Data from: Genome-wide association analysis for blood lipid traits measured in three pig populations revealed a substantial level of genetic heterogeneity

Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.

血脂与人类心肌梗死及心血管疾病密切相关。本研究针对血脂性状的遗传架构展开解析：我们对来自莱芜猪、二花脸猪以及杜洛克×（长白×约克夏）群体的1256头猪开展全基因组关联分析（genome-wide association studies, GWAS），并对来自5个不同群体的2400余头猪的GWAS结果进行荟萃分析。针对6项血脂性状，本研究在猪的11条染色体（Sus scrofa chromosome, SSC）上共检测到22个达到提示性显著水平的基因组位点。GWAS荟萃分析共鉴定出5个与血脂性状相关的新位点。对不同受试群体的GWAS位点进行比较后发现，猪血脂水平存在显著的遗传异质性。我们进一步评估了猪3号染色体（SSC3）上载脂蛋白B基因（apolipoprotein B, APOB）内部及其邻近区域的9个多态位点与血清低密度脂蛋白胆固醇（low-density lipoprotein cholesterol, LDL-C）和总胆固醇（total cholesterol, TC）水平的因果关联。在这9个多态位点中，1个插入缺失多态性（insertion-deletion polymorphism, indel）在莱芜猪群体中与LDL-C和TC水平呈现最显著的关联。但在白色杜洛克×二花脸F2资源群体中未检测到该显著关联，而该群体中同样在SSC3上检测到了LDL-C和TC的数量性状位点（quantitative trait locus, QTL）。这表明SSC3上的QTL可能存在群体特异性的信号。未来需开展进一步研究以验证这一假说。