Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations
Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations
复制标题
两个杜洛克猪群体腰部肌肉面积和腰部肌肉深度的全基因组关联研究的荟萃分析
DOI：
10.1371/journal.pone.0218263
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发表时间：
2019-06-12
期刊：
影响因子：
3.7
通讯作者：
Yang，Jie
中科院分区：
文献类型：
--
作者：
Zhuang，Zhanwei;Li，Shaoyun;Yang，Jie
胸肌面积和胸肌深度是影响种猪生产性能的重要性状。然而，这两个性状的遗传结构仍然知之甚少。为了明确LMA和LMD的遗传结构，收集了属于两个具有不同遗传背景的群体的6043头杜洛克猪的材料，并使用全基因组分布的50K单核苷酸多态性（SNPs）面板进行全基因组关联研究（GWAS）。为了提高常见SNP的检测能力，我们对这两个猪群进行了荟萃分析，并发现了其他重要的SNP。结果，我们在SSC 6、7、12、16和18上鉴定了LMA和LMD的75个显著SNP。其中，25个常见的SNPs与LMA和LMD相关。在SSC7上发现了一个影响LMA和LMD的多效数量性状基因座（QTL），该基因座位于SSC7上，间距为283 kb。标记ALGA 0040260是该QTL的一个关键SNP，分别解释了LMA和LMD表型变异的1.77%和2.48%。SSC16上的另一个遗传区域（709 kb）被检测到并显示与LMA显著相关，并且峰值SNP WU_10.2_16_35829257贡献了LMA的1.83%的表型方差。进一步的生物信息学分析确定了8个有希望的候选基因（GCLC、GPX8、DAXX、FGF21、TAF11、SPDEF、NUDT 3和PACSIN 1），它们在谷胱甘肽代谢、脂肪和肌肉组织发育以及脂质代谢中具有功能。本研究为杜洛克猪种的LMA和LMD提供了第一个GWAS，以通过大样本量分析潜在的遗传变异。这些发现进一步推进了我们的理解，并有助于阐明猪的LMA，LMD和生长相关性状的遗传结构。
Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.