Table_9_Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.XLSX

Selective breeding for athletic performance in various disciplines has resulted in population stratification within the American Quarter Horse (QH) breed. The goals of this study were to utilize high density genotype data to: (1) identify genomic regions undergoing positive selection within and among QH subpopulations; (2) investigate haplotype structure within each QH subpopulation; and (3) identify candidate genes within genomic regions of interest (ROI), as well as biological pathways, predicted to play a role in elite performance in each group. For that, 65K SNP genotyping data on 143 elite individuals from 6 QH subpopulations (cutting, halter, racing, reining, western pleasure, and working cow) were imputed to 2M SNPs. Signatures of selection were identified using FST-based (di) and haplotype-based (hapFLK) analyses, accompanied by identification of local haplotype structure and sharing within subpopulations (hapQTL). Regions undergoing positive selection were identified on all 31 autosomes, and ROI on 2 chromosomes were identified by all 3 methods combined. Genes within each ROI were retrieved and used to identify pathways and genes that might contribute to performance in each subpopulation. These included, among others, candidate genes associated with skeletal muscle development, metabolism, and central nervous system development. This work improves our understanding of equine breed development, and provides breeders with a better understanding of how selective breeding impacts the performance of QH populations.

针对不同竞技项目的运动性能开展的选择性育种，导致了美国夸特马（American Quarter Horse，QH）品种内出现群体分层。本研究旨在利用高密度基因型数据完成三项目标：(1) 鉴定美国夸特马亚群内部及亚群之间受到正选择的基因组区域；(2) 解析各美国夸特马亚群内的单倍型结构；(3) 鉴定目标基因组区域（regions of interest，ROI）内的候选基因，以及预测与各亚群精英运动表现相关的生物学通路。为此，本研究将来自6个美国夸特马亚群（截短赛、牵展赛、竞速赛、西部驭马术、西部休闲马术以及工作牧牛赛）的143匹精英个体的65K单核苷酸多态性（SNP）基因型数据，填充至2M个SNP位点。研究采用基于固定指数（Fixation Index，FST）的二倍体分析与基于单倍型的hapFLK分析，鉴定选择信号，并同步鉴定亚群内的局部单倍型结构与单倍型共享情况（hapQTL）。本研究在全部31条常染色体上均鉴定到了受到正选择的基因组区域，且通过三种方法联合分析，在2条染色体上鉴定到了目标基因组区域。随后检索各目标基因组区域内的基因，以此鉴定可能影响各亚群运动性能的通路与基因，其中包括与骨骼肌发育、代谢及中枢神经系统发育相关的候选基因。本研究增进了学界对马品种选育历程的认知，同时为育种从业者提供了关于选择性育种如何影响夸特马群体运动性能的全新理解。