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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01067

Landscape of loci and candidate genes for muscle fatty acid composition in pigs revealed by multiple population association analysis

Junjie Zhang1, Yifeng Zhang1, Huanfa Gong1, Leilei Cui1,  Junwu Ma1,  Congying Chen1,  Huashui Ai1,  Shijun Xiao1,  Lusheng Huang2* and  Bin Yang2*
  • 1State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, China
  • 2State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, China

Genome wide association analyses in diverse populations can identify complex trait loci that are specifically present in one population or shared across multiple populations, which help to better understand the genetic architecture of complex traits in a broader genetic context. In this study, we conducted GWAS and meta-analysis for 38 fatty acid composition traits with 12-19 million imputed genome sequence SNPs in 2446 pigs from six populations, encompassing White Duroc × Erhualian F2, Sutai, Duroc-Landrace-Yorkshire (DLY) three-way cross, Laiwu, Erhualian and Bamaxiang pigs that were originally genotyped with 60 K or 1.4 million SNP chips. The analyses uncovered 285 lead SNPs (P < 5 × 10-8), among which 78 locate more than 1 Mb to the lead chip SNPs were considered as novel, largely augmented the landscape of loci for porcine muscle fatty acid composition. Meta-analysis enhanced the association significance at loci near FADS2, ABCD2, ELOVL5, ELOVL6, ELOVL7, SCD and THRSP genes, suggesting possible existence of population shared mutations underlying these loci. Further haplotype analysis at SCD loci identified a shared 3.7 kb haplotype in F2, Sutai and DLY pigs showing consistent effects of decreasing C18:0 contents in the three populations. In contrast, at FASN loci, we found an Erhualian specific haplotype explaining the population specific association signals in Erhualian pigs. This study refines our understanding on landscape of loci and candidate genes for fatty acid composition traits of pigs.

Keywords: GWAS, sequence imputation, Meta-analysis, fatty acid composition, pig

Received: 16 Jun 2019; Accepted: 04 Oct 2019.

Copyright: © 2019 Zhang, Zhang, Gong, Cui, Ma, Chen, Ai, Xiao, Huang and Yang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Prof. Lusheng Huang, State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China, Lushenghuang@hotmail.com
Prof. Bin Yang, State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China, binyang@live.cn