AUTHOR=Zhang Junjie , Zhang Yifeng , Gong Huanfa , Cui Leilei , Ma Junwu , Chen Congying , Ai Huashui , Xiao Shijun , Huang Lusheng , Yang Bin 

TITLE=Landscape of Loci and Candidate Genes for Muscle Fatty Acid Composition in Pigs Revealed by Multiple Population Association Analysis

JOURNAL=Frontiers in Genetics

VOLUME=Volume 10 - 2019

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01067

DOI=10.3389/fgene.2019.01067

ISSN=1664-8021

ABSTRACT=<p>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 genome-wide association studies 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 F<sub>2</sub>, Sutai, Duroc-Landrace-Yorkshire (DLY) three-way cross, Laiwu, Erhualian, and Bamaxiang pigs that were originally genotyped with 60 K or 1.4 million single nucleotide polymorphism (SNP) chips. The analyses uncovered 285 lead SNPs (<italic>P</italic> &lt; 5 × 10<sup>-8</sup>), 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 <italic>FADS2, ABCD2, ELOVL5, ELOVL6, ELOVL7, SCD</italic>, and <italic>THRSP</italic> genes, suggesting possible existence of population shared mutations underlying these loci. Further haplotype analysis at <italic>SCD</italic> loci identified a shared 3.7 kb haplotype in F<sub>2</sub>, Sutai and DLY pigs showing consistent effects of decreasing C18:0 contents in the three populations. In contrast, at <italic>FASN</italic> 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.</p>