CN115029465A - KASP and dCAPS markers cosegregating with rape seed secondary dormancy major QTL and application thereof - Google Patents

KASP and dCAPS markers cosegregating with rape seed secondary dormancy major QTL and application thereof Download PDF

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CN115029465A
CN115029465A CN202210098380.1A CN202210098380A CN115029465A CN 115029465 A CN115029465 A CN 115029465A CN 202210098380 A CN202210098380 A CN 202210098380A CN 115029465 A CN115029465 A CN 115029465A
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赵祥祥
刘福霞
刘磊
吴德鹏
裔新
谷玉娟
毛丰
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Abstract

The invention discloses a KASP and dCAPS marker co-separated from a rape seed secondary dormancy major QTL and application thereof, belonging to the technical field of rape molecular breeding. Designing primer compositions of a KASP marker and a dCAPS marker based on a sequence of a flanking SNP marker A09-10470644 which is co-separated from a rape seed secondary dormancy major QTL qSSD.A09, and carrying out PCR amplification by taking genome DNA of a rape plant as a template so as to effectively convert the SNP marker into the KASP marker and the dCAPS marker. The detection system and the method provided by the invention can effectively predict the secondary dormancy characteristic of the rape seeds, assist in screening the excellent varieties or strains with weak secondary dormancy characteristic, effectively improve the breeding accuracy and accelerate the improvement of the secondary dormancy characteristic of the rape seeds.

Description

KASP and dCAPS markers cosegregating with rape seed secondary dormancy major QTL and application thereof
Technical Field
The invention belongs to the technical field of rape molecular breeding, relates to an SNP locus, a molecular marker developed based on the SNP locus and application of the molecular marker, and particularly relates to KASP and dCAPS markers which are co-separated from a rape seed secondary dormancy main effect QTL qSSD.A09 and application of the KASP and dCAPS markers in auxiliary selection of rape seed secondary dormancy characteristics.
Background
Rape is one of the most important oil crops in the world, provides more than 15 percent of edible vegetable oil in the world, and is also an important biofuel and feed. The mechanical action of the mechanical combined harvest in the rape production area can cause about 6000-9000 grains/m 2 The seeds are scattered in the field, and the manual harvest can cause more seeds to be scattered. The scattered seeds induce secondary dormancy due to adverse conditions such as drought and the like, can survive for several months or even ten years underground, cause the underground seed bank to exist for a long time, and once the external environment is proper, the secondary dormancy seeds germinate to form self-growing seedlings. On one hand, the rape self-growing seedlings can become weeds in the field, and the field management investment (manpower, herbicide and the like) is increased; on the other hand, rape is a common cross-pollinated crop, and rape self-growing seedlings cause variety mixing through pollen drift in the flowering period, so that the quality of the rape is reduced. More seriously, the self-growing seedlings of the transgenic rapes can cause gene drift and cause biological safety problems through cross pollination. The cultivation and application of new species with weak secondary dormancy is one of the most economic and effective ways to solve the problem.
Single Nucleotide Polymorphism (SNP) refers to a DNA sequence polymorphism caused by a change such as a transition, a transversion, an insertion, or a deletion at a specific nucleotide position in DNA in a genome. The SNP markers have the advantages of large quantity, wide distribution, uniform distribution in the whole genome and the like, and become the most widely applied molecular markers.
KASP is a novel genotyping technology with low cost and high throughput characteristics by competitive allele specific PCR (KASP) developed by LGC (Laboratory of the Government Chemist) (http:// www.lgcgenomics.com), carries out accurate double-allele genotyping on SNP and InDel markers by specific matching of terminal bases of primers, and is widely applied to molecular marker-assisted selection of crops such as rice, wheat, soybean and the like. dCAPS (modified purified amplified polymorphic sequences, dCAPS) molecular marker technology utilizes enzyme cutting sites formed by mutation to carry out enzyme cutting detection on the mutation site amplification products so as to judge the mutation condition. The method is simple to operate and low in cost, and can complete genotyping by combining with conventional laboratory equipment such as Polymerase Chain Reaction (PCR) and agarose gel electrophoresis.
The former people locate 4 Quantitative Trait Loci (QTL) related to secondary dormancy by linkage analysis, which are respectively located on chromosomes A05, C03, C05 and C08, but do not develop molecular markers which are tightly linked with the QTL and can be used for marker-assisted selective breeding. Therefore, the research utilizes the developed KASP and dCAPS markers co-separated from the main effect QTL qSSD.A09 related to the secondary dormancy of the rape seeds to accurately improve the secondary dormancy characteristics of the rape seeds, and has important significance in the production practice of the rape seeds.
Disclosure of Invention
Aiming at the problems in the prior art, the invention aims to provide a KASP and dCAPS marker which is co-separated from a rape seed secondary dormancy main effect QTL qSSD.A09; the second technical problem to be solved by the present invention is to provide a KASP-labeled primer composition and a dCAPS-labeled primer composition; the third technical problem to be solved by the invention is the application of KASP and dCAPS markers or primer compositions thereof in genetic analysis and fine positioning of rape seed secondary dormancy genes and in auxiliary selection or genetic improvement of rape seed secondary dormancy characteristics.
In order to solve the technical problems, the technical scheme adopted by the invention is as follows:
the method utilizes a PEG chemical induction method to identify the secondary dormancy rate of a backcross recombination inbred line group of 178 lines from 2017 to 2021, locates the QTL related to the secondary dormancy based on a complete interval mapping method built in IcMapping v4.2, screens out the main effect QTL qSSD.A09 of the secondary dormancy of rape seeds, and can explain 7.8-12.2% of phenotypic variation.
A flanking SNP marker A09-10470644 co-separated from a main QTL qSSD.A09 of the secondary dormancy of rape seeds, wherein the SNP marker and the QTL qSSD.A09 related to the secondary dormancy of the rape seeds are co-located in an interval of 4.9cM of a chromosome A09 of the rape, are located in 10.47-13.48Mb of a reference genome A09 of a double middle 11, and have polymorphism A/C.
Further, the invention also provides a method for developing KASP marker and dCAPS marker based on SNP locus, which takes the sequence of A09-10470644 as basic sequence, designs primer composition of KASP marker and primer composition of dCAPS marker, takes the genome DNA of rape plant as template to carry out PCR amplification, and makes the SNP marker effectively converted into KASP marker and dCAPS marker; the nucleotide sequence of the KASP-labeled primer composition is shown in SEQ ID NO. 1-3; the nucleotide sequence of the dCAPS labeled primer composition is shown in SEQ ID NO. 4-5.
A KASP marker Primer composition co-separated from a rape seed secondary dormancy main effect QTL qSSD.A09 comprises two specific primers PrimeR A and PrimeR C used for amplifying the KASP marker and a universal Primer Primer _ Common, wherein the nucleotide sequences of the primers are respectively shown as SEQ ID NO. 1-3.
The method comprises the following specific steps:
Figure BDA0003492363740000031
the application is that the 5' end of the nucleotide sequence of a specific primer SEQ ID NO.1-2 is respectively added with a fluorescent modification group FAM and a fluorescent modification group HEX.
A primer composition of a dCAPS marker co-separated from a rape seed secondary dormancy main effect QTLqSSD.A09, wherein a forward primer of the dCAPS marker is shown as SEQ ID NO.4, and a reverse primer of the dCAPS marker is shown as SEQ ID NO.5, and comprises the following components:
Figure BDA0003492363740000032
the primer composition of the KASP marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 or the KASP marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 is applied to genetic analysis and fine positioning of rape seed secondary dormancy genes.
The primer composition of the KASP marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 or the KASP marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 is applied to molecular marker-assisted breeding of the rape seed secondary dormancy characteristics.
The verification of the KASP marking efficiency by utilizing 178 group strains shows that the KASP marking can effectively predict the secondary dormancy characteristic of rape seeds, and a new variety with weak secondary dormancy characteristic can be selected in an auxiliary mode in production.
The primer composition of the dCAPS marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 or the dCAPS marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 is applied to genetic analysis and fine positioning of rape seed secondary dormancy genes.
The application of the dCAPS marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 or the primer composition of the dCAPS marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09 in molecular marker-assisted breeding of the rape seed secondary dormancy characteristics.
The efficiency of dCAPS marking is verified by using 47 randomly selected group strains, which shows that the dCAPS marking can effectively predict the secondary dormancy characteristic of rape seeds and can assist in screening of excellent varieties or strains with weak secondary dormancy characteristics.
A method for screening a weak dormancy genotype rape plant comprises the following steps: taking the genome DNA of a plant sample to be detected as a template, and carrying out PCR amplification on the template by using the primer composition of the KASP marker co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09, and carrying out genotype typing on the KASP amplification result; in the primer composition, different fluorescent modification groups are respectively added to the 5' ends of the primer sequences shown in SEQ ID NO.1-2, and the plants capable of reading the fluorescent groups marked by the SEQ ID NO.2 are identified as the rape plants with weak dormancy genotypes.
The PCR amplification system is as follows: template DNA 20ng/ul 2.5ul, 2x KASP Master mix 2.5ul, KASP Assay mix 0.07 ul.
The PCR amplification procedure was: 15min at 94 ℃; the annealing temperature is reduced by 0.6 ℃ for 10 cycles at 94 ℃ for 20s and 61-55 ℃ for 1 min; 26 cycles of 94 ℃ for 20s and 55 ℃ for 1 min.
A method of screening a canola plant for a weakly dormant genotype comprising the steps of: taking genome DNA of a plant sample to be detected as a template, carrying out PCR amplification on the template by using a dCAPS marked primer composition co-separated from the rape seed secondary dormancy main effect QTL qSSD.A09, carrying out enzyme digestion and electrophoresis detection on a PCR product by using restriction enzyme Taq I, screening a rape plant with a weak dormancy genotype according to an electrophoresis detection result, wherein the rape plant with the weak dormancy genotype is a rape plant with a strong dormancy genotype if the fragment is 89bp after enzyme digestion, and the rape plant with the weak dormancy genotype is a rape plant with the weak dormancy genotype if the fragment is 59bp and 30bp after enzyme digestion.
The PCR amplification system is as follows: mu.L template DNA, 10. mu.L 2 XKOD FX buffer, 4. mu.L 2mM dNTPs, 0.4. mu.L KOD FX, 10. mu. mol/L each of forward and reverse primers, 0.1. mu.L, 3.4. mu.L ddH 2 O。
The PCR amplification procedure was: 5min at 94 ℃; 10s at 98 ℃, 30s at 57 ℃, 2min at 68 ℃ and 32 cycles; 10min at 68 ℃; keeping the temperature at 4 ℃.
The enzyme cutting system is as follows: mu.L of PCR product, 1. mu.L of restriction enzyme Taq I10U/mL, 0.5. mu.L of 10x Buffer, 0.5. mu.L of ddH 2 And O, placing the enzyme digestion system at the constant temperature of 37 ℃ for 2 hours to obtain a product after enzyme digestion.
Further, a kit for identifying the secondary dormancy genotype of rape seeds comprising said KASP-tagged primer composition or said dCAPS-tagged primer composition is also within the scope of the present application.
Compared with the prior art, the invention has the beneficial effects that:
the invention discloses a main effect QTLqSSD.A09 coseparation KASP and dCAPS markers which are positioned on a rape A09 chromosome and related to the secondary dormancy of seeds, which can be used for detecting the secondary dormancy characteristics of the rape seeds.
Drawings
FIG. 1 is a QTL scanning result diagram of the secondary dormancy rate of BILs group rape in 5 environments in 2017-2021;
FIG. 2 is a diagram of KASP tag development and verification; AA: a strongly dormant parent genotype; CC: a weakly dormant parent genotype;
FIG. 3 is a graph showing the results of typing of dCAPS markers; in the figure, H: a weakly dormant parent; v: a strongly dormant parent; B1-B200: backcrossing and recombining partial strains of the inbred line group; marker: 20bp DNA Ladder (Code No. 3420A; TaKara); AA: a strongly dormant parent genotype; CC: a weakly dormant parent genotype.
Detailed Description
The invention is further described with reference to specific examples.
Example 1
Materials and field test
A secondary dormancy super-strong variety Huaiyou-SSD-V1 (V for short, secondary dormancy rate) with obvious secondary dormancy character difference>90 percent) and a secondary dormancy ultra-weak variety Huaiyou-WSD-H2 (H for short, the secondary dormancy rate is less than 5 percent) as parents for hybridization to obtain a hybrid F 1 By continuous multi-generation backcrossing with weak secondary dormancy parent, the method constructs the product containingA population of 178 lines of backcross recombinant inbred lines (BILs). Planting the group and the parents in a biological science and technology garden test base of Huaiyin academy of academic, Huai, in 2017-2021 for 5 years, wherein all tests are designed in a random block mode, and a seedling transplanting mode is adopted, wherein 2 lines are planted in each cell, and 15 plants are planted in each line. And field management is carried out according to a conventional production mode, in order to ensure the purity, rape flowering phase is subjected to bagging on sampled plants, after the seeds are completely mature, seeds of 10 plants are collected from each family, and the plants are naturally dried and stored.
Second, phenotypic evaluation
And (3) identifying the secondary dormancy rate of the population from 2017 to 2021 by adopting an optimized PEG chemical induction method (national invention patent: ZL201210108031.X, 2013).
Third, genetic linkage map construction and location
178 materials were genotyped using a rape 90K illuminium SNP chip. All SNP markers were screened as follows: (1) polymorphisms exist between parents; (2) the deletion ratio of the offspring genotype is not more than 50%; (3) minor Allele Frequency (MAF) greater than 5%; (4) the heterozygosity rate is not more than 20%; (5) the allele proportion of the donor parent is less than 25 percent, and 12,959 high-quality SNP markers are obtained in total. The probe sequences of these markers were aligned with the reference genome (version ZS11, http:// cbi. hzau. edu. cn/cgi-bin/rape/download _ ext) using blast software to obtain the positions of 12,339 SNP markers on 19 chromosomes of Brassica napus. Genetic map construction was performed using the JoinMap v4.0 software, and the recombination rate between markers was converted to genetic distance by Kosambi mapping function. Finally, a full-length 2031.98cM high-density genetic linkage map containing 5738 SNP markers is constructed, covering 19 chromosomes of rape, and the average map distance is 0.67 eM. The linkage group length is distributed in the range of 51.76-203.71cM, the number of markers in each linkage group is 42-1343, and the average number of markers is 302. Based on the high-density genetic linkage map, an Ichimapping v4.2 software built-In Complete Interval Mapping (ICIM) is utilized to locate the rape seed secondary dormancy related QTL, a threshold LOD is set to be more than or equal to 2.5, and finally, a main effective locus (shown in figure 1) which is stable in multi-environment is located on the chromosome A09 and named as qSSD.A 09. This QTL was identified in 5-environments in 2017-2021, accounting for 7.8-12.2% phenotypic variation. The QTL is positioned in the interval of 4.9cM of rape A09 chromosome, and the corresponding reference genome physical positions of the medium and double 11 rape are as follows: 10.47-13.48 Mb.
Four, KASP mark development and verification
A flanking SNP marker A09-10470644 for co-segregation of rape seed secondary dormancy major QTL QSSD.A09, and the marker polymorphism is A/C. KASP molecular marker Primer sequences were designed using Primer premier 5.0 software, including 2 specific primers (Primer A and Primer C) and 1 universal Primer (Primer _ Common). Wherein, the 5' ends of 2 specific primers are respectively added with different fluorescent modification groups, and the primer sequences and the fluorescent groups are shown in table 1. 178 strains of BILs groups are tested, genome DNA of a plant sample to be tested is extracted by a heaven root kit (DP305) to be used as a template, and the template is amplified by an LGC Hydrocycler-16PCR instrument by using the 3 primer mixtures and the KASP kit (KBS-1016, LGC), wherein the amplification system is as follows: template DNA (20ng/ul)2.5ul, 2 XKASP Master mix 2.5ul, KASP Assay mix 0.07ul, amplification program: 15min at 94 ℃; the annealing temperature is reduced by 0.6 ℃ for 10 cycles in each cycle at 94 ℃ for 20s and 61-55 ℃ for 1 min; 26 cycles of 94 ℃ for 20s and 55 ℃ for 1 min. After the reaction is finished, a Pherastar scanner is used for reading fluorescence data of the KASP product, and the result of fluorescence scanning is automatically converted into a graph. The BMG PHERstar instrument was used to detect the fluorescence signal and to look for typing.
TABLE 1 KASP primer sequences
Figure BDA0003492363740000071
As shown in FIG. 2, the KASP marker can accurately distinguish between individuals with different genotypes, wherein the average secondary dormancy rate of 26 individuals with a strong dormant genotype (AA) is 68.55%; the average secondary dormancy rate of 149 individuals with the weak dormancy genotype (CC) is 37.19%, and the difference of the secondary dormancy rate among different genotype individuals is extremely obvious (p is less than 0.001).
Development and verification of five and dCAPS markers
While the KASP marker has high flux, the KASP marker also has the characteristics of high cost, high hardware requirements required by fluorescence detection and the like, the dCAPS marker is simple to operate and low in cost, and typing can be completed by using conventional laboratory equipment such as a PCR instrument, agarose gel electrophoresis and the like.
Based on the method, the application aims at the flanking SNP marker A09-10470644 co-separated from the main effect QTL qSSD.A09 of the secondary dormancy of rape seeds and utilizes a dCAPS Finder 2.0 online tool (c) (http://helix.wustl.edu/dcaps/ dcaps.html) dCAPS primer development and endonuclease selection were performed while the corresponding downstream primers were designed using Primerpremier 5.0 software (Table 2). The primers were synthesized by Biotechnology engineering (Shanghai) Inc.
Performing PCR amplification by using genomic DNA of the parent and the material to be detected as a template, wherein the PCR amplification system is 20 mu L: mu.L template DNA, 10. mu.L 2 XKOD FX buffer, 4. mu.L 2mM dNTPs, 0.4. mu.L KOD FX, 0.1. mu.L (10. mu. mol/L) of each of the forward and reverse primers, and 3.4. mu.L ddH 2 And O. The amplification procedure was: 5min at 94 ℃; 10s at 98 ℃, 30s at 57 ℃, 2min at 68 ℃ and 32 cycles; 10min at 68 ℃; keeping the temperature at 4 ℃. After the PCR product is detected to be qualified by 1% agarose gel electrophoresis, the PCR product is cut by enzyme respectively, the enzyme cutting system is 5 mu L: 3 mu L PCR product, 1 mu L restriction enzyme (Taq I, 10U/mL), 0.5 mu L10x Buffer, 0.5 mu L ddH 2 And O, placing the enzyme digestion system at the constant temperature of 37 ℃ for 2 hours to obtain a product after enzyme digestion. The enzyme digestion products were detected by 6% polyacrylamide gel electrophoresis.
As shown in fig. 3, 47 BILs offspring were randomly picked for signature verification. Wherein, the number of strong secondary dormancy strains is 26, and the average secondary dormancy rate is 68.55%; 21 weak secondary dormancy strains with the average secondary dormancy rate of 27.63%; the difference of the secondary dormancy rates among individuals with different genotypes is extremely obvious (p is less than 0.001).
TABLE 2 dCAPS tagged primers
Figure BDA0003492363740000081
Sequence listing
<110> Huaiyin college of learning professions
<120> KASP and dCAPS markers coseparated with rape seed secondary dormancy major QTL and application thereof
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gaaggtgacc aagttcatgc tgtataacgt ccttcccttc ctact 45
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<213> PrimerC(artificial)
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gaaggtcgga gtcaacggat tgtataacgt ccttcccttc ctacg 45
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<211> 24
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<213> Primer_Common(artificial)
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atgaaaaatg agtctttgtc caac 24
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<213> dCAPS-F1(artificial)
<400> 4
acgtataacg tccttccctt ccttc 25
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<212> DNA
<213> dCAPS-R1(artificial)
<400> 5
agatcataaa attgatgaaa aatg 24

Claims (10)

1. A KASP marker and a dCAPS marker co-separated from a rape seed secondary dormancy major QTL, which is characterized in that the KASP marker and the dCAPS marker are based on a sequence of a flanking SNP marker A09_10470644 co-separated from a rape seed secondary dormancy major QTL qSSD.A09 as a base sequence, a primer composition of the KASP marker and a primer composition of the dCAPS marker are designed, and genome DNA of a rape plant is used as a template for PCR amplification, so that the SNP marker is effectively converted into the KASP marker and the dCAPS marker; the SNP marker and a QTL qSSD.A09 related to the secondary dormancy of rape seeds are co-located in an interval of 4.9cM of chromosome A09 of rape, located on 10.47-13.48Mb of chromosome A09 of a double 11 reference genome, and have polymorphism of A/C; the nucleotide sequence of the KASP-labeled primer composition is shown in SEQ ID NO. 1-3; the nucleotide sequence of the dCAPS labeled primer composition is shown in SEQ ID NO. 4-5.
2. A primer composition of KASP markers co-separated with a rape seed secondary dormancy major QTL is characterized by comprising two specific primers and a universal primer for amplifying the KASP markers, wherein the nucleotide sequences of the primers are respectively shown as SEQ ID NO. 1-3.
3. A dCAPS marked primer composition which is co-separated with a rape seed secondary dormancy main effect QTL, wherein a dCAPS marked forward primer is shown as SEQ ID NO.4, and a dCAPS marked reverse primer is shown as SEQ ID NO. 5.
4. Use of the primer composition of the KASP marker co-segregated with the major QTL of secondary dormancy of oilseed rape seed of claim 1 or the KASP marker co-segregated with the major QTL of secondary dormancy of oilseed rape seed of claim 2 for genetic analysis and fine localization of the secondary dormancy gene of oilseed rape seed.
5. Use of the primer composition of the KASP marker co-segregating with the secondary dormancy major QTL of canola seed of claim 1 or the KASP marker co-segregating with the secondary dormancy major QTL of canola seed of claim 2 for molecular marker assisted breeding for secondary dormancy traits of canola seeds.
6. Use of a primer composition of the dCAPS marker co-segregating with the rapeseed secondary dormancy major QTL of claim 1 or the dCAPS marker co-segregating with the rapeseed secondary dormancy major QTL of claim 3 in genetic analysis and fine mapping of a rapeseed secondary dormancy gene.
7. Use of a primer composition of a dCAPS marker co-segregating with a rape seed secondary dormancy major QTL as defined in claim 1 or a dCAPS marker co-segregating with a rape seed secondary dormancy major QTL as defined in claim 3 for molecular marker assisted breeding of a rape seed secondary dormancy trait.
8. A method of screening a canola plant for a weak dormant genotype comprising the steps of: carrying out PCR amplification on a template by using the genome DNA of a plant sample to be detected as the template and using the KASP marked primer composition coseparated with the rape seed secondary dormancy major QTL in claim 2, and carrying out genotyping by using the amplification result; in the primer composition, different fluorescent modification groups are respectively added to the 5' ends of the primer sequences shown in SEQ ID NO.1-2, and the plants capable of reading the fluorescent groups marked by SEQ ID NO.2 are identified as the rape plants with weak dormancy genotypes.
9. A method for screening a rape plant with a weak dormancy genotype is characterized by comprising the following steps: taking genome DNA of a plant sample to be detected as a template, carrying out PCR amplification on the template by using a dCAPS marked primer composition which is co-separated from the rape seed secondary dormancy main effect QTL and is described in claim 3, carrying out enzyme digestion and electrophoresis detection on a PCR product by using restriction enzyme TaqI, screening the rape plant with the weak dormancy genotype according to an electrophoresis detection result, wherein the rape plant with the strong dormancy genotype is obtained if the fragment after enzyme digestion is 89bp, and the rape plant with the weak dormancy genotype is obtained if the fragment after enzyme digestion is 59bp and 30 bp.
10. A kit for identifying a secondary dormancy genotype of a rape seed comprising the KASP-tagged primer composition of claim 2 or the dCAPS-tagged primer composition of claim 3.
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