Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.
Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations.
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DOI：
10.3389/fgene.2018.00249
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发表时间：
2018
影响因子：
3.7
通讯作者：
McCue ME
中科院分区：
文献类型：
--
作者：
Avila F;Mickelson JR;Schaefer RJ;McCue ME
在不同学科的运动表现的选择性育种导致了美国四分之一马（QH）品种内的人口分层。本研究的目标是利用高密度基因型数据：（1）鉴定QH亚群内和QH亚群之间经历正选择的基因组区域;（2）研究每个QH亚群内的单倍型结构;和（3）鉴定基因组感兴趣区域（ROI）内的候选基因，以及预测在每组中的精英表现中发挥作用的生物学途径。为此，将来自6个QH亚群（切割、笼头、比赛、缰绳、西方娱乐和工作牛）的143个精英个体的65 K SNP基因分型数据插补到2 M SNP。使用基于FST（di）和基于单体型（hapFLK）的分析，伴随着局部单体型结构和亚群内共享（hapQTL）的鉴定，鉴定选择的签名。在所有31个常染色体上鉴定了正选择区域，并通过所有3种方法组合鉴定了2条染色体上的ROI。检索每个ROI内的基因并用于鉴定可能有助于每个亚群中的性能的途径和基因。其中包括与骨骼肌发育、代谢和中枢神经系统发育相关的候选基因。这项工作提高了我们对马品种发展的理解，并为育种者提供了更好地了解选择性育种如何影响QH种群的表现。
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.