Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya

In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by <i>F</i>_ST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, <i>ITGAV, LRP4, CDH23, TPRN, RYR2</i> and <i>CELSR1</i> genes, involved in <i>embryonic morphogenesis</i>, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (<i>ITGAV</i>: c.38C &gt; T; <i>TPRN</i>: c.133A &gt; T, c.1192A &gt; G, c.1250A &gt; C; <i>CELSR1</i>: c.7640T &gt; C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.

本研究采用固定指数（F_ST）方法，对产羔数差异显著的两群北川白山羊群体的基因组拷贝数变异进行了评估，并在受正向选择的基因中鉴定出1739个基因及485个错义突变。通过功能富集分析发现，ITGAV、LRP4、CDH23、TPRN、RYR2及CELSR1等基因参与胚胎形态发生过程，与产羔数性状密切相关，受到广泛关注。此外，本研究还报道了这些基因的若干突变位点（ITGAV：c.38C>T；TPRN：c.133A>T、c.1192A>G、c.1250A>C；CELSR1：c.7640T>C），上述位点的等位基因频率在高繁殖力山羊群体中发生了显著变化。本研究同时发现，这些位点的新发突变可改变蛋白质的亲水性及三维结构。本研究鉴定出与北川白山羊产羔数相关的候选基因及其错义突变位点，这些候选基因有助于解析北川白山羊的繁殖力遗传机制，对未来山羊育种工作具有重要指导意义。