SNP (Single Nucleotide Polymorphism) molecular marker related to Duroc pig backfat thickness character and application of SNP molecular marker

Abstract

The invention belongs to the technical field of pig molecular markers, and particularly discloses an SNP (Single Nucleotide Polymorphism) molecular marker related to a pig backfat thickness character. DNA samples of 3571 Duroc pigs are collected, a pig 80K SNP high-density functional site chip is used for genetic typing, a molecular marker related to the back fat thickness character of the pigs is obtained through whole-genome association analysis and screening, the login number of the SNP molecular marker in an Ensepbl database is rs326953479, the polymorphic site is located at the 97618073 site of a chromosome 7, allele mutation of T / C exists, and the SNP molecular marker is a molecular marker related to the back fat thickness character of the pigs. When the nucleotide is mutated into C, the pig has a thinner back fat thickness character.

Description

TECHNICAL FIELD

[0001] The application belongs to the technical field of pig molecular markers, and particularly relates to a SNP molecular marker related to the backfat thickness trait of Duroc pigs, which can be used for the assisted selection and prediction of the backfat thickness trait of pigs. BACKGROUND

[0002] Pigs are important economic animals in China, and have a long history of domestication. China is a large pork consumer, and the annual pork consumption is among the highest in the world. In recent years, consumers' demand for healthy meat products has gradually increased, and therefore, pork products with thinner backfat are more popular, and breeding personnel tend to breed pigs with thinner backfat and higher lean meat rate. In recent years, the rapid development of breeding methods such as genomic selection has effectively shortened the generation interval of pigs, and improved the performance of breeding pigs (E.F.Knol, B.Nielsen, and P.W.Knap, Genomic selection in commercial pig breeding. Animal Frontiers 6 (2016) 15-22.). The principle is to calculate the genomic breeding value of individuals based on the genotype data of the population to determine the selection of individuals, and therefore, understanding the genetic mechanism of the target economic trait is crucial for breeding lean pigs using genomic selection, and analyzing the molecular marker related to the backfat thickness of pigs is conducive to better selection of excellent breeding pigs.

[0003] In the past fifteen years, genome-wide association study (GWAS) has been applied to various studies to explore the association between genetic molecular markers and target traits (A. Abdellaoui, L. Yengo, K. J. Verweij, and P. M. Visscher, 15 years of GWAS discovery: realizing the promise. The American Journal of Human Genetics 110 (2023) 179-194.). Through this method, it can be identified whether there is a significant association between different genetic variations and traits, and the effect value is calculated. At present, there have been many reports that quantitative trait loci (QTL) and candidate genes associated with backfat thickness have been discovered based on this method (R. Ding, Z. Zhuang, Y. Qiu, D. Ruan, J. Wu, J. Ye, L. Cao, S. Zhou, E. Zheng, and W. Huang, Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis. Journal of Animal Science 100 (2022) skac012.). The application of this method helps to further understand the genetic mechanism related to pig backfat thickness, thereby improving the breeding efficiency.

[0004] The application obtains genotype data by collecting Duroc pig ear samples from COFCO Jiajian Kang Pig Farm, extracting DNA, and then performing genotyping based on a pig 80K SNP functional site chip using a targeted capture technology. Combined with the collected backfat thickness phenotype determination data of 3571 Duroc pigs, the rMVP software (L. Yin, H. Zhang, Z. Tang, J. Xu, D. Yin, Z. Zhang, X. Yuan, M. Zhu, S. Zhao, X. Li, and X. Liu, rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study. Genomics Proteomics Bioinformatics 19 (2021) 619-628.) in the R environment is used to screen out SNP molecular markers related to the backfat thickness trait of Duroc pigs by using an MLM model, which provides new molecular markers for the assisted selection and prediction of improvement of the backfat thickness of Duroc pigs, and has important significance for the assisted selection of pigs. SUMMARY

[0005] The application aims to provide molecular markers related to the backfat thickness trait of Duroc pigs, screen out SNPs significantly related to the backfat thickness trait of pigs by combining the genotype and phenotype data of the Duroc pig population with genome-wide association analysis (GWAS), and provide new molecular markers for the selection of the backfat thickness trait of Duroc pigs.

[0006] In order to achieve the above-mentioned purpose, the technical scheme of the application is as follows:

[0007] The applicant screens out an SNP molecular marker (Ensembl database accession number rs326953479) significantly related to the backfat thickness trait of Duroc pigs by genome-wide association analysis, and obtains the nucleotide sequence of 100 bp upstream and downstream of the SNP site by referring to the pig reference genome (genome version 11.1) of the Ensmble database, the nucleotide sequence is shown as SEQ ID NO. 1 or 2, the SNP marker is located at the 101st position of the sequence, and the polymorphic site is T or C.

[0008] The molecular marker can be used as an assisted selection and prediction molecular marker for detecting the backfat thickness trait of pigs, and when the polymorphic site is C, the Duroc pig has thinner backfat. BRIEF DESCRIPTION OF DRAWINGS

[0009] Figure 1 It is the overall technical process of the application.

[0010] Figure 2is Manhattan plot of genome-wide association study. The plot is backfat thickness trait of Duroc pigs, SNP sites with strong correlation signal on the threshold line are selected for further analysis, and the screened SNP markers are located on pig chromosome 7 (SSC7).

[0011] Figure 3 is Manhattan local plot and haplotype block plot.

[0012] Figure 4 is Quantile-quantile plot (QQ plot) of genome-wide association study.

[0013] Figure 5 is the distribution plot of genotyping results of 3571 Duroc pigs at the SNP site screened in the application.

[0014] Among them, 0 / 0 represents genotype TT, 0 / 1 represents genotype TC, and 1 / 1 represents genotype CC, and there is a significant difference between the phenotype values of the three genotypes of the backfat thickness trait of the pigs. DETAILED DESCRIPTION

[0015] The sequence and genome-wide association analysis result in the application are based on the information of pig genome 11.1 version.

[0016] Example 1: Genotyping detection

[0017] (1) 3571 Duroc pigs from a certain pig farm of COFCO Jiajian Kang Food Co., Ltd. were collected, DNA was extracted and quality detection was performed, and SNP genotyping data were obtained by using pig 80K SNP high-density functional site chip provided by Wuhan Shadow Gene Technology Co., Ltd.

[0018] (2) The original genotype file was quality controlled by using Plink1.9 software: a, geno 0.1: remove SNP sites with call rate less than 90%; b, MAF 0.01: remove SNP sites with minimum allele frequency less than 0.01; c, chr 1-18: retain SNP sites with chromosome number 1-18. After quality control, the genotype file was filled by using Beagle5.4.

[0019] (3) The filled genotype data was quality inspected, and finally 3571 individuals and 88654 variation sites were retained for GWAS study of backfat thickness trait.

[0020] Example 2: Genome-wide association analysis of SNP molecular markers and backfat thickness trait

[0021] The backfat thickness of Duroc pigs was measured by Mylab Touch vet animal backfat measuring ultrasonic diagnostic instrument. Specifically, the thickness of the skin and subcutaneous fat at 5 cm from the middle line of the back and perpendicular to the middle line of the back between the 3rd and 4th ribs of the pig was measured. The backfat thickness phenotype data of 3571 Duroc pigs from a certain pig farm of COFCO Joy Luck Food Co., Ltd. were counted, and the backfat thickness was used as the phenotype for subsequent GWAS analysis.

[0022] The mixed linear model was used to perform the whole genome association analysis (GWAS) by using the MLM model in the MVP package of R language. The specific model is as follows: y = Xβ + Vα + Zu + e, wherein y represents the phenotype value of the individual, β represents the fixed effect of the principle component, and the first three principle components are added as fixed effects in this embodiment, α represents the SNP vector in this whole genome association analysis, μ represents the random effect subject to the distribution , wherein G represents the kinship matrix calculated from the SNPs of the corresponding individual, X, V and Z represent the correlation matrices of β, α and μ, e represents the residual vector, and the residual vector is subject to the distribution

[0023] Table 1: candidate SNP sites associated with the backfat thickness trait

[0024]

[0025] Table 1: When the marker P value is <0.05 / 88654 (Bonferroni correction), it is a significant marker

[0026] Table 2: Genotype frequency and phenotype value of rs326953479 in the population

[0027]

[0028] The Manhattan plot of the whole genome association analysis is shown in Figure 2 , and there is a significant signal peak on chromosome 7. Further analysis of the signal peak shows that Figure 3 In the whole genome association analysis using the MLM model, the rs326953479 marker is extremely significantly associated with the backfat thickness trait, reaching the whole genome significant level, Figure 4 The QQ plot shows that the MLM model fits well in this analysis. The difference between the genotypes of the marker and the corresponding backfat thickness phenotype is shown in Figure 5 and Table 2. It can be found that individuals with genotype CC are concentrated in the population with thinner backfat thickness, so the marker is significantly related to the backfat thickness trait of Duroc pigs, and when the marker is mutated to C, it is beneficial for the pig to have thinner backfat thickness.

Claims

1. Use of SNP markers in selection for backfat thickness in pigs, characterized in that, The nucleotide sequence containing the SNP marker is shown in SEQ ID NO. 1 or 2, the SNP marker is located at position 101 of the sequence, and the polymorphic site is T or C.

2. Use according to claim 1, characterized in that, The pig has a thinner backfat trait when the polymorphic site is C.

3. Use according to claim 1, characterized in that, The pig is of the Duroc breed.

4. A kit for detecting the backfat thickness trait in swine, characterized in that, The kit contains reagents for detecting the polymorphic site of the SNP marker of claim 1.

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