CN-121160880-B - SNP molecular marker related to growth traits of pyriform ring snails and application thereof

Abstract

The invention discloses an SNP molecular marker related to growth traits of pyriform ring-shaped conch and application thereof, and belongs to the technical field of molecular marker assisted breeding. The SNP molecular marker is located at the 131,293,660 th site (T > C variation) of the chromosome of the Cissus pyriform Chr4, wherein the T alleles (genotypes T/T and T/C) are obviously positively correlated with the growth rate and the quality. The invention screens key sites by integrating whole genome association analysis (GWAS) with XGBoost machine learning models, and designs specific primer pairs to realize accurate typing. Population verification shows that individuals carrying T alleles have significantly greater growth rates and average body mass than C/C genotype individuals. The marker can be used for early prediction of the growth performance of the pyriform ring snails, high-yield fine variety breeding and genetic map construction, and breaks through the bottleneck of long period and low efficiency of traditional breeding.

Inventors

• CAO XIAOJUAN
• ZHANG NAN
• SUN BING

Assignees

• 华中农业大学

Dates

Publication Date

20260505

Application Date

20251009

Claims (6)

1. 1. A specific primer pair is characterized in that the nucleotide sequence of a forward primer is shown as SEQ ID NO.1, the nucleotide sequence of a reverse primer is shown as SEQ ID NO.2, the primer pair is used for amplifying a DNA fragment containing SNP molecular markers in the pyriform ring edge screw genome DNA, the SNP molecular markers are related to the pyriform ring edge screw (Bellamya purificata) growth traits and are positioned at the 131,293,660 th locus of the pyriform ring edge screw Chr4 chromosome, the base type is T/T homozygosity, the site variant form is T > C, and a T allele is a dominant allele related to excellent growth traits.
2. 2. The use of the primer pair as claimed in claim 1 in auxiliary breeding of pyriform ring snails for screening varieties with excellent growth traits.
3. 3. The molecular marker assisted breeding method for the pyriform ring snails is characterized by comprising the following steps of: (1) Extracting genome DNA of the individual to be detected pyriform ring snail; (2) Performing PCR amplification by using the primer pair as set forth in claim 1 to obtain a DNA fragment containing SNP molecular markers; (3) Sequencing the DNA fragments and identifying the genotype of the SNP molecular marker; (4) Individuals with dominant alleles are screened as parents for breeding.
4. 4. The method according to claim 3, wherein the PCR amplification reaction system comprises 2X Hieff volumes PCRMasterMix. Mu.L, 1. Mu.L of forward primer, 1. Mu.L of reverse primer, 1. Mu.L of template and between 20. Mu.L and RNase-Free ddH 2 O.
5. 5. The method of claim 3, wherein the PCR amplification is performed in a reaction sequence of 95℃pre-denaturation for 5min, 95℃denaturation for 30s,57℃annealing for 30s, and 72℃extension for 12s,35 cycles.
6. 6. The method of claim 3, wherein if the identified genotype is T/T or T/C, it is determined as a high quality, fast growth rate, pyriform ring-screw variety.

Description

SNP molecular marker related to growth traits of pyriform ring snails and application thereof Technical Field The invention belongs to the technical field of molecular marker assisted breeding, and relates to a SNP molecular marker related to the growth trait of pyriform ring snails and application thereof. Background Pityrosporum pyriform (school name: bellamya purificata) commonly known as snails, river snails, dan Luo, etc., is the largest monomer type species in the genus Cytyrosporum. Taxonomically belonging to the genus Cinnamomum (Bellamya) of the family Cinnamomeraceae (VIVIPARIDAE) is widely distributed in the eastern, southern and Asia freshwater areas of China. As aquatic organisms with ecological and economic values, the pyriform ring snails are not only key components of natural feed raw materials, traditional Chinese medicinal material resources and fresh water ecosystems, but also serve as special dietary sources by the nutritional characteristics of high protein and low fat. The snail meat is deeply favored by consumers in fresh, tender and fine mouthfeel. However, the traditional seasonal fresh food mode has the limitations of short supply period and low industrial added value, the cultivation scale is rapidly enlarged, and the market demand is continuously expanded, so that the industrial supply and demand gap is obvious, and the urgency of innovation of fine variety breeding and large-scale cultivation technology is highlighted. The pyriform ring snail has the remarkable advantages of high yield, high growth rate and the like, and becomes the first choice for large-scale cultivation of snails. Currently, the germplasm resources of artificially cultured freshwater snails depend on wild populations, and the growth performance of the freshwater snails is difficult to meet the industrial production requirements. Therefore, the development of efficient and accurate molecular markers aiming at growth traits by means of the machine learning model XGBoost has a key meaning for promoting the genetic improvement of the pyriform ring snails and the upgrading of the aquaculture industry. In molecular biology and genetic research, single Nucleotide Polymorphism (SNP) markers have become the core tool for resolving biological genetic mechanisms. As the most common variant form in genome, SNP is usually caused by single nucleotide substitution, and has the characteristics of wide distribution, genetic stability and the like. Along with the iterative development of genomics and bioinformatics technologies, a SNP marker analysis method combined with XGBoost machine learning models is becoming a leading edge technology for revealing population genetic variation rules and constructing high-density genetic maps, and the models can accurately predict key SNP loci associated with growth traits by fusing gene conservation scores, haplotype block structures and regulatory network interaction characteristics, so that a more efficient genotype-phenotype association analysis scheme is provided for molecular marker assisted breeding. Disclosure of Invention The invention aims to provide SNP molecular markers and specific primer pairs thereof which are obviously related to the growth traits of the pyriform ring-shaped conch, which are used for rapidly screening individuals with growth advantages, and realizing molecular auxiliary breeding of the pyriform ring-shaped conch, including group breeding, parent screening and variety improvement. In order to achieve the above purpose, the invention adopts the following technical scheme: A SNP molecular marker related to the growth trait of the pyriform ring snail is positioned at the 131,293,660 th site of the chromosome of the pyriform ring snail Chr4, the position corresponds to the 53 rd site of the nucleotide sequence shown in SEQ ID NO.3, the base type is T/T homozygote, the allelic variant form of the position is T > C, wherein the T allele is a dominant allele related to the excellent growth trait, and an individual (genotype T/T or T/C) carrying the T allele is positively related to the growth rate and the quality. A nucleotide sequence of a forward primer is shown as SEQ ID NO.1, a nucleotide sequence of a reverse primer is shown as SEQ ID NO.2, and the primer pair is used for amplifying a DNA fragment containing the SNP molecular marker in the pyriform ring edge screw genome DNA, wherein the nucleotide sequence of the fragment is shown as SEQ ID NO. 3. The SNP molecular marker or the primer pair can be used for rapidly screening individuals with growth advantage, and molecular auxiliary breeding of the pyriform ring snails is realized. The invention further provides a molecular marker assisted breeding method for the pyriform ring-shaped conch, which comprises the following steps: (1) Extracting genome DNA of the individual to be detected pyriform ring snail; (2) Carrying out PCR amplification by adopting the primer pair to obtain a DNA fragment containing the SNP