A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Pingxian Wu,Xiaotian Qiu,Xuewei Li,Guoqing Tang,Dejuan Chen,Li Zhu,Anan Jiang,Yanzhi Jiang,Kai Wang,Jie Zhou

doi:10.1038/s42003-021-02416-3

Pingxian Wu, Xiaotian Qiu + Show 8 more

Open Access

https://doi.org/10.1038/s42003-021-02416-3

Copy DOI

Abstract

Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles ‘GGG’ for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.

Highlights

Affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging
Previous research has proven that many phenotypes are affected by both DGE and SGE and the contribution of SGE to total genetic variance is large in pigs, such as growth rate, body weight (BW)[6,7], feed intake, backfat thickness (BFT), muscle depth[2], behavior[8,9], and average daily gain (ADG)[10,11]
The main objectives of this study were (i) to construct haplotype loci based on imputed whole-genome sequences (WGS) data and identify associations between haplotype-DGE and haplotype-SGE by GWAS; (ii) to perform single-locus analysis to explore SNPs associated with socially affected traits by considering both DGE and SGE in Yorkshire pigs; (iii) to compare the results of GWAS based on haplotypes and SNPs for DGE and SGE; and (iv) to combine single-locus and haplotype-based GWAS to reveal important SNPs and genes for DGE and SGE in pigs

Summary

Introduction

Affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. In our previous study, a total of 27 SNPs associated with six growth traits were identified using whole-genome sequences (WGS) of 40 Yorkshire pigs (Zhejiang Tianpeng Group Co., Ltd. Zhejiang, China)[15]. To better investigate the genetic architecture of socially affected traits in pigs, the present study used both GWAS approaches to estimate the DGE and SGE on each trait by employing a social genetic model, WGS of 60 pigs, and genotyping of 1204 Yorkshire pigs with Illumina 50 K SNP chips. The main objectives of this study were (i) to construct haplotype loci based on imputed WGS data and identify associations between haplotype-DGE and haplotype-SGE by GWAS; (ii) to perform single-locus analysis to explore SNPs associated with socially affected traits by considering both DGE and SGE in Yorkshire pigs; (iii) to compare the results of GWAS based on haplotypes and SNPs for DGE and SGE; and (iv) to combine single-locus and haplotype-based GWAS to reveal important SNPs and genes for DGE and SGE in pigs

Objectives

Methods

Results

Conclusion