Zhang Junjie, Zhang Yifeng, Gong Huanfa, Cui Leilei, Ma Junwu, Chen Congying, Ai Huashui, Xiao Shijun, Huang Lusheng, Yang Bin
State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
Front Genet. 2019 Oct 25;10:1067. doi: 10.3389/fgene.2019.01067. eCollection 2019.
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, 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 ( < 5 × 10), 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 , and genes, suggesting possible existence of population shared mutations underlying these loci. Further haplotype analysis at loci identified a shared 3.7 kb haplotype in F, Sutai and DLY pigs showing consistent effects of decreasing C18:0 contents in the three populations. In contrast, at 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.
在不同种群中进行全基因组关联分析，可以识别出特定存在于一个种群或多个种群共有的复杂性状基因座，这有助于在更广泛的遗传背景下更好地理解复杂性状的遗传结构。在本研究中，我们对来自六个种群的2446头猪的38个脂肪酸组成性状进行了全基因组关联研究和荟萃分析，这些猪最初使用60K或140万个单核苷酸多态性（SNP）芯片进行基因分型，涵盖大白杜洛克×二花脸F1、苏太、杜洛克-长白-约克夏（DLY）三元杂交、莱芜、二花脸和巴马香猪，利用1200万至1900万个推算的基因组序列SNP。分析发现了285个先导SNP（<5×10），其中78个位于距先导芯片SNP超过1 Mb处，被认为是新发现的，大大扩展了猪肌肉脂肪酸组成的基因座图谱。荟萃分析增强了在、和基因附近位点的关联显著性，表明这些位点可能存在种群共享突变。在位点进行的进一步单倍型分析在F1、苏太和DLY猪中鉴定出一个共享的3.7 kb单倍型，在这三个种群中显示出一致的降低C18:0含量的效应。相比之下，在位点，我们发现了一个二花脸特异性单倍型，解释了二花脸猪中种群特异性的关联信号。本研究深化了我们对猪脂肪酸组成性状的基因座图谱和候选基因的理解。
