS gene; b) is a control of wild type rice (Oryza sativa L.japonica. cv. Nipponbare) .
  • 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.
  • 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
  • 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 ( Figure 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.
  • 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
  • target C4 is positioned in the second intron.
  • 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.
  • 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.
  • 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 12.5kb was recovered, and named HUN411.
  • primers with cohesive ends were synthesized as follows:
  • 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.
  • the structure of the recombinant plasmid pHUN411 -C3 was described as follows: the recombinant plasmid was obtained by substituting the small fragment (about 1.2kb) 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.
  • the structure of the recombinant plasmid pHUN411–C4 was described as follows: the recombinant plasmid was obtained by substituting the small fragment (about 1.2kb) 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.
  • 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) .
  • 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.
  • pEASY –Blunt vector TransGen Biotech Co., Ltd., catalogue number: CB101
  • the primers for respectively amplifying the gene containing the target sites C3 and C4 had sequences as follows:
  • Upstream primer OsEC3 -F 5 '-CTAGGAATTATCTCTCAAGTCAATC -3';
  • Downstream primer OsEC3 -R 5 '-CTCACTGTTCAGCAAGTTGTCC -3'.
  • Upstream primer OsEC4 -F 5 '-TTCTTAATAGCTTTGATCGCG -3';
  • Downstream primers OsEC4 -R 5 '-TAACCTTGCCACCAGGAAGTC -3'.
  • 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) .
  • T threonine
  • I isoleucine
  • P proline
  • S serine
  • the specific construction method of the donor vector was as follows:
  • 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.
  • OsEPSPS-DF 3 '5'-CCCTCTCCGAGGTGAGACG - (position 1-19 of SEQ ID No. 8) ;
  • OsEPSPS-DR 5 '-TAACCTTGCCACCAGGAAGTC -3' (a reverse complementary sequence of position 1179-1199 of SEQ ID No. 8) .
  • 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. colu.
  • a clone was selected and sent for 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.
  • OsEPSPS -TIPSF 5 '- -3';
  • OsEPSPS -TIPSR 5 '-TGCTGTCAAcGATCGCATTGCAATTCCAGCGTTCCCCAAG -3'.
  • 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.
  • 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.
  • OsEF1 5 '-CAACAGGATCCTCCTCCTCTC -3' (positioned at 30 bp upstream SEQ ID No. 8/6 in a rice genome) ;
  • OsER 5 '-TAACCTTGCCACCAGGAAGTC -3' (a sequence reverse complementary to position 1179 to 1199 of SEQ ID No. 6) .
  • PCR product was digested with a single enzyme PvuI, and the enzyme digestion result was shown in Figure 4a.
  • 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 Figure 4a, which also contain target bands (with the size of about 950bp and 270bp) from digestion of PvuI in addition to a PCR product band (with the size of about 1.2kb) ) , the remaining numbered plants (respectively corresponding to lanes 2, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15 and 16 in Figure 4) belonged to the wild type.
  • the sequencing results of mutants were shown in Figure 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.
  • 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.
  • Atsnc1 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.
  • the point mutation occurs in Exon 3 of Atsnc1 and the coding sequence of Exon 3 is SEQ ID No. 10.
  • SEQ ID No. 11 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) .
  • S1 sgRNA driven by the AtU626 promoter
  • S2 sgRNA driven by the AtU629 promoter
  • donor sequence containing one nucleotide substitution G1654-A
  • the donor sequence containing the nucleotide substitution is SEQ ID No. 14.
  • 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.

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Abstract

A method for obtaining glyphosate-resistant rice by a site-directed nucleotide substitution is provided, which 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. A method capable of generating a site-directed nucleotide substitution and a fragment substitution utilizing a CRISPR-mediated NHEJ pathway to substitute a region between two gRNA sites by designing the two gRNA sites is provided.

Description

Method for Obtaining Glyphosate-resistant Rice by Site-directed Nucleotide Substitution Technical field
The present invention belongs to the field of biotechnological breeding, relates to a method for obtaining glyphosate-resistant rice by site-directed nucleotide substitution, and also relates to a method for generating site-directed nucleotide substitution and fragment substitution.
Background
Rice is the main food crop in China and even the world. In our country, the total area, total yield and yield per unit area of rice top the list, and the planting area is about 500 million mu. In China, the paddy weeds occurrence area accounts for about 45％of the rice planting area. The yield of the rice is generally reduced by 5％to 15％in the absence of weed control, resulting in a loss about 10 million tons every year. In some severe situation, the yield may be reduced by 15％to 30％. In order to control paddy weeds, a lot of manpower and material resources and financial resources were input, and also a large amount of herbicide was applied. Therefore, it is of vital importance to develop herbicide-resistant rice. Traditional breeding is time-consuming, and the available germplasm resources are deficient. With the development of transgenic technology and genome editing technology, an effective way is provided for the breeding of glyphosate resistance rice.
The genome editing technology is a rising new technology in recent years, and mainly includes three types of sequence specific nucleases: zinc finger nuclease (ZFN) , transcription activator -like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas9) system. These artificial nucleases can generate DNA double-strand breaks (DSBs) at DNA target sites, and the DSBs generated after damage of DNA activate intracellular inherent non-homologous ending-joining (NHEJ) or homologous recombination (HR) as two different repair mechanisms to repair the damaged DNA: the probability of repair by HR is very low； the organism is mainly repaired by the NHEJ, where the broken chromosome will be re-joined, but the joining is usually not accurate, and the insertion or deletion of a few nucleotides will be generated at the break positions, resulting in a frameshift mutation or early termination of  protein translation, thus realizing the site-directed knockout of a target gene.
Glyphosate is a nonselective herbicide with the advantages of broad spectrum, high efficiency, low toxicity and low residue, nonselective for the majority of plants, and is the herbicide mostly used in the world currently. Its mechanism of action mainly lies in competitively inhibiting the activity of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) in the shikimic acid pathway, resulting in the block of aromatic amino acid synthesis, and eventually killing the plants.
Summary of the invention
The present invention discloses a method for obtaining a glyphosate-resistant plant.
The method for obtaining the glyphosate-resistant plants 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 amino acid sequence of the conserved region of the endogenous EPSPS protein of the target plant is set forth in SEQ ID No. 2.
The amino acid sequence of the conserved region obtained after the substitution is set forth in SEQ ID No. 7.
According to the method, the steps of “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) ” are realized by introducing the following a) , b) , c) , d) , e) or f) into a cell or tissue of the target plant, and then culturing the cell or tissue as obtained into complete plants；
a) a genetic material 1, a genetic material 2 and a donor vector: the genetic material 1 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 1； the genetic material 2 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 2；
b) a genetic material 12 and a donor vector: the genetic material 12 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing the sequence specific nuclease 1 and also expressing the sequence specific nuclease 2；
c) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is an mRNA capable of expressing the sequence specific nuclease 1；  the non-genetic material 2 is an mRNA capable of expressing the sequence specific nuclease 2；
d) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is the protein of the sequence specific nuclease 1 expressed in vitro； the non-genetic material 2 is the protein of the sequence specific nuclease 2 expressed in vitro；
e) a donor vector；
f) a donor vector capable of expressing the sequence specific nuclease 1 and also capable of expressing the sequence specific nuclease 2；
the donor vector is a vector carrying a mutation target sequence； 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 target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide mutation； the target fragment 1 is positioned in an intron region (denoted as intron region 1) 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； the target fragment 2 is positioned in an intron region (denoted as intron region 2) 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； the nucleotide mutation 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) .
The mutation target sequence may be a DNA fragment sequence corresponding to a sequence in the genome of the target plant from the 5’end of a target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide mutation； and may further contains an upstream and/or downstream homologous sequence, wherein the upstream homologous sequence is a segment of sequence positioned in the upstream of the target fragment 1 in the genome of the target plant, the downstream homologous sequence is a segment of sequence positioned in the downstream of the target fragment 2 in the genome of the target plant.
The sequence specific nuclease 1 is able to specifically cleave the target fragments 1 in the genome of the target plant and the donor vector； the sequence specific nuclease 2 is able to specifically cleave the target fragments 2 in the genome of the target plant and the donor  vector； when the sequence specific nuclease 1 and the sequence specific nuclease 2 cleave the target fragments 1 and the target fragments 2 in the genome of the target plant and the donor vector at the same time, the fragment containing the substituted nucleotide between two target sites of the donor vector can be inserted between the two target sites of the genome of the target plant, thus obtaining a genome sequence with a site-directed nucleotide substitution.
The sequence specific nuclease (such as the sequence specific nuclease 1 or the sequence specific nuclease 2) specifically cleaves the target fragments in the genome of the target plant and the donor vector at the same time, which possibly results in an insertion mutation, and /or a deletion mutation of several nucleotides, but such mutation is positioned in the prompter region, and/or intron region, and/or UTR region (Untranslated Region) , and thus generally the function of the protein will not be affected； when the two sequence specific nucleases (such as the sequence specific nuclease 1 or the sequence specific nuclease 2) cleave the target fragments 1 and the target fragments 2 in the genome of the target plant and the donor vector at the same time, a nucleotide substitution mutation of the sequence between two target sites can be generated.
Both the sequence specific nuclease 1 and the sequence specific nuclease 2 may be a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any sequence specific nuclease capable of realizing genome editing； the sequence specific nuclease 1 and the sequence specific nuclease 2 may be of the same type or may be of different type.
According to the method, the plant may be a monocotyledon or dicotyledon. The monocotyledon may be a gramineous plant. Specifically, the gramineous plant may be rice.
In an embodiment of the present invention, specifically, the plant is rice (Oryza sativa L.japonica. cv. Nipponbare) .
Accordingly, at the genomic DNA level, the residues to be mutated (position 8 and position 12) in the amino acid sequence of the conserved region of the endogenous EPSPS protein of the target plant are positioned in the second exon of the endogenous EPSPS protein of the target plant； the intron region 1 is the first intron, the nucleotide sequence of which corresponds to position 1-704 of SEQ ID No. 3 in the sequence listing； the intron region 2 is the second intron, the nucleotide sequence of which corresponds to position 950-1030 of SEQ ID No. 3 in the sequence listing. Both the sequence specific nuclease 1 and the sequence specific nuclease 2 are CRISPR/Cas9 nucleases, and the target fragment 1 is a fragment complying with the formula 5 '-NX -NGG -3'or 5 '-CCN -NX -3'within the  nucleotide sequence corresponds to position 1-704 of SEQ ID No. 3 in the sequence listing； N represents any one of A, G, C, and T； 14≤X≤30 and X is an integer (e.g., X is 20) ； and NX represents X consecutive nucleotides. The target fragment 2 is a fragment complying with the formula 5 '-NX -NGG -3'or 5 '-CCN -NX -3'within the nucleotide sequence corresponds to position 950-1030 of SEQ ID No. 3 in the sequence listing； N represents any one of A, G, C, and T； 14≤X≤30 and X is an integer (e.g., X is 20) ； and NX represents X consecutive nucleotides.
Furthermore, the nucleotide sequence of the target fragment 1 is set forth in SEQ ID No. 4 in the sequence listing； the nucleotide sequence of the target fragment 2 is set forth in SEQ ID No. 5 in the sequence listing.
Accordingly, according to the present invention, specifically, the genetic material 1 is a recombinant plasmid (pHUN411-C3) obtained by substituting the small fragment between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID No. 4 in the sequence listing； specifically, the genetic material 2 is a recombinant plasmid (pHUN411-C4) obtained by substituting the small fragment between two restriction enzymes BsaI of the pHUN411 vector with a DNA fragment corresponds to position 1-20 of SEQ ID No. 5 in the sequence listing.
Specifically, the nucleotide sequence of the mutation target sequence carried by the donor vector is SEQ ID No. 6 in the sequence listing. Specifically, the donor vector is a recombinant plasmid (pEPSPS-donor) obtained by inserting a DNA fragment shown in SEQ ID No. 6 No. 6 in the sequence listing into a pEASY -Blunt vector (TransGen Biotech Co., Ltd, catalogue number: CB101) 
According to the present invention, the pHUN411-C3, the pHUN411-C4 and the pEPSPS-donor are introduced into rice calluses (Oryza sativa L. japonica. cv. Nipponbare) , at a molar ratio of 1: 1: 2.
According to the method, the cell may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture； the tissue may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture. Specifically, for example, the cell may be a protoplast cell or suspension cell； for example, the tissue may be callus, immature embryo or mature embryo.
According to the method, the approach for introducing a) , b) , c) , d) or e) into the cell or tissue of the target plant may be a gene gun approach, an Agrobacterium infection approach, a PEG-mediated protoplast transformation approach or any other introduction  approach.
Any one of the following biological materials also falls within the protection scope of the present invention:
(1) a protein formed by only substituting threonine (T) at position 8 of the amino acid sequence of a conserved region of rice endogenous EPSPS protein with isoleucine (I) , and substituting proline (P) at position 12 with serine (S) ； the amino acid sequence of the conserved region of the rice endogenous EPSPS protein is SEQ ID No. 2 in the sequence listing；
(2) a coding gene of said protein；
(3) an expression cassette recombinant vector, recombinant bacterium or transgenic cell line containing said coding gene.
Said transgenic cell line is a non-propagating material.
The present invention also provide a method for substituting a target nucleotide in a target gene, wherein the target nucleotide may be one or more non-consecutive nucleotides, and may also be a fragment formed by a plurality of consecutive nucleotides.
In the method for substituting a target nucleotide in a target gene, the step of substituting the target nucleotide in the target gene of a target organism is realized by introducing the following a) , b) , c) , d) or e) into a cell or tissue of the target organism:
a) a genetic material 1, a genetic material 2 and a donor vector: the genetic material 1 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 1； the genetic material 2 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 2；
b) a genetic material 12 and a donor vector: the genetic material 12 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing the sequence specific nuclease 1 and also expressing the sequence specific nuclease 2；
c) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is an mRNA capable of expressing the sequence specific nuclease 1； the non-genetic material 2 is an mRNA capable of expressing the sequence specific nuclease 2；
d) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is a protein of the sequence specific nuclease 1 expressed in vitro； the non-genetic material 2 is a protein of the sequence specific nuclease 2 expressed in  vitro；
e) a donor vector capable of expressing the sequence specific nuclease 1 and also expressing the sequence specific nuclease 2；
the donor vector is a vector carrying a mutation target sequence； the mutation target sequence contains a DNA fragment sequence corresponding to a sequence in the genome of the target organism from the 5’end of a target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide substitution； the target fragment 1 is positioned in an intron region or a promoter region upstream the target nucleotide of the target gene in the genome of the target organism； the target fragment 2 is positioned in an intron region or a 3’-UTR region downstream the target nucleotide of the target gene in the genome of the target organism. The target sites of the two sequence specific nucleases are positioned in the prompter region, and/or the intron region, and/or a UTR region (Untraslated Region) , and the expression of the target genet generally will not be affected by an insertion and a deletion of a small number of nucleotides in such regions.
The mutation target sequence may be a DNA fragment sequence corresponding to a sequence in the genome of the target organism from the 5’end of a target fragment 1 to the 3’end of a target fragment 2, which contains the desired nucleotide substitution； and may further contains an upstream and/or downstream homologous sequence, wherein the upstream homologous sequence is a segment of sequence positioned in the upstream of the target fragment 1 in the genome of the target organism, the downstream homologous sequence is a segment of sequence positioned in the downstream of the target fragment 2 in the genome of the target organism.
The sequence specific nuclease 1 is able to specifically cleave the target fragments 1 in the genome of the target organism and the donor vector； the sequence specific nuclease 2 is able to specifically cleave the target fragments 2 in the genome of the target organism and the donor vector. The donor vector is directed to the target gene in the genome of the target organism by the upstream and downstream homologous sequences in the donor vector. When the sequence specific nuclease 1 and the sequence specific nuclease 2 cleave the target fragments 1 and the target fragments 2 in the genome of the target organism and the donor vector at the same time, a fragment containing the nucleotide to be substituted between two target sites of the donor vector can be inserted between the two target sites of the genome of the target organism, thus obtaining a genome sequence with a site-directed nucleotide substitution.
The target organism may be a target plant, target animal or target microorganism. Both the sequence specific nuclease 1 and the sequence specific nuclease 2 may be a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any sequence specific nuclease capable of realizing genome editing. The sequence specific nuclease 1 and the sequence specific nuclease 2 may be of the same type and may also be of different types.
In some embodiments, said target organism is a plant, including monocotyledon or dicotyledon, such as rice or Arabidopsis. The cell may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture； the tissue may be any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture. Specifically, for example, the cell may be a protoplast cell or suspension cell； for example, the tissue may be callus, immature embryo or mature embryo. The approach for introducing a) , b) , c) , d) or e) into the cell or tissue of the target plant may be a gene gun approach, an Agrobacterium infection approach, a PEG-mediated protoplast transformation approach or any other introduction approach.
In one specific embodiment, said plant is Arabidopsis； said target gene is Atsnc1 (At4g16890) of SEQ ID NO. 9； said sequence specific nuclease 1 comprises a sgDNA corresponding to SEQ ID NO. 12； said sequence specific nuclease 2 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 the plant the resistance against Pseudomonas syringae pv maculicola ES4326 and Peronospora parasitica Noco2.
In the present invention, according to the CRISPR-mediated NHEJ pathway, two gRNA sites respectively positioned in the first intron and the second intron of EPSPS gene are designed, the two gRNAs cleave the target fragments 1 and 2 in the genome and the donor vector at the same time through CRISPR/Cas9 technology, a fragment corresponding to the sequence between the target sites in which the nucleotide (s) is substituted has a chance to be inserted between the target sites in the genome to substitute the second exon of rice, so that the site-directed mutation of two amino acids in the conserved region is realized, and thus rice with glyphosate resistance is produced. It is of great significance in breeding new herbicide-resistant plant varieties.
The present invention also provides a method for site-directed substitution of a target nucleotide in a target gene.
Brief description of the drawings
Figure 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.
Figure 2 shows the detection of activity of C3 and C4 targeting OsEPSPS in rice protoplasts and corresponding sequencing results. a) shows the PCR/RE detection results of the target site C3 in the protoplast, b) shows the corresponding sequencing results of the target site C3, c) shows the PCR/RE detection results of the target site C4 in the protoplast, d) shows the corresponding sequencing results of the target site C4. 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.
Figure 3 is a schematic diagram showing the structure of a donor vector (pEPSPS -donor) containing substitutions. a) shows a DNA sequence in a conserved region of EPSPS in a genome of rice and the coded amino acid sequence of the conserved region, b) shows the DNA sequence and the coded amino acid sequence of the conserved region of EPSPS 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.
Figure 4 shows the detection of T0-generation mutants of CRISPR-mediated site-directed mutation rice OsEPSPS gene by using PCR/RE and the sequencing results. a) 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) ； b) 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. "-" represents a deletion mutation, "+" represents an insertion mutation, the number after "-/+" represents the number of deleted or inserted nucleotides (lowercase letters represent inserted nucleotides) .
Figure 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 T0-1 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
Unless otherwise specified, experimental methods used in the following examples are all conventional methods.
Unless otherwise specified, materials, reagents, etc. used in the following examples are commercially available.
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
I.Selection of an OsEPSPS target site
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 (Figure 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.
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.
C3: 5 '-TACTAAATATACAATCCCTTGGG -3' (SEQ ID No. 4) ；
C4: 5 '-AAAATATGTATGGAATTCATGGG -3' (SEQ ID No. 5) .
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.
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 C4target 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.
II. Construction of recombinant vectors
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 12.5kb was recovered, and named HUN411.
2. According to C3 and C4 target site sequences designed by step I, primers with cohesive ends (underlined) were synthesized as follows:
C3 -F: 5 '-GGCGTACTAAATATACAATCCCTT -3'；
C3 -R: 5 '-AAACAAGGGATTGTATATTTAGTA -3'.
C4 -F: 5 '-GGCGAAAATATGTATGGAATTCAT -3'；
C4 -R: 5 '-AAACATGAATTCCATACATATTTT -3'.
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.
The structure of the recombinant plasmid pHUN411 -C3 was described as follows: the recombinant plasmid was obtained by substituting the small fragment (about 1.2kb) 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.
The structure of the recombinant plasmid pHUN411–C4 was described as follows: the recombinant plasmid was obtained by substituting the small fragment (about 1.2kb) 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
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.
The primers for respectively amplifying the gene containing the target sites C3 and C4 had sequences as follows:
Upstream primer OsEC3 -F: 5 '-CTAGGAATTATCTCTCAAGTCAATC -3'；
Downstream primer OsEC3 -R: 5 '-CTCACTGTTCAGCAAGTTGTCC -3'.
Upstream primer OsEC4 -F: 5 '-TTCTTAATAGCTTTGATCGCG -3'；
Downstream primers OsEC4 -R: 5 '-TAACCTTGCCACCAGGAAGTC -3'.
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.
The enzyme digestion results for detecting the activity of the C3 recombinant vectors in the protoplasts were shown in Figure 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 (Figure 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.
The enzyme digestion results for detecting the activity of the C4 recombinant vectors in the protoplasts through were shown in Figure 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 (Figure 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
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:
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.
OsEPSPS-DF: 3 '5'-CCCTCTCCGAGGTGAGACG - (position 1-19 of SEQ ID No. 8) ；
OsEPSPS-DR: 5 '-TAACCTTGCCACCAGGAAGTC -3' (a reverse complementary sequence of position 1179-1199 of SEQ ID No. 8) .
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. colu. 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.
A schematic diagram showing the structure of PEPSPS-donor was shown in Figure 3.
OsEPSPS -TIPSF: 5 '-
Figure PCTCN2016095307-appb-000001
-3'；
OsEPSPS -TIPSR: 5 '-TGCTGTCAAcGATCGCATTGCAATTCCAGCGTTCCCCAAG -3'.
Mutattion 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
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.
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.
OsEF1: 5 '-CAACAGGATCCTCCTCCTCTC -3' (positioned at 30 bp upstream SEQ ID No. 8/6 in a rice genome) ；
OsER: 5 '-TAACCTTGCCACCAGGAAGTC -3' (a sequence reverse complementary to position 1179 to 1199 of SEQ ID No. 6) .
PCR product was digested with a single enzyme PvuI, and the enzyme digestion result was shown in Figure 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 Figure 4a, which also contain target bands (with the size of about 950bp and 270bp) from digestion of PvuI in addition to a PCR product band (with the size of about 1.2kb) ) , the remaining numbered plants (respectively corresponding to  lanes  2, 3, 4, 6, 8, 9, 10, 11, 12, 13, 14, 15 and 16 in Figure 4) belonged to the wild type.
Furthermore, the sequencing results of mutants were shown in Figure 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
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.
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) . Figure 5a shows TIPS EPSPS site mutated T0-1, and Figure 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
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.
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.
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) .
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.
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.

Claims (14)

  1. A method for obtaining a glyphosate-resistant plant, which 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 amino acid sequence of the conserved region of the endogenous EPSPS protein of the target plant is set forth in SEQ ID No. 2.
  2. The method according to claim 1, characterized in that the steps of “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) ” are realized by introducing the following a) , b) , c) , d) , e) or f) into a cell or tissue of the target plant, and then culturing the cell or tissue as obtained into a complete plant:
    a) a genetic material 1, a genetic material 2 and a donor vector: the genetic material 1 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 1； the genetic material 2 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 2；
    b) a genetic material 12 and a donor vector: the genetic material 12 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing the sequence specific nuclease 1 and also capable of expressing the sequence specific nuclease 2；
    c) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is an mRNA capable of expressing the sequence specific nuclease 1； the non-genetic material 2 is an mRNA capable of expressing the sequence specific nuclease 2；
    d) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is a protein of the sequence specific nuclease 1 expressed in vitro； the non-genetic material 2 is a protein of the sequence specific nuclease 2 expressed in vitro；
    e) a donor vector； or
    f) a donor vector capable of expressing the sequence specific nuclease 1 and also  capable of expressing the sequence specific nuclease 2；
    the donor vector is a vector carrying a mutation target sequence； 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 target fragment 1 to the 3’ end of a target fragment 2, which contains the desired nucleotide mutation； the target fragment 1 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； the target fragment 2 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； the nucleotide mutation 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) ；
    the sequence specific nuclease 1 is able to specifically cleave the target fragments 1 in the genome of the target plant and the donor vector； the sequence specific nuclease 2 is able to specifically cleave the target fragments 2 in the genome of the target plant and the donor vector.
  3. The method according to claim 2, characterized in that the sequence specific nuclease 1 is a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any nuclease capable of realizing genome editing； the sequence specific nuclease 2 is a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any nuclease capable of realizing genome editing.
  4. The method according to any one of claims 1 to 3, characterized in that the plant is a monocotyledon or dicotyledon； specifically, the monocotyledon is a gramineous plant； more specifically, the gramineous plant is rice.
  5. The method according to claim 4, characterized in that the target fragment 1 is positioned in an intron 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 which is denoted as intron region 1； the nucleotide sequence of intron region 1 corresponds to position 1-704 of SEQ ID No. 3； both the sequence specific nuclease 1 and the sequence specific nuclease 2 are CRISPR/Cas9 nucleases, and the target fragment 1 is a fragment complying with the formula of 5' -NX-NGG-3' or 5' -CCN-NX-3' within the nucleotide sequence corresponds to position 1-704 of SEQ ID No. 3； N represents any one  of A, G, C, and T； 14≤X≤30 and X is an integer； and NX represents X consecutive nucleotides； and /or
    the target fragment 2 is positioned in an intron region in the genome of the target plant downstream of the nucleotide sequence encoding the amino acid sequence of the conserved region of the endogenous EPSPS protein which is denoted as intron region 2； the nucleotide sequence of intron region 2 corresponds to position 950-1030 of SEQ ID No. 3； both the sequence specific nuclease 1 and the sequence specific nuclease 2 are CRISPR/Cas9 nucleases, and the target fragment 2 is a fragment complying with the formula of 5' -NX-NGG-3' or 5' -CCN-NX -3' within the nucleotide sequence corresponds to position 950-1030 of SEQ ID No. 3； N represents any one of A, G, C, and T； 14≤X≤30 and X is an integer； and NX represents X consecutive nucleotides.
  6. The method according to claim 5, characterized in that the nucleotide sequence of the target fragment 1 is SEQ ID No. 4； the nucleotide sequence of the target fragment 2 is SEQ ID No. 5.
  7. The method according to claim 6, characterized in that the genetic material 1 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； the genetic material 2 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
    the nucleotide sequence of the mutation target sequence carried by the donor vector is set forth in SEQ ID No. 6.
  8. The method as set forth in any one of claims 2 to 7, characterized in that the cell is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture； the tissue is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture；
    specifically, the cell is a protoplast cell or suspension cell； the tissue is a callus, a immature embryo or a mature embryo；
    the approach for introducing the a) , b) , c) , d) , e) or f) into the cell or tissue of the target plant is a gene gun approach, an agrobacterium infection approach, a PEG-mediated protoplast transformation approach or any other introduction approachs.
  9. Any one of the following biological materials:
    (1) a protein formed by only substituting threonine (T) at position 8 of the amino  acid sequence of a conserved region of rice endogenous EPSPS protein with isoleucine (I) , and substituting proline (P) at position 12 with serine (S) ； the amino acid sequence of the conserved region of the rice endogenous EPSPS protein is SEQ ID No. 2 in the sequence listing；
    (2) a coding gene of said protein；
    (3) an expression cassette, recombinant vector, recombinant bacterium or transgenic cell line containing said coding gene .
  10. A method for substituting a target nucleotide in a target gene of a target organism, comprising the step of introducing the following a) , b) , c) , d) or e) into a cell or tissue of the target organism:
    a) a genetic material 1, a genetic material 2 and a donor vector: the genetic material 1 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 1； the genetic material 2 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing a sequence specific nuclease 2；
    b) a genetic material 12 and a donor vector: the genetic material 12 is a circular DNA plasmid, a linear DNA fragment or an RNA transcribed in vitro capable of expressing the sequence specific nuclease 1 and also capable of expressing the sequence specific nuclease 2；
    c) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is an mRNA capable of expressing the sequence specific nuclease 1； the non-genetic material 2 is an mRNA capable of expressing the sequence specific nuclease 2；
    d) a non-genetic material 1, a non-genetic material 2 and a donor vector: the non-genetic material 1 is a protein of the sequence specific nuclease 1 expressed in vitro； the non-genetic material 2 is a protein of the sequence specific nuclease 2 expressed in vitro；
    e) a donor vector capable of expressing the sequence specific nuclease 1 and also capable of expressing the sequence specific nuclease 2；
    the donor vector is a vector carrying a mutation target sequence； the mutation target sequence contains a DNA fragment sequence corresponding to a sequence in the genome of the target organism from the 5’ end of a target fragment 1 to the 3’ end of a target fragment 2, which contains the desired nucleotide substitution； the target fragment 1 is positioned in an  intron region or a promoter region upstream the target nucleotide of the target gene in the genome of the target organism； the target fragment 2 is positioned in an intron region or a 3’ -UTR region downstream the target nucleotide of the target gene in the genome of the target organism ；
    the sequence specific nuclease 1 is able to specifically cleave the target fragments 1 in the genome of the target organism and the donor vector； the sequence specific nuclease 2 is able to specifically cleave the target fragments 2 in the genome of the target organism and the donor vector.
  11. The method according to claim 10, characterized in that the sequence specific nuclease 1 is a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any nuclease capable of realizing genome editing； the sequence specific nuclease 2 is a CRISPR/Cas9 nuclease, a TALEN nuclease, a zinc finger nuclease or any nuclease capable of realizing genome editing.
  12. The method according to claim 10 or 11, characterized in that said target organism is a plant, including monocotyledon or dicotyledon, such as rice or Arabidopsis.
  13. The method according to claim 12, characterized in that the cell is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture； the tissue is any cell that can be used as an introduction recipient and can be regenerated into a complete plant by tissue culture；
    specifically, the cell is a protoplast cell or suspension cell； the tissue is a callus, a immature embryo or a mature embryo；
    the approach for introducing the a) , b) , c) , d) , e) or f) into the cell or tissue of the target plant is a gene gun approach, an agrobacterium infection approach, a PEG-mediated protoplast transformation approach or any other introduction approachs.
  14. The method according to claim 13, said plant is Arabidopsis； said target gene is Atsnc1 (At4g16890) of SEQ ID NO. 9； said sequence specific nuclease 1 comprises a sgDNA corresponding to SEQ ID NO. 12； said sequence specific nuclease 2 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 the plant the resistance against Pseudomonas syringae pv maculicola ES4326 and Peronospora parasitica Noco2.
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