CN107988337A - A kind of labeling method and its application of rice blast resistant rice identification method and gene - Google Patents

A kind of labeling method and its application of rice blast resistant rice identification method and gene Download PDF

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CN107988337A
CN107988337A CN201711080527.XA CN201711080527A CN107988337A CN 107988337 A CN107988337 A CN 107988337A CN 201711080527 A CN201711080527 A CN 201711080527A CN 107988337 A CN107988337 A CN 107988337A
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pid2
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孙丁
孙一丁
许明辉
马继琼
杨奕
李进斌
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Biotechnology and Germplasm Resource Institute of Yunnan Academy of Agricultural Sciences
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Abstract

The invention belongs to crops molecular genetic breeding field, and in particular to a kind of labeling method and its application of rice blast resistant rice identification method and gene, include the following steps:Detect Pid2 gene order FJ915121.1 sequences and its end of homologous sequence 5 ' in No. 6 chromosome of rice to be measured and play SNP site at the 5352nd and 5353 bases, SNP types at the 5352nd and 5353 bases are played to Pid2 gene order FJ915121.1 sequences in No. 6 chromosome of rice and its end of homologous sequence 5 ' by PCR amplification and digestion with restriction enzyme and are identified.Whether the present invention can contain blast resistant gene Pid2 with rice plant selected by accurate judgement, profit can be effective against the selection of rice blast ospc gene pid2 genotype in this way, not only it can be used for the evaluation and screening of rice pest insects, but also can be used for the molecular breeding of rice blast resistant gene Pid2.

Description

A kind of labeling method and its application of rice blast resistant rice identification method and gene
Technical field
The invention belongs to crops molecular genetic breeding field, is related to a kind of rice blast resistant rice identification method and gene Labeling method and its application.
Background technology
Rice is cereal crops important in the world, and rice blast is one of each rice region in world disease the most serious, seriously It has impact on the yield of rice.Due to the variability and unstability of Pyricularia oryzae, cause newly to be bred as has single resistance The resistant variety of gene just becomes susceptible variety after several years of popularizing planting, this becomes the important of Rice Production sustainable development Obstacle, excavates the basis that Resistance genes of vice resource is blast resisting breeding.It is identified at present by extensive genetic analysis With located 84 rice blast resistance genes, at least 24 major gene resistances are cloned by separation in succession.As paddy DNA is sequenced The extensive use of technology, different resistances(Phenotype)The sequence alignment of cultivar origin is by as the method for definite new function gene (Yudai Okuyama et al., 2011), the development of rice genome examining order again will be promoted greatly including rice blast Gene Isolation clone's process including resistant gene(Xu et al., 2011).
Pid2 is located at the nearly centromere region of the 6th chromosome of rice, be cloned in China's rice variety " paddy " for main effect Blast resistant gene, shows China rice blast biological strain ZB15 higher resistance to leaf blast, is south China rice blast breeding Important anti-source.From the point of view of the rice blast resistance gene structure cloned, Pi-d2 is different from traditional " R " gene.The anti-rice of main effect Seasonal febrile diseases gene Pi-d2 is derived from rice variety " paddy ", shows China rice blast biological strain ZB15 higher resistance to leaf blast (Chen, 2010).Pi-d2 is positioned at the nearly centromere region of the 6th chromosome of rice, is single copy gene, and one length of coding is The transmembrane receptor protein kinases (RLK) of 825 amino acid, the kinases aminoterminal contain hydrophobic signal peptide, B-lectin structures Domain, PAN domains and TM domains, c-terminus are a typical serine/threonine kinase domains(STK).Due in the past in rice RLK is not found containing the outer B-lectin structures of film, therefore Pi-d2 belongs to new disease-resistant gene type.
Digestion amplification polymorphism sequence(C1eaved Amplified Polymorphic Sequences, CAPS)It is one Codominant molecular labeling of the class based on PCR, its basic principle be first go to design with the DNA sequence dna of known site it is a set of Specific PCR primer(19~27 bp), then remove to expand a certain DNA fragmentation on the site using these primers, then use Amplified band obtained by the restriction enzyme cleavage of one species specificity simultaneously carries out rflp analysis.It discloses freeze-draw method DNA The information that restriction enzyme site makes a variation in sequence, can detect the mode of DNA polymorphism, while also have quick, simple and direct, high The advantages that effect.
Traditional routine field phenotypic evaluation is low to the efficiency of selection of blast resistant gene, and accuracy is poor;It is badly in need of a kind of anti-rice The high-efficient breeding method of seasonal febrile diseases rice.
The content of the invention
To solve the above-mentioned problems, the present invention provide a kind of rice blast resistant rice identification method and gene labeling method and its Using.Profit can be effective against the selection of rice blast ospc gene pid2 genotype in this way, both can be used for rice pest insects Evaluation and screening, and can be used for the molecular breeding of rice blast resistant gene Pid2.
Concrete technical scheme is:
A kind of rice blast resistant rice identification method, is realized by following steps:
(1)PCR amplification and PCR product sequencing are carried out to the allele of Rice Resources Pid2 code areas;
(2)Pid2 gene order FJ915121.1 sequences and its end of homologous sequence 5 ' play the in No. 6 chromosome of rice Two Pid2 specificity SNP sites are obtained at 5352 and 5353 bases;
(3)Described two Pid2 specificity SNP site bases have three kinds of situations:1)Base type is " AT ", 2)Base type is " GC ", 3)Base type is " GT ";
(4)If 5352 and 5353 site base of rice material to be measured is " AT ", which is to contain blast resistant gene Pid2 Rice or candidate be the rice containing blast resistant gene Pid2;If base base class at 5352 and 5353 site of rice to be measured Type is " GC " or " GT ", then the rice material be do not contain blast resistant gene Pid2 rice or candidate not contain anti-rice blast The rice of ospc gene Pid2.
Preferably, the labeling method of the rice blast resistant rice gene, that is, detect rice Pid2 gene orders FJ915121.1 The method that the 5352nd and 5353 bases are played in sequence and its end of homologous sequence 5 ' is as follows:
(1)Using the genomic DNA of rice to be measured as template, molecular labeling primer using rice blast resistance gene Pid2 genes is draws Thing, carries out PCR amplification, obtains the pcr amplification product of 700bp sizes;
(2)Digestion is carried out to the pcr amplification product respectively with restriction enzyme Fau1 and Mlu1, its result has following several Situation:
1)The pcr amplification product only shows 1 DNA band by two kinds of digestion with restriction enzyme rear electrophoresis, then water to be measured It is homozygous " AT " that the 5352nd and 5353 bases are played in rice gene order FJ915121.1 sequences and its end of homologous sequence 5 ';
2)The pcr amplification product can show two DNA bands by restriction enzyme Fau1 digestion rear electrophoresis, and restricted Restriction endonuclease Mlu1 digestion rear electrophoresis show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured and its homologous sequence It is homozygous " GC " that the 5352nd and 5353 bases are played in the end of row 5 ';
3)The pcr amplification product can show two DNA bands by restriction enzyme Mlu1 digestion rear electrophoresis, and restricted Restriction endonuclease Fau1 digestion rear electrophoresis show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured and its homologous sequence It is homozygous " GT " that the 5352nd and 5353 bases are played in the end of row 5 ';
4)The pcr amplification product can show three DNA bands by restriction enzyme Fau1 digestion rear electrophoresis, and restricted Restriction endonuclease Mlu1 digestion rear electrophoresis show 1 DNA band, then the homologous sequence of rice genome sequence FJ915121.1 sequences to be measured It is heterozygosis base " AT/GC " that the 5352nd and 5353 bases are played in 5 ' ends;
5)If the pcr amplification product can show 3 DNA bands by restriction enzyme Mlu1 digestion rear electrophoresis, and be limited Property restriction endonuclease Fau1 digestion rear electrophoresis processed show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured is homologous It is heterozygosis base " AT/GT " that the 5352nd and 5353 bases are played in the end of sequence 5 ';
6)The pcr amplification product shows 3 DNA bands by two kinds of digestion with restriction enzyme rear electrophoresis, then rice to be measured It is heterozygosis " GC/GT " that the 5352nd and 5353 bases are played in the end of homologous sequence 5 ' of gene order FJ915121.1 sequences;
Preferably, the primer is the primer for the molecular labeling that can expand rice blast resistance gene Pid2, its sequence is:
DF:5’- AAGCTTGGTCAGGGAGGGTT-3’;
Pid2 DR:5’-TGTCATTGTACTTCA GCTTGGC-3’.
Preferably, the nucleotide sequence of the rice blast disease-resistant gene Pid2 molecular labelings is located at FJ915121.1 and its same Rise in the sequence shown in the 4870th and 5570 nucleotide the end of source sequence 5 '.
Preferably, identified using the primer and method, screen anti-rice blast rice.
Preferably, rice blast resistant gene molecular breeding is carried out using the primer and method.
Compared with prior art, the present invention has following advantages:
(1)Different rice blast Race Identification rice blast resistance allele differences, the present invention are inoculated with from traditional utilization The molecular labeling Pid2CAPS of offer is located at the code area of Pid2 genes, genetically with Pid2 disease resistances in isolating, selects Efficiency can reach 100%, not only may determine that whether target material contains Pid2 genes, also can detect that target material Pid2 genotype is heterozygosis or homozygosis, with the existing method phase being detected by Uneven PCR to Pid2 linked markers Than highly efficient.
(2)Molecular labeling provided by the invention can be distinguished by restriction enzyme Fau1 and Mlu1 digestion, always Tri- kinds of banding patterns of shared 700bp, 425bp and 225bp, can directly be detected using 1.5% agarose gel electrophoresis, can be extensive In the colony different applied to genetic background.The method that existing Uneven PCR are detected Pid2 is just for same a group What the sequence polymorphism of the different parents of body two was developed, these marks are limited in other colony's applicabilities.
(3)Rapid identification is carried out to blast resistant gene Pid2 allelotypes in Rice Germplasm Resources using this method. Need not repeat the screening of parent's polymorphism using the method for the present invention, can accelerate the selection and breeding of anti-rice blast rice kind into Degree, the transgenic breeding of rice restorer and sterile line backbone parent material suitable for China's large-area applications, gene pyramiding And the resistance breeding based on MAS technologies.
Brief description of the drawings
Fig. 1 be downloaded from public database the Pid2 genes published and sequencing rice varieties 93-11, The Pid2 allelic sequences specificity SNP site of Nipponbare and remaining 41 kind is analyzed, and dark block is 3 type gene pieces Section base same section;Light color is identical for two types base;
Fig. 2 is to carry out digestion to PCR product successively using restriction enzyme Mlu1 and Fau1, then digestion products are carried out agar Sugared detected through gel electrophoresis figure;
Fig. 3 is the genomic DNA progress PCR amplification of transgenic paddy rice and Nipponbare, and gained PCR product uses restriction enzyme respectively Enzyme Fau1 carries out digestion, and each digestion products are carried out electrophoresis detection figure on Ago-Gel.
Embodiment
A kind of rice blast resistant rice identification method, is realized by following steps:
(1)PCR amplification and PCR product sequencing are carried out to the allele of Rice Resources Pid2 code areas;
(2)Pid2 gene order FJ915121.1 sequences and its end of homologous sequence 5 ' play the in No. 6 chromosome of rice Two Pid2 specificity SNP sites are obtained at 5352 and 5353 bases;
(3)Described two Pid2 specificity SNP site bases have three kinds of situations:1)Base type is " AT ", 2)Base type is " GC ", 3)Base type is " GT ";
(4)If 5352 and 5353 site base of rice material to be measured is " AT ", which is to contain blast resistant gene Pid2 Rice or candidate be the rice containing blast resistant gene Pid2;If base base class at 5352 and 5353 site of rice to be measured Type is " GC " or " GT ", then the rice material be do not contain blast resistant gene Pid2 rice or candidate not contain anti-rice blast The rice of ospc gene Pid2.
Preferably, the labeling method of the rice blast resistant rice gene, that is, detect rice Pid2 gene orders FJ915121.1 The method that the 5352nd and 5353 bases are played in sequence and its end of homologous sequence 5 ' is as follows:
(1)Using the genomic DNA of rice to be measured as template, molecular labeling primer using rice blast resistance gene Pid2 genes is draws Thing, carries out PCR amplification, obtains the pcr amplification product of 700bp sizes;
(2)Digestion is carried out to the pcr amplification product respectively with restriction enzyme Fau1 and Mlu1, its result has following several Situation:
1)The pcr amplification product only shows 1 DNA band by two kinds of digestion with restriction enzyme rear electrophoresis, then water to be measured It is homozygous " AT " that the 5352nd and 5353 bases are played in rice gene order FJ915121.1 sequences and its end of homologous sequence 5 ';
2)The pcr amplification product can show two DNA bands by restriction enzyme Fau1 digestion rear electrophoresis, and restricted Restriction endonuclease Mlu1 digestion rear electrophoresis show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured and its homologous sequence It is homozygous " GC " that the 5352nd and 5353 bases are played in the end of row 5 ';
3)The pcr amplification product can show two DNA bands by restriction enzyme Mlu1 digestion rear electrophoresis, and restricted Restriction endonuclease Fau1 digestion rear electrophoresis show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured and its homologous sequence It is homozygous " GT " that the 5352nd and 5353 bases are played in the end of row 5 ';
4)The pcr amplification product can show three DNA bands by restriction enzyme Fau1 digestion rear electrophoresis, and restricted Restriction endonuclease Mlu1 digestion rear electrophoresis show 1 DNA band, then the homologous sequence of rice genome sequence FJ915121.1 sequences to be measured It is heterozygosis base " AT/GC " that the 5352nd and 5353 bases are played in 5 ' ends;
5)If the pcr amplification product can show 3 DNA bands by restriction enzyme Mlu1 digestion rear electrophoresis, and be limited Property restriction endonuclease Fau1 digestion rear electrophoresis processed show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured is homologous It is heterozygosis base " AT/GT " that the 5352nd and 5353 bases are played in the end of sequence 5 ';
6)The pcr amplification product shows 3 DNA bands by two kinds of digestion with restriction enzyme rear electrophoresis, then rice to be measured It is heterozygosis " GC/GT " that the 5352nd and 5353 bases are played in the end of homologous sequence 5 ' of gene order FJ915121.1 sequences;
Preferably, the primer is the primer for the molecular labeling that can expand rice blast resistance gene Pid2, its sequence is:
DF:5’- AAGCTTGGTCAGGGAGGGTT-3’;
Pid2 DR:5’-TGTCATTGTACTTCA GCTTGGC-3’.
Preferably, the nucleotide sequence of the rice blast disease-resistant gene Pid2 molecular labelings is located at FJ915121.1 and its same Rise in the sequence shown in the 4870th and 5570 nucleotide the end of source sequence 5 '.
Preferably, identified using the primer and method, screen anti-rice blast rice.
Preferably, rice blast resistant gene molecular breeding is carried out using the primer and method.
Embodiment 1, the design of primers of blast resistant gene Pid2 specific Cs APS marks Pid2caps and detection
First, Pid2 gene orders specificity SNP site is analyzed
Downloaded from public database the Pid2 genes published and sequencing rice varieties 93-11, Nipponbare and The Pid2 allelic sequences of remaining 41 kind, are compared these sequences, examination Pid2 it is special, the position can be different from The SNP of point allele.As described in Figure 1, wherein after Pid2 gene start codons+2057 and+2058 sites base For " AT ", the genotype of remaining all kind has two types, and type one is base " GC ", and type two is base " GT ".And this The SNP changes in two sites just cause the Pid2 allelotypes of type one to be known in the position by restriction enzyme Mlu1 Do not cut and at+2051, the Pid2 allelotypes of type two can the position by restriction enzyme Fau1 identify and+ Cut at 2051, Pid2 genes cannot then be identified and cut by both restriction enzymes.The two SNP sites and Pid2 and Sequence space in its allelotype in remaining Mlu1 and Fau1 site is more than 700bp, meets the condition of CAPS marker developments.
2nd, design of primers and synthesis
The design pairing primer at Pid2 gene+2057bp site upstream 480bp department levels downstream 219bp
Pid2 DF:5’- AAGCTTGGTCAGGGAGGGTT-3’;
Pid2 DR:5’-TGTCATTGTACTTCA GCTTGGC-3’.
(One)Select rice material
The related Rice Resources Pid2 gene orders downloaded in Indigenous Rice Genotypes In Yunnan Province and public database.
(Two)PCR amplification and digestion detection
Each rice material genomic DNA in extraction step three, respectively using it as template, using the primer of step 2 as amplimer PCR amplification is carried out, gained clip size is 700bp, which is Pid2caps marks.Present invention amplification obtains The sequence of Pid2caps marks has three kinds, the first base at 481 and 482bp is " AT ", alkali at second 481 and 482bp Base is " GC ", the third base at 481 and 482bp is " GT ".
Digestion is carried out to PCR product respectively using restriction enzyme Mlu1 and Fau1, then digestion products are subjected to agar Sugared detected through gel electrophoresis, as a result as Fig. 1 is shown.
PCR amplification system is 25 μ L:DdH2O15.75 μ L, DNA1 μ L, 10mmol/L primers each 1 μ L, 10 × PCRbuffer2.5 μ L, dNTP(2.5mmol/L)2 μ L, Mgcl2(25mmol/L)1.5 μ L, archaeal dna polymerase(5U/µl)0.25μ L.PCR amplification program is 95 DEG C of pre-degeneration 5min;94 DEG C denaturation 45s, 57 DEG C(SFL)Or 53 DEG C(Bar)Anneal 45s, and 72 DEG C are prolonged 1min is stretched, totally 30 circulations;72 DEG C of extension 10min.
Digestion is carried out to PCR product successively using restriction enzyme Mlu1 and Fau1, then digestion products are subjected to agar Sugared detected through gel electrophoresis, the results are shown in Figure 2.
In Fig. 2,1,2,4,7, No. 9 material can be cut by Fau1, and cannot be cut by Mlu1, these materials after sequencing Base is " GC " at 481 and 482bp;3rd, 5,6, No. 8 materials can be cut by Mlu1, and cannot be cut by Fau1, these materials warp Base is " GT " at 481 and 482bp after sequencing;No. 10 materials cannot be cut by Fau1 and Mlu1, after sequencing its 481 and Base is " AT " at 482bp.
Embodiment 2, blast resistant gene Pid2 specific Cs APS marks testing in the rice for turning Pid2 gene coding regions Card and application
(One), using the rice varieties Nipponbare without blast resistant gene Pid2 as transgene receptor, by anti-rice
The high expression under Nipponbare background of the CDS regions of seasonal febrile diseases gene Pid2, is prepared into the rice for turning Pid2 gene coding regions.
(Two), transgenic paddy rice that extraction step one obtains and Nipponbare genomic DNA, respectively using it as template, make PCR amplification is carried out with the primer of embodiment 1, gained PCR product carries out digestion with restriction enzyme Fau1 respectively, by each enzyme Cut product and electrophoresis detection is carried out on Ago-Gel.
The results are shown in Figure 3, and No. 1 swimming lane is Nipponbare nontransgenic plants, can by Fau1 digestions, show 255bp and Two band of 475bp;No. 2 swimming lanes are Pid2 transfer-gen plants, have 3 band after Fau1 digestions.

Claims (6)

1. a kind of rice blast resistant rice identification method, it is characterised in that realized by following steps:
(1)PCR amplification and PCR product sequencing are carried out to the allele of Rice Resources Pid2 code areas;
(2)Pid2 gene order FJ915121.1 sequences and its end of homologous sequence 5 ' play the in No. 6 chromosome of rice Two Pid2 specificity SNP sites are obtained at 5352 and 5353 bases;
(3)Described two Pid2 specificity SNP site bases have three kinds of situations:1)Base type is " AT ", 2)Base type is " GC ", 3)Base type is " GT ";
(4)If 5352 and 5353 site base of rice material to be measured is " AT ", which is to contain blast resistant gene Pid2 Rice or candidate be the rice containing blast resistant gene Pid2;If base base class at 5352 and 5353 site of rice to be measured Type is " GC " or " GT ", then the rice material be do not contain blast resistant gene Pid2 rice or candidate not contain anti-rice blast The rice of ospc gene Pid2.
A kind of 2. rice blast resistant rice identification method according to claim 1, it is characterised in that the rice blast resistant rice gene Labeling method, that is, detect rice Pid2 gene order FJ915121.1 sequences and its end of homologous sequence 5 ' and play the 5352nd He The method of 5353 bases is as follows:
(1)Using the genomic DNA of rice to be measured as template, molecular labeling primer using rice blast resistance gene Pid2 genes is draws Thing, carries out PCR amplification, obtains the pcr amplification product of 700bp sizes;
(2)Digestion is carried out to the pcr amplification product respectively with restriction enzyme Fau1 and Mlu1, its result has following several Situation:
1)The pcr amplification product only shows 1 DNA band by two kinds of digestion with restriction enzyme rear electrophoresis, then water to be measured It is homozygous " AT " that the 5352nd and 5353 bases are played in rice gene order FJ915121.1 sequences and its end of homologous sequence 5 ';
2)The pcr amplification product can show two DNA bands by restriction enzyme Fau1 digestion rear electrophoresis, and restricted Restriction endonuclease Mlu1 digestion rear electrophoresis show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured and its homologous sequence It is homozygous " GC " that the 5352nd and 5353 bases are played in the end of row 5 ';
3)The pcr amplification product can show two DNA bands by restriction enzyme Mlu1 digestion rear electrophoresis, and restricted Restriction endonuclease Fau1 digestion rear electrophoresis show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured and its homologous sequence It is homozygous " GT " that the 5352nd and 5353 bases are played in the end of row 5 ';
4)The pcr amplification product can show three DNA bands by restriction enzyme Fau1 digestion rear electrophoresis, and restricted Restriction endonuclease Mlu1 digestion rear electrophoresis show 1 DNA band, then the homologous sequence of rice genome sequence FJ915121.1 sequences to be measured It is heterozygosis base " AT/GC " that the 5352nd and 5353 bases are played in 5 ' ends;
5)If the pcr amplification product can show 3 DNA bands by restriction enzyme Mlu1 digestion rear electrophoresis, and be limited Property restriction endonuclease Fau1 digestion rear electrophoresis processed show 1 DNA band, then rice genome sequence FJ915121.1 sequences to be measured is homologous It is heterozygosis base " AT/GT " that the 5352nd and 5353 bases are played in the end of sequence 5 ';
6)The pcr amplification product shows 3 DNA bands by two kinds of digestion with restriction enzyme rear electrophoresis, then rice to be measured It is heterozygosis " GC/GT " that the 5352nd and 5353 bases are played in the end of homologous sequence 5 ' of gene order FJ915121.1 sequences.
A kind of 3. labeling method of rice blast resistant rice gene according to claim 2, it is characterised in that the primer For that can expand the primer of the molecular labeling of rice blast resistance gene Pid2, its sequence is:
DF:5’- AAGCTTGGTCAGGGAGGGTT-3’;
Pid2 DR:5’-TGTCATTGTACTTCA GCTTGGC-3’.
A kind of 4. labeling method of rice blast resistant rice gene according to claim 2, it is characterised in that the rice blast The nucleotide sequence of sick disease-resistant gene Pid2 molecular labelings is located at FJ915121.1 and its 4870th He is played in the end of homologous sequence 5 ' In sequence shown in 5570 nucleotide.
5. a kind of primer for the molecular labeling that can expand rice blast resistance gene Pid2 according to claim 3, its It is characterized in that, is identified using the primer and method, screens anti-rice blast rice.
6. a kind of primer for the molecular labeling that can expand rice blast resistance gene Pid2 according to claim 3, its It is characterized in that, rice blast resistant gene molecular breeding is carried out using the primer and method.
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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109402236A (en) * 2018-11-12 2019-03-01 长江大学 The detection method of blast resistant gene Pi-25 in a kind of rice breed
CN112725518A (en) * 2021-03-01 2021-04-30 广西壮族自治区农业科学院 PARMS marker based on SNP mutation of coding region of rice blast resistance gene Pid2 and application

Citations (3)

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