College of Animal Science and Technology, Southwest University, Chongqing, 400715, China.
Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
Anim Genet. 2021 Aug;52(4):550-555. doi: 10.1111/age.13092. Epub 2021 May 24.
As one of the best-known commercial goat breeds in the world, Boer goat has undergone long-term artificial selection for nearly 100 years, and its excellent growth rate and meat production performance have attracted considerable worldwide attention. Herein, we used single nucleotide polymorphisms (SNPs) called from the whole-genome sequencing data of 46 Australian Boer goats to detect polymorphisms and identify genomic regions related to muscle development in comparison with those of 81 non-specialized meat goat individuals from Europe, Africa, and Asia. A total of 13 795 202 SNPs were identified, and the whole-genome selective signal screen with a π ratio of nucleotide diversity (π /π ) and pairwise fixation index (F ) was analyzed. Finally, we identified 1741 candidate selective windows based on the top 5% threshold of both parameters; here, 449 candidate genes were only found in 727 of these regions. A total of 433 genes out of the 449 genes obtained were annotated to 2729 gene ontology terms, of which 51 were directly linked to muscle development (e.g., muscle organ development, muscle cell differentiation) by 30 candidate genes (e.g., JAK2, KCNQ1, PDE5A, PDLIM5, TBX5). In addition, 246 signaling pathways were annotated by 178 genes, and two pathways related to muscle contraction, including vascular smooth muscle contraction (ADCY7, PRKCB, PLA2G4E, ROCK2) and cardiac muscle contraction (CACNA2D3, CASQ2, COX6B1), were identified. The results could improve the current understanding of the genetic effects of artificial selection on the muscle development of goat. More importantly, this study provides valuable candidate genes for future breeding of goats.
作为世界上最知名的商业山羊品种之一，布尔山羊经过近 100 年的人工选择，其出色的生长速度和产肉性能引起了全球的广泛关注。在此，我们利用来自 46 只澳大利亚布尔山羊全基因组测序数据中的单核苷酸多态性（SNP），与来自欧洲、非洲和亚洲的 81 只非专门化肉用山羊个体进行比较，检测多态性和与肌肉发育相关的基因组区域。共鉴定出 13795202 个 SNP，利用核苷酸多样性（π /π）和成对固定指数（F）的全基因组选择信号筛选，分析了整个基因组的选择信号。最后，我们根据这两个参数的前 5%阈值，确定了 1741 个候选选择窗口，其中 449 个候选基因仅在这 727 个区域中的 433 个基因中被发现。这 449 个基因中有 433 个基因被注释到 2729 个基因本体论术语，其中 51 个基因直接与肌肉发育（如肌肉器官发育、肌肉细胞分化）相关，由 30 个候选基因（如 JAK2、KCNQ1、PDE5A、PDLIM5、TBX5）编码。此外，178 个基因注释了 246 个信号通路，其中两条与肌肉收缩相关的通路被鉴定出来，包括血管平滑肌收缩（ADCY7、PRKCB、PLA2G4E、ROCK2）和心肌收缩（CACNA2D3、CASQ2、COX6B1）。这些结果可以提高我们对人工选择对山羊肌肉发育遗传影响的认识。更重要的是，本研究为未来山羊的选育提供了有价值的候选基因。
