Brassica napus stem diameter major QTL linked SNP marker and application thereof

Abstract

The invention discloses a cabbage type rape stem diameter major QTL (quantitative trait loci) linked SNP (single nucleotide polymorphism) marker and application thereof, the SNP marker comprises a first SNP marker and an optional second SNP marker, the first SNP molecular marker is located at the 9132080th-9132180th basic group of a second chromosome of a cabbage type rape genome A and is polymorphic, and the basic group of the first SNP molecular marker is T or C; the base of the second SNP molecular marker located at the 3808136-3808236 sites of the No.8 chromosome of the brassica napus C genome is polymorphic, and the base is A or G; brassica napus' ZS11 'is used as a reference genome of the SNP molecular marker. Based on the advantages of a PARMS detection technology, a primer group containing allele specific primers and reverse amplification primers of a target site is designed according to 100-500bp sequences in upstream and downstream of SNP linked with QTL, so that the stem diameter character of the brassica napus is rapidly identified or assisted in identification, and the requirements of brassica napus breeding or assisted breeding, breeding cycle shortening and the like are met.

Description

Technical Field

[0001] The present invention relates to the field of biotechnology, and particularly to SNP markers linked to major QTLs for stem diameter in Brassica napus and their applications. Background Art

[0002] China is a large consumer of edible vegetable oil. In 2023, the consumption was approximately 38.5 million tons, while the domestic production was about 14 million tons, with a self-sufficiency rate of about 36.4% (data source: China National Grain and Oils Information Center), and an import dependence rate of about 63.6%. Rapeseed is the largest oil crop in China. In 2023, the planting area was approximately 7.65 million hectares, and rapeseed oil accounted for 42%-45% of domestic edible vegetable oil (data source: National Bureau of Statistics). Therefore, vigorously developing rapeseed production is of great strategic significance for ensuring the supply security of national edible oil.

[0003] As the supporting structure of rapeseed, the thickness of the stem directly affects lodging resistance, and lodging will lead to yield reduction. The thicker the stem, the stronger the lodging resistance. Secondly, the thickness of the stem is related to material transportation. The degree of development of vascular bundles affects the transportation of water and nutrients, and thus affects yield. In addition, the stem may be related to the distribution of photosynthetic products. A thick stem can store more nutrients, thereby promoting inflorescence differentiation and grain filling. Therefore, increasing stem thickness through genetic improvement is of great significance for improving the lodging resistance and yield of rapeseed.

[0004] Rapeseed in China is divided into two ecological regions: spring rapeseed and winter rapeseed. Spring rapeseed is mainly distributed in high-altitude or high-latitude regions such as the northwest and southwest of China, accounting for about 8% of the total national area. Qinghai is the first province in China to carry out the improvement of spring rapeseed varieties. The Qingza series of varieties developed have advantages such as high yield and wide adaptability, and the annual planting area accounts for about 50% of the total area of spring rapeseed in China. However, they have weak lodging resistance and are prone to lodging in areas with sufficient fertilizer and water, which is not conducive to stable production and mechanical harvesting. Therefore, increasing stem thickness through genetic improvement is of great significance for improving the lodging resistance and stable production of spring rapeseed varieties.

[0005] Based on the above background, scientists at home and abroad have carried out research on QTL mapping of stem diameter in Brassica napus. Shen et al. (2018) used a DH population constructed from an intertribal introgression line Y689 derived from a wild germplasm resource and Westar as materials to conduct QTL mapping of three stem traits, namely plant height (PH), branch initiation height (BIH), and stem diameter (SD). A total of 102 QTLs were identified in six environments, of which 16 QTLs were related to stem diameter, and a single QTL explained a phenotypic variation rate of 4.10 - 17.48%. However, only 2 QTLs were repeatedly detected in two environments, and a candidate gene BnaA02g02560 (atGASA4) related to stem diameter, plant height, and flowering time was obtained. Li et al. (2018) investigated four stem lodging-related traits of 472 rapeseed germplasms, including stem breakage resistance (SBR), stem diameter (SD), stem strength (SS), and lodging coefficient (LC), and conducted a genome-wide association study (GWAS) on stem lodging-related traits using the Brassica 60K SNP chip, identifying 67 related quantitative trait loci (QTLs) and 71 candidate genes. Among them, 16 QTLs were related to the regulation of stem diameter (SD), but the contribution rate of a single QTL to the phenotype was relatively low (3.58 - 5.28%), and few QTLs were stably detected repeatedly in multiple environments. Four candidate genes for stem diameter were identified on chromosome C08. Xu Liang et al. (2022) constructed a DH population using two Brassica napus varieties (lines) G922 and Zhongshuang 11 with significant differences in stem diameter as parents, and conducted QTL analysis on the stem-related traits of this population. A total of 6 QTLs for stem diameter were detected in 4 environments. Among them, the major QTL for stem diameter, cqSD.C8-1, could be repeatedly detected in 4 environments, with a contribution rate to phenotypic variation of 14.67%. Four QTLs for stem diameter on chromosome A2 could be repeatedly detected in three environments and formed a QTL cluster cqSD.A2, and two QTL loci were verified in the natural population and could be used for the breeding / assistant breeding of molecular markers for stem diameter in Brassica napus. However, the SNPs in the QTL interval could only be detected using the 60K SNP chip developed by the American company Illumina, with a high detection cost (about 400 yuan / sample) and a long cycle (2 - 3 months), while spring rapeseed only takes 2 months from emergence to flowering, which is not suitable for large-scale and rapid molecular marker-assisted selection of breeding materials. Therefore, it is necessary to develop a high-throughput, low-cost, and rapid detection technology for SNPs linked to stem diameter QTLs.

[0006] The PARMS (Penta-primer amplification refractory mutation system) detection technology is a detection technology based on the amplification refractory mutation system PCR (ARMS PCR). Different from the conventional ARMS PCR, the PARMS detection technology adds two detection primers with different fluorescences, which can respectively detect the complementary sequences at the 5' ends of the two allele forward primers. After PCR amplification with the same reverse primer, the polymorphism of the locus to be detected can be detected through different fluorescence signals. The PARMS detection has the advantages of high throughput (detecting more than 5,000 samples per day on average), low cost (about 2 yuan per sample), and accurate data, and can be applied to molecular marker-assisted breeding. Summary of the Invention

[0007] For the reasons mentioned above, based on the PARMS technology, the present invention develops a primer set that can detect the SNP loci linked to the major QTL of the stem diameter of Brassica napus, and detects it in a natural population to verify the selection effect of the primer set on the stem diameter trait.

[0008] To achieve the object of the present invention, the present invention provides SNP markers linked to the major QTL of the stem diameter of Brassica napus and their applications. Also, based on the advantages of the PARMS detection technology, according to the sequences of 100 - 500 bp upstream and downstream of the SNP linked to the major QTL, a primer set containing allele-specific primers and reverse amplification primers for the target locus is designed to quickly identify or assist in identifying the stem diameter trait of Brassica napus, meeting the needs of Brassica napus breeding or assisted breeding, shortening the breeding cycle, etc.

[0009] After research, the technical solutions provided by the present invention are as follows:

[0010] In the first aspect, the present invention provides an SNP marker linked to the major QTL of the stem diameter of Brassica napus. The SNP marker includes a first SNP marker and an optional second SNP marker. Among them, the first SNP marker has polymorphism in the bases at positions 9,132,080 - 9,132,180 on chromosome 2 of the A genome of Brassica napus, and the bases are T or C; the second SNP marker has polymorphism in the bases at positions 3,808,136 - 3,808,236 on chromosome 8 of the C genome of Brassica napus, and the bases are A or G; the SNP molecular markers are all based on the reference genome of Brassica napus "ZS11".

[0011] In some preferred embodiments, the base at position 9132130 on chromosome 2 of the Brassica napus A genome of the first SNP marker is polymorphic, and the base is T or C; the base at position 3808186 on chromosome 8 of the Brassica napus C genome of the second SNP marker is polymorphic, and the base is A or G.

[0012] In a second aspect, the present invention provides a set of SNP marker primers, comprising primers for amplifying or detecting SNP markers linked to the major QTL of the stem diameter of Brassica napus as described above, and the primers included in the primer set are designed according to the sequences of 100 - 500 bp upstream and downstream of the SNP linked to the major QTL of the stem diameter of Brassica napus respectively.

[0013] In some preferred embodiments, the set of SNP marker primers comprises a first set of SNP marker primers and, optionally, a second set of SNP marker primers, wherein the first set of SNP marker primers comprises a first SNP marker allele - specific primer 1, a first SNP marker allele - specific primer 2, and a first SNP marker reverse amplification primer;

[0014] The first SNP marker allele - specific primer 1 is (a1) or (a2):

[0015] (a1) The single - stranded DNA shown in SEQ ID No.1;

[0016] (a2) The single - stranded DNA which is obtained by substituting and / or deleting and / or adding one or several nucleotides in SEQ ID No.1 and has the same function as SEQ ID No.1;

[0017] The first SNP marker allele - specific primer 2 is (a3) or (a4):

[0018] (a3) The single - stranded DNA shown in SEQ ID No.2;

[0019] (a4) The single - stranded DNA which is obtained by substituting and / or deleting and / or adding one or several nucleotides in SEQ ID No.2 and has the same function as SEQ ID No.2;

[0020] The first SNP marker reverse amplification primer is (a5) or (a6):

[0021] (a5) The single - stranded DNA shown in SEQ ID No.3;

[0022] (a6) The single - stranded DNA which is obtained by substituting and / or deleting and / or adding one or several nucleotides in SEQ ID No.3 and has the same function as SEQ ID No.3;

[0023] The second SNP marker primer set includes a second SNP marker allele-specific primer 1, a second SNP marker allele-specific primer 2, and a second SNP marker reverse amplification primer;

[0024] The second SNP marker allele-specific primer 1 is (b1) or (b2):

[0025] (b1) single-stranded DNA shown in SEQ ID No. 4;

[0026] (b2) single-stranded DNA which is obtained by substitution and / or deletion and / or addition of one or several nucleotides in SEQ ID No. 4 and has the same function as SEQ ID No. 4;

[0027] The second SNP marker allele-specific primer 2 is (b3) or (b4):

[0028] (b3) single-stranded DNA shown in SEQ ID No. 5;

[0029] (b4) single-stranded DNA which is obtained by substitution and / or deletion and / or addition of one or several nucleotides in SEQ ID No. 5 and has the same function as SEQ ID No. 5;

[0030] The second SNP marker reverse amplification primer is (b5) or (b6):

[0031] (b5) single-stranded DNA shown in SEQ ID No. 6;

[0032] (b6) single-stranded DNA which is obtained by substitution and / or deletion and / or addition of one or several nucleotides in SEQ ID No. 6 and has the same function as SEQ ID No. 6.

[0033] In some preferred embodiments, the primers included in the SNP marker primer set are shown in the following table:

[0034]

[0035] In the present invention, the SNP marker primer set is a PARMS primer set, and each PARMS marker primer set further includes a fluorescent probe linker sequence. In some preferred embodiments, each PARMS marker primer set includes two fluorescent probe linker sequences. In some more preferred embodiments, each PARMS marker primer set includes two fluorescent probe linker sequences, one of which is a FAM fluorescent probe linker sequence and the other is a HEX fluorescent probe linker sequence.

[0036] In a third aspect, the present invention provides a reagent or kit for detecting SNP markers linked to major QTLs for the stem diameter of Brassica napus, comprising the SNP marker primer sets described above.

[0037] In a fourth aspect, the present invention provides the use of the SNP markers linked to major QTLs for the stem diameter of Brassica napus described above, the SNP marker primer sets described above, or the reagent or kit of the SNP markers described above in detecting or assisting in the detection of the stem diameter trait of Brassica napus.

[0038] In a fifth aspect, the present invention provides the use of the SNP markers linked to major QTLs for the stem diameter of Brassica napus described above, the SNP marker primer sets described above, or the reagent or kit of the SNP markers described above in genotyping, screening, identification or assisting in identification, breeding or assisting in breeding of Brassica napus.

[0039] In a sixth aspect, the present invention provides a method for detecting the genotype of the stem diameter of Brassica napus, the method comprising: detecting the nucleotide at positions 9132080 - 9132180 corresponding to chromosome 2 in the A genome of the Brassica napus to be tested. If the Brassica napus to be tested shows FAM fluorescence, the nucleotide at this site is the TT genotype, and the major QTL for stem diameter linked to it is an increasing effect, which can promote the thickening of the rapeseed stem; if the Brassica napus to be tested shows HEX fluorescence, the nucleotide at this site is the CC genotype, and the major QTL for stem diameter linked to it is a decreasing effect, which is a thin-stem genotype; if the Brassica napus to be tested shows both FAM fluorescence and HEX fluorescence, the nucleotide at this site is the TC genotype, and the major QTL for stem diameter linked to it is a heterozygous genotype; and / or

[0040] detecting the nucleotide at positions 3808136 - 3808236 corresponding to chromosome 8 in the C genome of the Brassica napus to be tested. If the Brassica napus to be tested shows FAM fluorescence, the nucleotide at this site is the AA genotype, and the major QTL for stem diameter linked to it is an increasing effect, which can promote the thickening of the rapeseed stem; if the Brassica napus to be tested shows HEX fluorescence, the nucleotide at this site is the GG genotype, and the major QTL for stem diameter linked to it is a decreasing effect, which is a thin-stem genotype; if the Brassica napus to be tested shows both FAM fluorescence and HEX fluorescence, the nucleotide at this site is the AG genotype, and the major QTL for stem diameter linked to it is a heterozygous genotype.

[0041] In some preferred embodiments, the nucleotide at position 9132130 corresponding to chromosome 2 in the A genome of the Brassica napus to be tested is detected.

[0042] In some preferred embodiments, the nucleotide at position 3808186 corresponding to chromosome 8 in the C genome of the Brassica napus to be tested is detected.

[0043] In some preferred embodiments, a method for detecting the genotype of the stem diameter of Brassica napus includes: detecting the nucleotide at position 9132130 corresponding to chromosome 2 in the A genome of the Brassica napus to be tested. If the Brassica napus to be tested shows FAM fluorescence, the nucleotide at this site is the TT genotype, and the major QTL for stem diameter linked to it is an increasing effect, which can promote the thickening of the rapeseed stem; if the Brassica napus to be tested shows HEX fluorescence, the nucleotide at this site is the CC genotype, and the major QTL for stem diameter linked to it is a decreasing effect, which is a thin-stem genotype; if the Brassica napus to be tested shows both FAM fluorescence and HEX fluorescence, the nucleotide at this site is the TC genotype, and the major QTL for stem diameter linked to it is a heterozygous genotype; and / or detecting the nucleotide at position 3808186 corresponding to chromosome 8 in the C genome of the Brassica napus to be tested. If the Brassica napus to be tested shows FAM fluorescence, the nucleotide at this site is the AA genotype, and the major QTL for stem diameter linked to it is an increasing effect, which can promote the thickening of the rapeseed stem; if the Brassica napus to be tested shows HEX fluorescence, the nucleotide at this site is the GG genotype, and the major QTL for stem diameter linked to it is a decreasing effect, which is a thin-stem genotype; if the Brassica napus to be tested shows both FAM fluorescence and HEX fluorescence, the nucleotide at this site is the AG genotype, and the major QTL for stem diameter linked to it is a heterozygous genotype.

[0044] The beneficial effects of the present invention at least include:

[0045] The present invention provides SNP markers linked to the major QTL of the stem diameter of Brassica napus and their applications. Based on the advantages of the PARMS detection technology, a primer set containing allele-specific primers and reverse amplification primers for the target site is designed according to the sequences of 100 - 500 bp upstream and downstream of the SNP linked to the major QTL, so as to quickly identify or assist in identifying the stem diameter traits of Brassica napus, meeting the needs of Brassica napus breeding or assisted breeding and shortening the breeding cycle.

[0046] Other features and advantages of the present invention will be described in detail in the subsequent specific implementation section. Description of the Drawings

[0047] Figure 1 The fluorescence signal genotyping result diagram showing the identification of the SNP locus SDA02-p7893901 in Example 2.

[0048] Figure 2 The fluorescence signal genotyping result diagram showing the identification of the SNP locus SDA02-p10176749 in Example 2.

[0049] Figure 3 The fluorescence signal genotyping result diagram showing the identification of the SNP locus SDA02-p10668400 in Example 2.

[0050] Figure 4 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDA02-p8849037 in Example 2.

[0051] Figure 5 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDA02-p9195997 in Example 2.

[0052] Figure 6 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDA02-p9608319 in Example 2.

[0053] Figure 7 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDA02-p10228189 in Example 2.

[0054] Figure 8 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDC08-p221008 in Example 2.

[0055] Figure 9 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDC08-p502660 in Example 2.

[0056] Figure 10 Show the fluorescence signal genotyping result diagram of identifying SNP locus SDC08-p289292 in Example 2.

[0057] Figure 11 [[ID=3l]]Show the fluorescence signal genotyping result diagram of identifying SNP locus SDC08-p90999 in Example 2.

[0058] Figure 12 Show the fluorescence signal SNP genotyping diagram of identifying SNP locus SDC08-p366585 in Example 2.

[0059] Figure 13 Show the SNP genotyping diagram detected by the primer set for identifying SNP locus SDA02-p9608319 in 130 natural population resources in Example 3.

[0060] Figure 14 Show the SNP genotyping diagram detected by the primer set for identifying SNP locus SDC08-p289292 in 130 natural population resources in Example 3. Detailed implementation mode

[0061] To make the objectives, technical solutions and beneficial effects of the present invention clearer, the present invention will be further described in detail below in conjunction with the accompanying drawings and specific embodiments. Examples of the embodiments are shown in the accompanying drawings. It should be understood that the specific embodiments described in the following embodiments of the present invention are only illustrative descriptions of the specific embodiments of the present invention, and are intended to explain the present invention, rather than limiting the present invention.

[0062] In the scope disclosed in the present invention, the endpoints and any values of the range are not limited to the exact range or value. These ranges or values should be understood to include values close to these ranges or values. For numerical ranges, between the endpoint values of each range, between the endpoint values of each range and individual point values, and between individual point values, they can be combined with each other to obtain one or more new numerical ranges, and these numerical ranges should be regarded as specifically disclosed herein. In the description of this application, unless otherwise specified, the meaning of similar terms such as "multiple / various" is two / kinds or more than two / kinds.

[0063] In the following examples, the experimental methods, unless otherwise specified, are all conventional methods, and are carried out according to the techniques or conditions described in the literature in this field or according to the product instructions. The materials, reagents, instruments, etc. used in the following examples, unless otherwise specified, can all be obtained from commercial channels. In the following examples, for quantitative tests, three repeated experiments are set, and the results are averaged. In the following examples, unless otherwise specified, the first position of each nucleotide sequence in the sequence list is the 5'-terminal nucleotide of the corresponding DNA / RNA, and the last position is the 3'-terminal nucleotide of the corresponding DNA / RNA.

[0064] All Brassica napus in the following examples are biological materials that can be obtained by the public from the applicant. The biological materials are only used for repeating the relevant experiments of the present invention and cannot be used for other purposes.

[0065] Example 1 Development of SNP Markers Linked to the Major QTL for Stem Diameter in Brassica napus

[0066] Using two Brassica napus parents, Zhongshuang 11 (ZS11) and G922, with significant differences in stem diameter as materials, a DH population was constructed. The phenotypes of this population and the two parents were identified in 4 environments over 2 years. The stem diameter (SD, mm) at 20 cm above the cotyledon node at maturity was measured using a digital display vernier caliper. All materials were genotyped using the Brassica napus 60K SNP chip developed by Illumina. The genetic linkage map was constructed and QTL mapping was performed using WinQTLcartographer 2.5 software.

[0067] A total of six major QTLs related to stem diameter and their SNP loci that could be repeatedly detected in multiple environments were mapped (see Table 1), which were distributed on chromosomes A2, C3, and C8. cqSD.C8-1 could be detected in four environments, and its contribution rate to phenotypic variation was 14.67%, which was a major QTL. The four major QTLs on chromosome A2 formed a QTL cluster (cqSD.A2), which was located in the interval of 84.91 - 107.10 cM, and the phenotypic variation explained by a single locus was 7.41% - 10.35%.

[0068] Table 1 Basic information of major QTLs for stem diameter and their linked SNP loci

[0069]

[0070] Example 2 Design of primer sets for SNP markers linked to major QTLs of stem diameter in Brassica napus

[0071] According to the previous research results, 12 SNP loci were selected in the confidence intervals of the mapped major QTLs for stem diameter. Based on the flanking sequence information of the SNP loci, sequence alignment was performed using Brassica napus ZS11 as the reference genome, and sequences with uniqueness on the reference genome were selected to design locus-specific primers, including two allele-specific primers and one reverse common primer. In this way, a total of 12 primer sets for SNP loci were designed (see Table 2).

[0072] Table 2 Sequence information on both sides of SNPs in the confidence intervals of stem diameter QTLs and designed primer sequences

[0073]

[0074]

[0075]

[0076]

[0077] In the submitted sequence list, [T / C] is represented by m, [A / G] is represented by k, [T / G] is represented by r, and [A / C] is represented by s.

[0078] The results showed that when the primer sets of 12 SNP loci were used to identify in the parents with known genotypes and 30 offspring, only the primer sets of 10 SNP loci obtained good genotyping results, among which the primer sets of SDA02-p10176749 and SDA02-p10668400 did not obtain good genotyping results (as Figures 1 to 12 shown).

[0079] Example 3: Verification of the Effect of a Primer Set of SNP Markers Linked to a Major QTL for Stem Diameter in Brassica napus

[0080] Using the 10 SNP primer sets that yielded favorable typing results from Example 2, SNP detection was performed on 130 accessions of Brassica napus. The phenotypic values for stem diameter at 20 cm above ground at maturity were also evaluated for all 130 accessions (randomized block design, three replicates, 10 plants per plot, and the average of the three replicates). The selective effects of all primer sets on stem diameter in natural populations were evaluated. The results are shown in Table 3.

[0081] Table 3 Identification results of the primer set of the present invention in 130 resources

[0082]

[0083]

[0084] The results showed that when the SNPs screened by the primer sets SDA02-p9608319 and SDC08-p289292 were TT and GG, respectively, the main effect QTLs of stem diameter contained in the screened materials were all homozygous increasing genotypes, and the average stem diameter was 14.68 mm. When the SNPs screened by the primer sets SDA02-p9608319 and SDC08-p289292 were CC and AA, respectively, the main effect QTLs of stem diameter contained in the screened materials were all homozygous decreasing genotypes, and the average stem diameter was 13.4 8mm, and the average stem diameters of the two groups of homozygous genotypes were extremely significantly different; however, when the two groups of materials screened by the SDA02-p9608319 and SDC08-p289292 primer sets (one group was a homozygous enhancing genotype for the major effect QTL of stem diameter on chromosome A02, and a homozygous reducing genotype for the major effect QTL of stem diameter on chromosome C08; the other group was a homozygous reducing genotype for the major effect QTL of stem diameter on chromosome A02, and a homozygous increasing genotype for the major effect QTL of stem diameter on chromosome C08) had no significant difference in average stem diameters.

[0085] These experiments showed that only the primer set for the single SNP site SDA02-p9608319 claimed in the claims of the present invention, and the primer set of SDA02-p9608319 and SDC08-p289292 were effective for selecting the stem diameter of Brassica napus (e.g., Figure 13 and Figure 14 Therefore, the accuracy of stem diameter molecular marker-assisted breeding selection is high. However, the stem diameter differences between the two homozygous SNP loci identified by the primer sets for other single SNP loci did not reach significance (p greater than 0.05) between the material groups. The P values for detecting stem diameter differences in germplasm materials screened using these SNP markers were all too large, thus the accuracy of stem diameter molecular marker-assisted breeding selection is low.

[0086] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention and do not constitute a limitation to the content of the present invention. Within the scope of the technical concept of the present invention, various simple modifications can be made to the technical solutions of the present invention, including any other suitable combination of each technical feature. These simple modifications and combinations should also be regarded as the content disclosed by the present invention and fall within the protection scope of the present invention.

Claims

1. A SNP marker linked to the major QTL for stem diameter in Brassica napus, characterized in that, The SNP marker includes a first SNP marker and, optionally, a second SNP marker, wherein, The first SNP molecular marker is polymorphic at the base positions 9132080 - 9132180 on chromosome 2 of the Brassica napus A genome, and the base is T or C; The second SNP molecular marker is polymorphic at the base positions 3808136 - 3808236 on chromosome 8 of the Brassica napus C genome, and the base is A or G; The SNP molecular markers are all based on the Brassica napus "ZS11" reference genome.

2. The SNP marker linked to the major QTL for stem diameter in Brassica napus according to claim 1, characterized in that, Wherein, The first SNP marker is polymorphic at the base position 9132130 on chromosome 2 of the Brassica napus A genome, and the base is T or C; The second SNP marker is polymorphic at the base position 3808186 on chromosome 8 of the Brassica napus C genome, and the base is A or G.

3. A SNP marker primer set, characterized in that, Primers for amplifying or detecting the SNP markers linked to the major QTL of the Brassica napus stem diameter according to claim 1 or 2, and the primers included in the primer set are designed based on the sequences of 100 - 500 bp upstream and downstream of the SNP markers linked to the major QTL of the Brassica napus stem diameter respectively.

4. The SNP marker primer set according to claim 3, characterized in that, Includes a first SNP marker primer set and, optionally, a second SNP marker primer set, wherein, The first SNP marker primer set includes a first SNP marker allele - specific primer 1, a first SNP marker allele - specific primer 2, and a first SNP marker reverse amplification primer; The first SNP marker allele - specific primer 1 is (a1) or (a2): (a1) The single - stranded DNA shown in SEQ ID No.1; (a2) The single - stranded DNA which is obtained by substitution and / or deletion and / or addition of one or several nucleotides in SEQ ID No.1 and has the same function as SEQ ID No.1; The first SNP marker allele - specific primer 2 is (a3) or (a4): (a3) The single - stranded DNA shown in SEQ ID No.2; (a4) The single - stranded DNA which is obtained by substitution and / or deletion and / or addition of one or several nucleotides in SEQ ID No.2 and has the same function as SEQ ID No.2; The first SNP marker reverse amplification primer is (a5) or (a6): (a5) The single - stranded DNA shown in SEQ ID No.3; (a6) The single - stranded DNA which is obtained by substitution and / or deletion and / or addition of one or several nucleotides in SEQ ID No.3 and has the same function as SEQ ID No.3; The second SNP marker primer set includes a second SNP marker allele - specific primer 1, a second SNP marker allele - specific primer 2, and a second SNP marker reverse amplification primer; The second SNP marker allele - specific primer 1 is (b1) or (b2): (b1) The single - stranded DNA shown in SEQ ID No.4; (b2)A single-stranded DNA that has undergone substitution and / or deletion and / or addition of one or more nucleotides and has the same function as SEQ ID No. 4; The second SNP marker allele-specific primer 2 is (b3) or (b4): (b3) The single-stranded DNA shown in SEQ ID No. 5; (b4) A single-stranded DNA that has undergone substitution and / or deletion and / or addition of one or more nucleotides and has the same function as SEQ ID No. 5; The second SNP marker reverse amplification primer is (b5) or (b6): (b5) The single-stranded DNA shown in SEQ ID No. 6; (b6) A single-stranded DNA that has undergone substitution and / or deletion and / or addition of one or more nucleotides and has the same function as SEQ ID No.

6.

5. The SNP marker primer set according to claim 4, wherein The primers included are shown in the following table:

6. The SNP marker primer set according to claim 5, characterized in that The SNP marker primer set is a PARMS primer set, and each PARMS primer set further includes a fluorescent probe adapter sequence.

7. A reagent or kit for detecting SNP markers linked to a major QTL for stem diameter in Brassica napus, characterized in that: It includes the SNP marker primer set according to any one of claims 3-6.

8. Use of the SNP marker linked to the major QTL of the stem diameter of Brassica napus according to claim 1 or 2, the SNP marker primer set according to any one of claims 3-6, or the reagent or kit of the SNP marker according to claim 7 in detecting or assisting in detecting the stem diameter trait of Brassica napus.

9. Use of the SNP marker linked to the major QTL of the stem diameter of Brassica napus according to claim 1 or 2, the SNP marker primer set according to any one of claims 3-6, or the reagent or kit of the SNP marker according to claim 7 in genotyping, screening, identifying or assisting in identifying, breeding or assisting in breeding of Brassica napus.

10. A method for detecting the genotype of the stem diameter of Brassica napus, characterized in that: The method includes: Detecting the nucleotide at position 9132130 on chromosome 2 corresponding to the A genome of the Brassica napus to be tested. If the Brassica napus to be tested shows FAM fluorescence, the nucleotide at this site is the TT genotype, and the QTL of the linked stem diameter is an enhancing effect, which can promote the thickening of the rapeseed stem; if the Brassica napus to be tested shows HEX fluorescence, the nucleotide at this site is the CC genotype, and the QTL of the linked stem diameter is a reducing effect, which is a thin-stem genotype; if the Brassica napus to be tested shows both FAM fluorescence and HEX fluorescence, the nucleotide at this site is the TC genotype, and the QTL of the linked stem diameter is a heterozygous genotype; and / or Detecting the nucleotide at position 3808186 on chromosome 8 corresponding to the C genome of the Brassica napus to be tested. If the Brassica napus to be tested shows FAM fluorescence, the nucleotide at this site is the AA genotype, and the QTL of the linked stem diameter is an enhancing effect, which can promote the thickening of the rapeseed stem; if the Brassica napus to be tested shows HEX fluorescence, the nucleotide at this site is the GG genotype, and the QTL of the linked stem diameter is a reducing effect, which is a thin-stem genotype; if the Brassica napus to be tested shows both FAM fluorescence and HEX fluorescence, the nucleotide at this site is the AG genotype, and the QTL of the linked stem diameter is a heterozygous genotype.

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