荣昌猪初产繁殖性状的全基因组关联研究

doi:10.11843/j.issn.0366-6964.2023.01.010

摘要/Abstract

摘要： 旨在鉴定荣昌猪初产繁殖性状的重要变异位点和基因，为荣昌猪繁殖性状的遗传改良提供重要的分子标记和基因资源。本研究选取429头荣昌母猪进行猪50K芯片基因分型，经过质量控制和基因型填充后，保留35046个SNPs用于分析。采用主成分分析法研究群体结构，利用混合线性模型(mixed-linear model，MLM)将出生年、出生月作为固定效应，将主成分值作为协变量对总产仔数、活产仔数、死胎数和初生窝重性状进行全基因组关联分析(GWAS)。结果显示，在全基因组显著水平上鉴定出2个影响荣昌猪初生窝重的SNPs和1个影响荣昌猪死胎数的SNP；在潜在显著水平上鉴定到5个影响荣昌猪总产仔数的SNPs，3个影响荣昌猪活产仔数的SNPs和10个影响荣昌猪死胎数的SNPs。通过全基因组关联分析筛选到1个显著的SNP(SSC17:57 315 180bp)同时影响荣昌猪总产仔数、活产仔数和初生窝重，1个显著的SNP(SSC1:279 214 647bp)同时影响荣昌猪活产仔数和总产仔数，暗示基因在不同性状间具有一因多效性。本研究根据候选基因的相关分子生物学功能，确定BMP7基因为影响荣昌猪总产仔数、活产仔数和初生窝重的重要候选基因，MSH3和CBLB基因为影响荣昌猪死胎数的重要候选基因。以上结果为荣昌猪繁殖性状提供了重要的遗传变异位点和候选基因，也为荣昌猪繁殖性状的基因组选择提供了重要的理论基础。

关键词: 荣昌猪, 全基因组关联分析, 产仔数, 死胎数, 初生窝重

Abstract: The aim of this study was to identify genetic variant loci and genes which associated with reproductive traits at first farrowing in Rongchang pigs, and provide important molecular markers and genes for improving pig reproductive traits in Rongchang pigs. In this study, a total of 429 Rongchang sows were genotyped using porcine 50K SNP chip. After quality control, 35 046 SNPs were generated for subsequent genome-wide association study (GWAS). Then, the population structure was analyzed using principal component analysis, and GWAS was performed for total number born (TNB), total number born alive (NBA), number of stillborn (NS) and litter weight born alive (LWB) using a mixed-linear model (MLM). The birth year and birth month were used as fixed effects, and principal component values were used as a covariate in this model. The results showed that a total of 2 and 1 genome-wide significant SNPs were detected for LWB and NS, respectively. Furthermore, a total of 5, 3 and 10 suggestive SNPs were found for TNB, NBA and NS, respectively. Of these, one locus located on SSC17 (position: 57 315 180 bp) were evaluated to affect TNB, NBA and LWB and one locus located on SSC1 (position: 279 214 647 bp) were evaluated to affect both NBA and TNB, indicating the pleiotropism of genes in different reproductive traits. Considering the function of candidate genes, BMP7 gene was suggested as the promising candidate genes for TNB, NBA and LWB, and two genes(MSH3 and CBLB) were suggested as the important candidate genes for NS. These results provided novel variant loci and potential candidate genes for reproductive traits, and provided important theoretical basis for improving reproductive traits using genomic selection in Rongchang pigs.

Key words: Rongchang pig, GWAS, number of piglets, number of stillborn, litter weight born alive

中图分类号:

S828.2

吴平先, 陈力, 龙熙, 柴捷, 张廷焕, 徐顺来, 郭宗义, 王金勇. 荣昌猪初产繁殖性状的全基因组关联研究[J]. 畜牧兽医学报, 2023, 54(1): 103-112.

WU Pingxian, CHEN Li, LONG Xi, CHAI Jie, ZHANG Tinghuan, XU Shunlai, GUO Zongyi, WANG Jinyong. Genome-wide Association Studies for Reproductive Traits at First Farrowing in Rongchang Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 103-112.

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