Watermelon male flower pedicel length related snp marker and application thereof

Abstract

The application belongs to the technical field of molecular markers, and relates to a SNP marker related to the length of a male flower stalk of watermelon and application thereof. The SNP marker is a single nucleotide at the 15321651th position of the 10th chromosome of the genome V2 of watermelon 97103, and the nucleotide is C or T. The length of the male flower stalk of watermelon with the TT genotype of the SNP site is longer than 12.00 mm, and the length of the male flower stalk of watermelon with the CC genotype of the SNP site is less than or equal to 12.00 mm. By comparing the genotype and the actual length of the male flower stalk, the accuracy of the SNP marker provided by the application in detecting the length of the male flower stalk of watermelon is 95.6%. By judging the genotype of the SNP site, the length of the male flower stalk of watermelon can be accurately and quickly identified at the seedling stage without the male flower growing on the plant. The breeding efficiency can be improved, the breeding time can be shortened, and the application is suitable for genetic identification and breeding of watermelon.

Description

Technical Field

[0001] This invention belongs to the field of molecular marker technology and relates to SNP markers for the length of male flower pedicels in watermelon and their applications. Background Technology

[0002] As an important cucurbitaceous crop, watermelon is a vital fruit for quenching thirst and cooling off in summer, holding a very important position among horticultural crops worldwide. China is the world's largest producer and consumer of watermelons. The length of the male flower stalk is one of the important agronomic traits of watermelons. Longer male flower stalks facilitate flower collection and reduce pollen shedding during artificial hybridization and pollination. However, research on the length of watermelon male flower stalks has not yet been reported.

[0003] Molecular markers are genetic markers based on single nucleotide polymorphisms (SNPs), which are changes in DNA sequence caused by mutations in a single nucleotide at the genomic level. Widely distributed across the genome, they possess advantages such as high throughput, simplicity, stability, and high sensitivity, making them a highly promising genetic marker method in assisted breeding.

[0004] With the advent of the genomic era, clarifying the functions of watermelon genes and their impact on agronomic traits, identifying key genes controlling these traits, and developing corresponding molecular markers are important aspects of current watermelon breeding work. Utilizing SNP markers is significant for screening watermelons with superior traits and promoting the breeding of new varieties. Therefore, developing molecular markers related to the length of watermelon male flower pedicels and applying them to watermelon breeding will also help accelerate the watermelon breeding process. Summary of the Invention

[0005] Since longer male flower stalks reduce pollen shedding and improve the effectiveness of artificial pollination, breeding plants with longer male flower stalks is an important way to improve artificial pollination. Based on this, the present invention provides a SNP marker related to the length of watermelon male flower stalks and uses this SNP marker in watermelon breeding.

[0006] This invention first provides an application of an SNP marker in watermelon breeding, which is related to the length of the male flower pedicel of watermelon; it is located at position 15321651 on chromosome 10 of the watermelon 97103 genome V2 version.

[0007] Furthermore, the genotype of the above SNP marker is T or C.

[0008] Furthermore, the male flower pedicels of watermelon plants with the genotype TT of the above-mentioned SNP markers are >12.00 mm long; the male flower pedicels of watermelon plants with the genotype CC of the above-mentioned SNP markers are ≤12.00 mm long.

[0009] To improve the effectiveness of artificial pollination and reduce pollen shedding, those skilled in the art can select watermelon plants with the TT genotype as parents for breeding to obtain watermelon plants with longer male flower stalks, which makes it easier to remove the male flower stalks during the pollination period.

[0010] To expand the application of the SNP marker, this invention also claims protection for a primer pair for detecting SNP markers, wherein the primer pair is used to detect SNP markers in watermelon to obtain watermelon genotyping; the SNP marker is related to the length of the male flower peduncle of watermelon, and the SNP marker is located at position 15321651 on chromosome 10 of watermelon reference genome version 97103v2; the watermelon genotyping is TT or CC.

[0011] This invention also claims protection for a probe for detecting SNP markers in watermelon to obtain watermelon genotyping; the SNP marker is related to the length of the male flower peduncle of watermelon, and the SNP marker is located at position 15321651 on chromosome 10 of watermelon reference genome version 97103v2; the watermelon genotyping is TT or CC.

[0012] This invention also claims protection for a chip for detecting SNP markers, the chip being used to detect SNP markers in watermelon to obtain watermelon genotyping; the SNP markers are related to the length of the male flower pedicel of watermelon, the SNP markers are located at position 15321651 on chromosome 10 of watermelon reference genome version 97103v2; the watermelon genotyping is TT or CC.

[0013] Compared with existing technologies, the present invention "SNP markers related to the length of male flower pedicels of watermelon and their application" has the following beneficial effects:

[0014] Based on the fact that longer male flower stalks in watermelons facilitate pollination and effectively reduce pollen shedding during artificial hybridization, this invention provides a SNP marker related to the length of watermelon male flower stalks. By analyzing the genotype of this SNP marker locus, the length of watermelon male flower stalks can be accurately and quickly determined at the seedling stage, without requiring the plant to produce male flowers. Comparing the genotype with the actual male flower stalk length, the accuracy rate of the SNP marker provided by this invention in detecting the length of watermelon male flower stalks is 95.6%. This invention can effectively improve watermelon breeding efficiency, shorten breeding time, and is applicable to watermelon genetic identification and breeding work. Attached Figure Description

[0015] Figure 1 Manhattan plot of watermelon male flower pedicel length based on genome-wide association study (GWAS). Figure 1The vertical axis represents the negative logarithm of the p-value for each SNP; the smaller the p-value, the higher the significance and the higher the position in the graph. The horizontal axis represents the chromosome location of the SNP. The horizontal line in the graph is the p-value threshold, representing the significance level. As shown in the graph, the gene for male flower pedicel length in watermelon is located on chromosome 10, Cla97Chr10. This region contains one significant SNP with a p-value less than 10. -8 It has high significance. Detailed Implementation

[0016] The present invention will now be described in conjunction with embodiments, providing a clear and complete description of the technical solutions in these embodiments. Obviously, the described embodiments are only a part of the embodiments of the present invention, and not all of them. All other embodiments obtained by those skilled in the art based on the embodiments of the present invention without creative effort are within the scope of protection of the present invention.

[0017] This embodiment provides a specific method for mining SNP markers related to the length of male flower pedicels of watermelon based on GWAS analysis.

[0018] 1. Preparation of test materials

[0019] The test materials consisted of 159 natural watermelon populations obtained from the National Watermelon and Melon Mid-term Bank, as shown in Table 1.

[0020] Table 1. Male flower pedicel length and genotype of 159 watermelon natural populations.

[0021]

[0022]

[0023]

[0024]

[0025]

[0026]

[0027]

[0028]

[0029] 2. Determination of the length of male flower pedicels in natural watermelon populations.

[0030] The 159 natural population materials in the table above were continuously planted for 3 years. Five plants were selected from each material, and male flowers near the 7th to 10th leaves were selected during the peak flowering period. The length of the male flower stalks of watermelon was measured using vernier calipers. The measurement was repeated for 3 years, and the average length of the male flower stalks was taken as the corresponding length of the male flower stalks for each material (see Table 1). Male flowers with a stalk length >12.00 mm were marked as long stalks; male flowers with a stalk length ≤12.00 mm were marked as short stalks.

[0031] 3. GWAS analysis was performed on 159 natural watermelon populations using TASSEL 3.0 software. The results are as follows: Figure 1 . Figure 1 The vertical axis represents the negative logarithm of the p-value for each SNP; the smaller the p-value, the higher the significance and the higher the position in the graph. The horizontal axis represents the chromosome location of the SNP. The horizontal line in the graph is the p-value threshold, representing the significance level. As shown in the graph, the gene for male flower pedicel length in watermelon is located on chromosome 10, Cla97Chr10. This region contains one significant SNP with a p-value less than 10. -8 It has high significance.

[0032] 4. Obtaining the target SNP

[0033] Analysis of the 150kb interval upstream and downstream of this significant SNP locus revealed only one gene, Cla97C10G191780, encoding a zinc finger protein, which may be associated with the length of the male flower pedicel in watermelon. Therefore, the SNP marker associated with the length of the male flower pedicel in watermelon is located at nucleotide 15321651 on chromosome 10 of the watermelon genome (http: / / cucurbitgenomics.org / , V2), and is either T or C. The homozygous genotypes of this SNP marker are TT and CC, respectively. The CC genotype corresponds to watermelons with short male flower pedicels, while the TT genotype corresponds to watermelons with long male flower pedicels.

[0034] The genotype of nucleotide 15321651 on chromosome 10 of the above 159 natural population materials was detected. By comparing the genotype with the actual length of the male flower pedicel, the accuracy of the SNP marker provided by this invention in detecting the length of the male flower pedicel of watermelon was 95.6%.

[0035] The embodiments described above are only some, not all, of the embodiments of the present invention. The detailed description of the embodiments of the present invention is not intended to limit the scope of the claimed invention, but merely to illustrate selected embodiments. All other embodiments obtained by those skilled in the art through related deductions and substitutions based on the inventive concept, without inventive effort, are within the scope of protection of the present invention.

Claims

1. An application of SNP markers in watermelon breeding, characterized in that, The SNP markers are related to the length of the male flower pedicel of watermelon; The SNP marker is located at position 15321651 on chromosome 10 of the watermelon 97103 genome V2 version; The SNP marker has a genotype of T or C; The homozygous genotypes of the SNP markers are TT genotype and CC genotype, respectively. The TT genotype is for long-stalked watermelon, and the CC genotype is for short-stalked watermelon. The male flower stalk of the long-stalked watermelon has a length >12.00mm, while the male flower stalk of the short-stalked watermelon has a length ≤12.00mm.

Images