CN109196123A - SNP marker combination and its application for paddy gene parting - Google Patents
SNP marker combination and its application for paddy gene parting Download PDFInfo
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Abstract
The present invention is provided to the combinations of the SNP marker of paddy gene parting, are made of 56606 SNP markers, and the number of the SNP marker is respectively SNP1~SNP56606, their nucleotide sequence is respectively as shown in SEQ ID NO:1-56606.Molecular labeling fingerprint analysis can be carried out to variety resources of rice, genotype identification is carried out to hybrid Population offspring, is identified variety authentication, breeding material genetic background is analyzed and screened, is associated analysis to economical character by being combined using SNP marker of the invention, be had broad application prospects.
Description
Technical field
The present invention relates to genomics, molecular biology, bioinformatics and Molecular Plant Breeding fields, specifically,
It is related to the SNP marker combination and its application for paddy gene parting.
Background technique
Molecular marking technique (Molecular marker technologies) is the important tool in molecular breeding.It passes
System molecular marking technique, such as RFLP (Restriction Fragment Length Polymorphism, Restriction Fragment Length
Polymorphism) and SSR (Simple Sequence Repeat, simple sequence repeats) technology once played in functional genome research
Important function.But there are many limitations for traditional molecular marking technique, as flux is low, quantity is few, operating process is numerous
It is trivial, it is not able to satisfy the demand of large-scale commercial breeding.In order to accurately be controlled target gene, have to genetic background
Effect selection, is accurately analyzed and is identified to breeding kind, need to develop and utilize high-throughput molecular marking technique.Currently, high
Flux molecular marking technique platform specifically includes that second generation sequencing technologies, biochip technology and the detection of single SNP marker
System, such as Taqman and KASP label.
Summary of the invention
The object of the present invention is to provide the SNP marker combinations and its application for paddy gene parting.
It is a further object of the present invention to provide a kind of rice full-length genome breeding chips.
In order to achieve the object of the present invention, the present invention is provided to the SNP marker of paddy gene parting, the SNP divides
Shown in the nucleotide sequence such as SEQ ID NO:1-56606 of son label is any, every the 36th bit base of sequence is SNP mutation position
Point.
Then the present invention is provided to the combination of the SNP marker of paddy gene parting, the SNP marker group is combined into
Any two or multiple combinations in above-mentioned SNP marker.It is preferred that the combination is made of 56606 SNP markers.
The present invention utilizes two generation DNA sequencing technologies, to 3024 parts of rice samples from global 89 countries and regions into
Full-length genome of having gone resurveys sequence, obtains the sequencing data of 17T, minimum sequencing depth is 4 ×, reach 10 × sample be 2322
Part, average sequencing depth be 14 ×.Using OryzasativaLcv.Nipponbare MSU7.0 as reference sequences, it is compared using BWA is soft, mean coverage is
94%, average comparison rate is 92.5%.SNP detection is carried out to 3024 parts of samples using GATK process (Fig. 1), obtains 18.9M high
The SNP and Indel of quality, construct the phylogenetic tree (Fig. 2) of 3024 parts of rice, and rice is divided into 17 group:Group1
(421 parts), Group2 (454 parts), Group3 (250 parts), Group4 (331 parts), Group5 (310 parts), Group6 (221
Part), Group7 (223 parts), Group8 (145 parts), Group9 (266 parts), Group10 (171 parts), Group11 (101 parts),
Group_Africa_cultivation (5 parts), Group_aro_G10_Ind (30 parts), Group_aro_G10_Jap (36
Part), Group_aus_aro (46 parts), Group_near7 (7 parts), Group_near8 (7 parts).Based on 500 parts of typical cases of 3K rice
SNP polymorphic site screening (the rice functional genome breeding database (RFGB): 3K rice SNP and InDel subdata of material
Library), and representational 192 rice varieties has been selected to do further screening to high quality SNP site, it selects
56606 core SNP sites, to 192 parts of rice materials carry out clustering the result shows that, only with this 56606 SNP sites
Genotype information be enough to distinguish above-mentioned 192 parts of Rice Germplasm Resources.
The present invention also provides SNP marker combinations to prepare the application in rice full-length genome breeding chip.
The present invention also provides rice full-length genome breeding chip (rice 56K chips), include 56606 SNP sites, tool
There is nucleotide sequence shown in SEQ ID NO:1-56606.
The answering in rice varieties identification the present invention also provides the SNP marker/combination or the rice 56K chip
With.
The present invention also provides the SNP marker/combinations or the rice 56K chip in detection rice breed
Application.
The present invention also provides the SNP marker/combinations or the rice 56K chip in the association point of rice full-length genome
Application in analysis.
The present invention also provides the SNP marker/combinations or the rice 56K chip to educate in rice molecular label auxiliary
Application in kind.
The present invention also provides the SNP marker/combinations or the rice 56K chip to refer in Rice Germplasm Resources gene
Application in line analysis.
The present invention also provides the SNP marker/combinations or the rice 56K chip in Rice Progenies genotype
Application in identification.
Compared with other Markers for Detection systems, the present invention has the following advantages and effects:
(1) compared with conventional molecular is marked such as SSR marker, there are the advantages such as flux is high, single marking data are at low cost.
(2) genotype data is accurate and reliable, genetic stability and reproducible.
(3) automatic detection easy to accomplish reduces human cost.
(4) it can satisfy the integration of multiple genotype data result.
Detailed description of the invention
Fig. 1 is the screening basic flow chart of rice 56K chip of the present invention.
Fig. 2 is the Xian round-grained rice type of 192 test samples of the invention.
Fig. 3 is the geographic origin distribution map of 192 test samples of the invention.
Fig. 4 is distribution and the source of rice 56K chip of the present invention.
Fig. 5 is the distribution (number of SNP probe in the section 10Kb) of SNP site of the present invention on chromosome.
Fig. 6 is number distribution of the SNP site of the present invention on 12 chromosomes.
Fig. 7 is SNP effect of the present invention annotation (using snpeff tool).
Fig. 8 is the clustering figure of 192 test samples of the invention；Wherein, A: gathered with by the 1100K SNP of QC
Alanysis；B: clustering is carried out with the 53K SNP filtered out.
Specific embodiment
The following examples are used to illustrate the present invention, but are not intended to limit the scope of the present invention..Unless otherwise specified, embodiment
According to conventional laboratory conditions, such as Sambrook molecular cloning experiment handbook (Sambrook J&Russell DW,
Molecular Cloning:a Laboratory Manual, 2001), or according to the condition of manufacturer's specification suggestion.
The exploitation that embodiment 1 is combined for the SNP marker of paddy gene parting
One, the acquisition for resurveying sequence and SNP site of 3024 parts of Rice Germplasm Resources
1, the library construction of 3024 parts of Rice Germplasm Resources and sequencing:
The DNA sequence dna of 24 random samples is added to the joint sequence of 6 bp respectively, and mixes building mixing
The library index, joint sequence are used to distinguish the DNA sequence dna of each sample.The library built carries out on HiSeq2000 machine
PE90 sequencing, 6 lane are at least surveyed in each library, to ensure the available enough data of each sample.Then according to connector
Sequence splits data, and the read reading length after each sample can be split is 83bp (83=90-6-1,1 is connection base " T ").Most
Remove the reads and low-quality reads (base mass value≤5) polluted by connector afterwards, obtains the clean of high quality
reads.
2, it compares and SNP/Indel is detected
2.1 will obtain sam text using BWA software in clean reads comparison to OryzasativaLcv.Nipponbare (IRGSP-1.0) genome
Part, alignment parameters are " 10000-o of aln-m, 1-e, 10-t 4 ", other defaults.Using samtools by each sample
Sam file mergences, in addition index obtains bam file.Bam file is ranked up using Picard software, removal does not compare
On reads, while marking duplicate reads.It is compared again using the IndelRealigner order of GATK software package,
BaseRecalibrator carries out base quality value calibration.
2.2 detect the genotype and Indel of each sample using the UnifiedGenotyper order of GATK software package, make
With parameter are as follows:-stand_call_conf 50.0 ,-stand_emit_conf 10.0 ,-dcov 50；Use following parameter pair
Data are filtered: Mapping_quality > 20, Variant quality > 50, Read supported for every
Base > 2.
2.3 detect group SNP and Indel using the UnifiedGenotyper order of GATK software package, use parameter
Are as follows:-stand_call_conf 50.0 ,-stand_emit_conf 30.0 ,-dcov 50；Further use Mapping_
Quality > 20, Depth > 2 and MAF > 0.001 is filtered group's SNP data, finally obtains 18.9M high quality
SNP and Indel.
Full base has been carried out to 3024 parts of rice samples from global 89 countries and regions using two generation DNA sequencing technologies
Because group resurveys sequence, obtain the sequencing data of 17T, minimum sequencing depth is 4 ×, reach 10 × sample be 2322 parts, it is average to survey
Sequence depth 14 ×.Using OryzasativaLcv.Nipponbare MSU7.0 as reference sequences, BWA is soft to be compared, mean coverage 94%, average comparison rate
92.5%.SNP detection is carried out to 3024 parts of samples using GATK process, 18.9M SNP site is obtained, constructs 3024 parts of rice
Phylogenetic tree, rice is divided into 17 group:Group1 (421 parts), Group2 (454 parts), Group3 (250 parts),
Group4 (331 parts), Group5 (310 parts), Group6 (221 parts), Group7 (223 parts), Group8 (145 parts), Group9
(266 parts), Group10 (171 parts), Group11 (101 parts), Group_Africa_cultivation (5 parts), Group_
Aro_G10_Ind (30 parts), Group_aro_G10_Jap (36 parts), Group_aus_aro (46 parts), Group_near7 (7
Part), Group_near8 (7 parts).
Two, the preliminary screening of SNP site
SNP polymorphic site based on 500 parts of typical materials of 3K rice screens (rice functional genome breeding database
(RFGB): 3K rice SNP and InDel subdata base), the standard and condition of design are as follows:
1, genetic background and chadogram information based on 3K rice select 500 parts of typical materials to represent Rice Population
Polymorphism.
2, using japonica rice variety Nipponbare as reference sequences, according to the VCF file of each individual, each site is calculated
Allele frequency, low quality site and deletion segment.For SNP site, it is desirable that >=50 Variant quality,
>=20 mapping quality；2 <=<=200 read depth；>=20 genotype quality；For
The site genotype, it is desirable that >=30 reference allele quality；>=20 mapping quality.
3, it is reference sequences with rice variety 9311, according to the condition in step 2, equally calculates the allele in each site
Frequency, low quality site and deletion segment.
4, low quality site and deletion segment are all classified as missing data by the statistical result based on step 2, selection
It is polymorphic to obtain japonica rice SNP altogether for polymorphic site of the polymorphic site of missing data < 0.2, MAF > 0.05 as japonica rice
2910585, site of property.
5, low quality site and deletion segment are all classified as missing data by the statistical result based on step 3, selection
Polymorphic site of the polymorphic site of missing data < 0.2, MAF > 0.05 as long-grained nonglutinous rice.Extract long-grained nonglutinous rice polymorphic position
On point upstream and downstream 250bp (total 501bp=250+1+250) sequence alignment to Nipponbare genome, the position of unpmap is selected
It selects as distinctive (uniq) the SNP polymorphic site of long-grained nonglutinous rice, obtains such 4107, site altogether.
6, the flanking sequence for extracting SNP site upstream and downstream 35bp is used to the probe of design chips, and SNP site retains Major
With minor base type.
The 2.9MSNP polymorphic site information for obtaining high quality altogether, based on the genetic background of japonica rice, while joined Xian
The distinctive polymorphic site of rice.
Three, the screening of Affymetrix gene typing chips
Genotyping product of the Affymetrix based on chip is the various applications from Whole genome analysis to routine screening
Total solution, and accuracy and repeated highest are provided, process is simple, and cost is minimum.
The purposes and unique advantage of the GeneTitan genetic chip of Affymetrix company are mainly reflected in:
In the field SNP (single nucleotide polymorphism) analysis field, GeneTitan platform customizes different seeds in which can be convenient
Gene SNP typing chip, number can be suitble to different from 1500 SNP/ samples, to 670,000 SNP/ samples with flexible customization
Research field.Such as 500 SNP/ sample specification be suitble to seed screening, identification of transgenosis etc. application；5,000 SNP/ samples
The specification of product is suitble to the identification of molecular breeding and merit；The specifications of 50,000 SNP/ samples be suitble to gene positioning and
The confirmation of character site；500,000 SNP/ samples to 670,000 SNP/ samples are suitble to the positioning and novel character phase in feature site
The discovery of correlation gene.In conclusion the genetic chip of various specifications has different application fields, terminal client and market, and
The GeneTitan platform of Affymetrix company can all carry out the customization of chip according to above-mentioned specification requirement.And
Affymetrix ensures the homogeneity of all sites of every similar chip using photoetching technique using laser grating,
Avoid difference between batch that chip data is caused to lose, this is unique in terms of genetic chip platform.
The screening basic procedure of rice 56K chip is as follows:
According to the site 2.9MSNP obtained is screened early period from 3K SNP, by preliminary screening, the SNP of 2.5M is obtained
Site is used for the screening of early period, and representational 192 rice varieties is selected to screen the site of this 2.5M, with
Obtain the SNP site (Fig. 1) of high quality.
The effect of Screening chip: the SNP site of best quality is 1. found out；2. screen out the false positive that gets of sequencing and
The site of monomorphism；3. estimating the MAF/LD value etc. of SNP site, the site of more high heritability is found out, the chip of final design is made
Cost performance is higher；4. 192 samples is only needed early period to scan, the later period can do more multisample under same cost；5. faster
Ground obtains as a result, saving time and cost.
Four, the essential information of 192 rice samples used in Screening
Select representational 192 rice varieties during chip screening, the 133 of medium rice type
A, 47 of japonica rice type, 5 of Aus/boro type, Basmati and intermediate form are each 3 (Fig. 2).Come from geographical distribution
See: 192 parts of materials are from global 33 countries, mainly with based on the kind of China, from country in Southeast Asia
Kind is taken second place, and America, Africa, Europe and Oceania (Fig. 3) are combined.It include being widely applied in the kind of China
Kind, hybrid rice parents, molecular breeding parent and Mini core collection etc..
Five, the Screening result of 192 rice samples
It includes 4 kinds of different designs that Axiom_Rice3K55 customizes project altogether, and 2,467,017 probe groups pass through affy
The probe groups of detection have 1,142,678 (46.3%), wherein 811 specifically refer to genomic source SNP site for 9311, it is other
It is OryzasativaLcv.Nipponbare as the SNP site (table 1) for referring to genome.
1 Affy tetra- of table opens number of probes on chip and controls situation by quality
4 kinds of different designs of Affy 3K2MAX chip include about 2500K SNP site altogether, wherein 192 samples are final
It shares 178 samples and has all passed through QC detection (table 2) in all 4 kinds designs.
2 Affy tetra- of table opens on chip 192 samples and controls situation by quality
Six, the determination of rice 56K chip finally screened with SNP site
4 kinds of different designs of Affy 3K2MAX chip include about 2500K SNP site altogether, and about 1100K SNP site is logical
Cross the control of affymetrix SNP mass.Target is that screening meets item from recommendation SNP detection probe all in this 4 chips
The 56K probe of part.
1, screening criteria
1) it has verified that or disclosed SNP site
1. the SNP site that magnificent intelligence laboratory proofing is crossed
2. the SNP site in other public data/chips
3. the SNP site of cloning rice gene (means such as map based cloning, forward genetics, reverse genetics)
4. deriving from the SNP site of rice 9311
2) other SNP sites controlled by quality
1. creating scoring system, comprehensive score is carried out to all SNP controlled by quality:
A) base mutation type
B) PIC value (site information content)
C) SNP annotation information
2. LD block is analyzed, redundancy SNP is removed
3. other SNP are added, it is uniformly distributed whole SNP site in genome
2, detailed screening process
1) it has verified that or disclosed SNP site
1. the SNP marker (3.1K) of magnificent intelligence laboratory proofing
A) 2021 pass through affy quality test
B) it 1085 is not tested or not by test, is added in final chip design.
2. the SNP site in other public data/chips
A) 2161 pass through affy test in open 1: 3000 site of SNP data set
B) 3506 pass through affy test in open 2: 6000 sites of SNP data set
C) 6251 pass through affy test in open 3: 9000 sites of SNP data set
After above data merges, total acquisition 10790 has verified that or disclosed SNP site, these sites will all be selected in
Chip designs final scheme.
2) other SNP sites controlled by quality
For other SNP sites controlled by quality, we create a scoring system, pass through quality control to all
The SNP of system carries out comprehensive score:
1. base mutation type
a)A/G；A/C；T/G；Mutation (weight 20) between T/C；
b)A/T；G/C is mutated (weight 0), because A/T, C/G use identical fluorescence signal, so the hybridization of affy probe is such as
Fruit will distinguish A/T；Mutation between G/C has to place 2 probe groups, therefore its weighted.
2. PIC value (polymorphism information content, weight 40).
Although 192 parts of test sample, the sample that 4 kinds of chip quality inspections all pass through only has 179, finally according to this 179
The PIC value of sample calculating SNP.The value is similar to Rare allele frequency MAF.
3. SNP annotation information -- SNP annotation genomic locations according to locating for SNP give weight:
Intergenic region (2)
Introne (3)
Promoter (15)
5`-UTR(15)
3`-UTR(15)
If SNP is located at gene extron sub-district:
Same sense mutation (4)
Nonsynonymous mutation (10)
Nonsense mutation (20).
3, important agronomic genes SNP site
We have screened nearly 60 Main Agronomic Characters genes, and downstream 2k and gene regions select highest scoring 20 on it
SNP, inadequate 20 then all selections.Finally it is selected in SNP site 940 (table 3) according to the standard.
3 Main Agronomic Characters gene SNP number of probes of table
4, the functional gene SNP site cloned
We, which have collected, clones the gene delivered about by means such as map based cloning, forward genetics and reverse genetics
2372.2 SNP sites that highest scoring is selected from the SNP site of each gene (including upstream and downstream 2k), amount to and obtain
4729 SNP sites.
5, from 9311 SNP site
These sites are present in initial design, amount to 811 SNP and are controlled by quality, all selected.
6, the section LD block interior label SNP is screened
1) be removal redundancy SNP, we with 178 parts of detection material genotyping results to by the SNP probe of quality testing into
The LD block that gone is calculated, and obtaining 1,012,772 SNP adjacent thereto altogether, there are the SNP sites of LD.If the section LD block
Less than 10kb, we will select the SNP of highest scoring as Tag SNP inside it；It, will be if LD block is greater than 10k
Its internal every 10kb selects the SNP of a highest scoring as the Tag SNP in this section.According to the method, it selects in total
43005 SNP sites being located in LD block.
2) by analyzing SNP distribution in every section 10Kb, it has been found that there is 2312 section >, 2 SNP.In order to balance core
Piece site total amount, genome be evenly distributed, LD block block information.We will select one by every 5kb in 2312 sections
The high SNP site of score is as representative.So finally obtaining 36510 SNP sites in the section LD.
7, genome is uniformly distributed SNP screening
To ensure that SNP chip design is uniformly distributed within the scope of rice full-length genome, it is not divided into any LD from 128,620
The SNP site of block has carried out screening of filling a vacancy.By the way that chromosome to be divided into the section of 10k, if without containing any in the region
1-5 walks the SNP filtered out, then selects the SNP site of a non-LD block of highest scoring in the area.It can protect in this way
Demonstrate,prove every section 10Kb will have at least one SNP be selected in (on condition that there is the presence of SNP in the library 1M SNP in the section).According to the mark
Standard is filled a vacancy altogether selects 1736 SNP sites.
Seven, rice 56K chip design result
1,56K chip SNP site carrys out source distribution
By the above various methods, we screen 55,312 SNP sites, the SNP site that each step is contributed in total
And ratio situation is as shown in Figure 4.
2, the chromosome distribution of 56K chip SNP site
Distribution of the 56K chip screened on 12 chromosomes is counted, it is found that the SNP site of 56K is uniform
Be distributed on 12 chromosomes of rice, spacing average value is 6.84K, median 5.3K to SNP site on chromosome, important
The SNP site number of agronomic genes location proximate design is more (Fig. 5).
Number of the 56K chip screened on 12 chromosomes is counted, finds the SNP site of 56K
One and third chromosome on site it is more, respectively 6833 and 6082；Number on the chromosome of the 9th, 10 and 12 compared with
It is few, respectively 3148,3214 and 3329 (Fig. 6).
3, Fig. 4 is shown in distribution of the 56K chip SNP site in different genes region.Effect is carried out to SNP using snpeff tool
Annotation, is as a result shown in Fig. 7.
4, screening front and back SNP site clustering
The SNP site of (56K) carries out clustering to 192 test samples after (1.1M) before screening and screening, finds
The result that screening front and back obtains is closely similar.Select K=5, test sample can be divided into 5 subgroups, 2 japonica rice (temperate zone and
The torrid zone) and 3 long-grained nonglutinous rice groups.Show that the SNP site of the 56K filtered out is representative (Fig. 8) with higher.
Although above the present invention is described in detail with a general description of the specific embodiments,
On the basis of the present invention, it can be modified or is improved, this will be apparent to those skilled in the art.Cause
This, these modifications or improvements, fall within the scope of the claimed invention without departing from theon the basis of the spirit of the present invention.
Industrial applicibility
Molecular labeling fingerprint analysis, right can be carried out to variety resources of rice using SNP marker combination of the invention
Hybrid Population offspring carry out genotype identification, variety authentication is identified, breeding material genetic background is analyzed and
Screening is associated analysis to economical character, has broad application prospects.
Claims (10)
1. being used for the SNP marker of paddy gene parting, which is characterized in that the nucleotide sequence of the SNP marker is such as
Shown in SEQ ID NO:1-56606 is any, every the 36th bit base of sequence is SNP mutation site.
2. the SNP marker for paddy gene parting combines, which is characterized in that the SNP marker group is combined into right
It is required that any two or multiple combinations in 1 SNP marker.
3. the combination of SNP marker described in claim 2 is preparing the application in rice full-length genome breeding chip.
4. rice full-length genome breeding chip, which is characterized in that include 56606 SNP sites, with SEQ ID NO:1-
Nucleotide sequence shown in 56606.
5. core described in the combination of SNP marker described in SNP marker, claim 2 described in claim 1 or claim 4
Application of the piece in rice varieties identification.
6. core described in the combination of SNP marker described in SNP marker, claim 2 described in claim 1 or claim 4
Application of the piece in detection rice breed.
7. core described in the combination of SNP marker described in SNP marker, claim 2 described in claim 1 or claim 4
Application of the piece in rice whole-genome association.
8. core described in the combination of SNP marker described in SNP marker, claim 2 described in claim 1 or claim 4
Application of the piece in rice molecular marker-assisted breeding.
9. core described in the combination of SNP marker described in SNP marker, claim 2 described in claim 1 or claim 4
Application of the piece in Rice Germplasm Resources genetic fingerprinting.
10. core described in the combination of SNP marker described in SNP marker, claim 2 described in claim 1 or claim 4
Application of the piece in Rice Progenies genotype identification.
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| PCT/CN2017/100768 WO2019047074A1 (en) | 2017-09-06 | 2017-09-06 | Snp molecular marker combination for rice genotyping, and application thereof |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN109196123A true CN109196123A (en) | 2019-01-11 |
| CN109196123B CN109196123B (en) | 2022-03-08 |
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Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110527736A (en) * | 2019-08-19 | 2019-12-03 | 中国农业科学院作物科学研究所 | It combines and its applies for the SNP marker of Rice Germplasm Resources and cultivar identification |
| CN110699484A (en) * | 2019-12-03 | 2020-01-17 | 天津市农作物研究所(天津市水稻研究所) | SNP molecular marker for detecting rice stripe disease resistant STV11 gene and application |
| CN111676270A (en) * | 2020-07-09 | 2020-09-18 | 四川省自然资源科学研究院 | Method for screening polymorphic SNP molecular marker, polymorphic SNP molecular marker and primer pair |
| CN112662796A (en) * | 2020-11-04 | 2021-04-16 | 中国水稻研究所 | Combined SNP core locus for rice variety identification and application |
| CN112941216A (en) * | 2020-12-29 | 2021-06-11 | 武汉基诺赛克科技有限公司 | Development method and breeding application of 1K SNP-Panel of rice |
| CN113493853A (en) * | 2021-02-23 | 2021-10-12 | 双绿源创芯科技(佛山)有限公司 | SNP marker combination for rice variety resource identification |
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| CN112501339B (en) * | 2020-12-11 | 2023-06-27 | 华智生物技术有限公司 | SNP molecular marker of rice blast resistance gene Pi5 and application thereof |
| CN113151544B (en) * | 2021-03-19 | 2024-02-23 | 海南大学 | Primer group, kit and method for detecting Xa23 gene by utilizing functional markers |
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| WO2023058064A1 (en) * | 2021-10-07 | 2023-04-13 | National Institute Of Plant Genome Research | Pan-genome genotyping array and uses thereof |
| CN114480705A (en) * | 2022-01-13 | 2022-05-13 | 宁波市农业科学研究院 | SNP molecular marker of rice bacterial blight resistant gene XA23 and amplification primer and application thereof |
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| CN1675373A (en) * | 2002-06-10 | 2005-09-28 | 株式会社植物基因组研究中心 | Method of distinguishing rice varieties |
| CN102747138B (en) * | 2012-03-05 | 2014-03-19 | 中国种子集团有限公司 | Rice whole genome SNP chip and application thereof |
| CN104328507B (en) * | 2014-10-11 | 2016-03-30 | 中国水稻研究所 | A kind of SNP chip, Preparation method and use for rice varieties qualification |
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| CN104024438B (en) * | 2012-09-28 | 2015-06-17 | 未名兴旺系统作物设计前沿实验室（北京）有限公司 | Snp loci set and usage method and application thereof |
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- 2017-09-06 CN CN201780006971.9A patent/CN109196123B/en active Active
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN1675373A (en) * | 2002-06-10 | 2005-09-28 | 株式会社植物基因组研究中心 | Method of distinguishing rice varieties |
| CN102747138B (en) * | 2012-03-05 | 2014-03-19 | 中国种子集团有限公司 | Rice whole genome SNP chip and application thereof |
| CN104328507B (en) * | 2014-10-11 | 2016-03-30 | 中国水稻研究所 | A kind of SNP chip, Preparation method and use for rice varieties qualification |
Cited By (8)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110527736A (en) * | 2019-08-19 | 2019-12-03 | 中国农业科学院作物科学研究所 | It combines and its applies for the SNP marker of Rice Germplasm Resources and cultivar identification |
| CN110699484A (en) * | 2019-12-03 | 2020-01-17 | 天津市农作物研究所(天津市水稻研究所) | SNP molecular marker for detecting rice stripe disease resistant STV11 gene and application |
| CN111676270A (en) * | 2020-07-09 | 2020-09-18 | 四川省自然资源科学研究院 | Method for screening polymorphic SNP molecular marker, polymorphic SNP molecular marker and primer pair |
| CN111676270B (en) * | 2020-07-09 | 2023-07-25 | 四川省自然资源科学研究院 | Screening method of polymorphic SNP molecular markers, polymorphic SNP molecular markers and primer pair |
| CN112662796A (en) * | 2020-11-04 | 2021-04-16 | 中国水稻研究所 | Combined SNP core locus for rice variety identification and application |
| CN112662796B (en) * | 2020-11-04 | 2022-06-10 | 中国水稻研究所 | Combined SNP core locus for rice variety identification and application |
| CN112941216A (en) * | 2020-12-29 | 2021-06-11 | 武汉基诺赛克科技有限公司 | Development method and breeding application of 1K SNP-Panel of rice |
| CN113493853A (en) * | 2021-02-23 | 2021-10-12 | 双绿源创芯科技(佛山)有限公司 | SNP marker combination for rice variety resource identification |
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| WO2019047074A1 (en) | 2019-03-14 |
| CN109196123B (en) | 2022-03-08 |
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