Single-Locus and Multi-Locus Genome-Wide Association Studies for Intramuscular Fat in Duroc Pigs
Single-Locus and Multi-Locus Genome-Wide Association Studies for Intramuscular Fat in Duroc Pigs
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杜洛克猪肌内脂肪的单基因座和多基因座全基因组关联研究
DOI：
10.3389/fgene.2019.00619
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发表时间：
2019-06-28
影响因子：
3.7
通讯作者：
Yang, Jie
中科院分区：
文献类型：
--
作者：
Ding, Rongrong;Yang, Ming;Yang, Jie
肌内脂肪（IMF）是肉的重要数量性状，影响着猪肉的感官特性和营养价值。为了更好地了解IMF的遗传决定因素，我们使用了一种复合策略，包括单位点和多位点关联分析，对1,490头杜洛克公猪的IMF进行了全基因组关联研究（GWAS）。我们估计IMF的基因组遗传度为0.23 ± 0.04。共发现30个单核苷酸多态性（SNPs）与IMF显著相关。单位点混合线性模型（MLM）和多位点方法多位点随机SNP效应混合线性模型（mrMLM），快速多位点随机SNP效应有效混合模型关联（FASTMrEMMA）和综合确定独立筛选期望最大化贝叶斯最小绝对收缩和选择算子模型（ISIS EM-BLASSO）分析分别确定了5，9，8和21个显著SNP。有趣的是，SSC 7上的一个新的数量性状位点（QTL）被发现影响IMF。此外，基于其在IMF中的潜在功能作用，发现10个候选基因（BDKRB 2、GTF 2IRD 1、UTRN、TMEM 138、DPYD、CASQ2、ZNF 518 B、S1PR 1、GPC 6和GLI 1）与IMF相关。GO分析表明，大部分基因与肌肉和器官发育有关。据报道，一种显著富集的KEGG途径，即鞘脂信号传导途径，与脂肪沉积和肥胖相关。新的变异和功能基因的鉴定将促进我们对IMF遗传机制的理解，并为猪的标记辅助或基因组选择提供特定的机会。在一般情况下，这样的复合单位点和多位点的战略GWAS可能是有用的了解经济性状的家畜的遗传结构。
Intramuscular fat (IMF) is an important quantitative trait of meat, which affects the associated sensory properties and nutritional value of pork. To gain a better understanding of the genetic determinants of IMF, we used a composite strategy, including single-locus and multi-locus association analyses to perform genome-wide association studies (GWAS) for IMF in 1,490 Duroc boars. We estimated the genomic heritability of IMF to be 0.23 ± 0.04. A total of 30 single nucleotide polymorphisms (SNPs) were found to be significantly associated with IMF. The single-locus mixed linear model (MLM) and multiple-locus methods multi-locus random-SNP-effect mixed linear model (mrMLM), fast multi-locus random-SNP-effect efficient mixed model association (FASTmrEMMA), and integrative sure independence screening expectation maximization Bayesian least absolute shrinkage and selection operator model (ISIS EM-BLASSO) analyses identified 5, 9, 8, and 21 significant SNPs, respectively. Interestingly, a novel quantitative trait locus (QTL) on SSC 7 was found to affect IMF. In addition, 10 candidate genes (BDKRB2, GTF2IRD1, UTRN, TMEM138, DPYD, CASQ2, ZNF518B, S1PR1, GPC6, and GLI1) were found to be associated with IMF based on their potential functional roles in IMF. GO analysis showed that most of the genes were involved in muscle and organ development. A significantly enriched KEGG pathway, the sphingolipid signaling pathway, was reported to be associated with fat deposition and obesity. Identification of novel variants and functional genes will advance our understanding of the genetic mechanisms of IMF and provide specific opportunities for marker-assisted or genomic selection in pigs. In general, such a composite single-locus and multi-locus strategy for GWAS may be useful for understanding the genetic architecture of economic traits in livestock.