Avila Felipe, Mickelson James R, Schaefer Robert J, McCue Molly E
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.
Front Genet. 2018 Jul 19;9:249. doi: 10.3389/fgene.2018.00249. eCollection 2018.
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 -based ( ) 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.
对不同学科运动性能的选择性育种导致了美国夸特马（QH）品种内的群体分层。本研究的目的是利用高密度基因型数据：（1）识别QH亚群内部和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；（3）识别感兴趣的基因组区域（ROI）内的候选基因以及预计在每组精英性能中起作用的生物学途径。为此，将来自6个QH亚群（切割、挽具、赛马、驯马、西部休闲和工作奶牛）的143个精英个体的65K SNP基因分型数据推算至2M SNPs。使用基于统计量的方法（ ）和基于单倍型的方法（hapFLK）分析来识别选择特征，并伴随着识别亚群内的局部单倍型结构和共享情况（hapQTL）。在所有31条常染色体上都识别出了经历正选择的区域，并且通过三种方法的组合在2条染色体上识别出了ROI。检索每个ROI内的基因，并用于识别可能有助于每个亚群性能的途径和基因。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。这项工作增进了我们对马品种发展的理解，并为育种者提供了对选择性育种如何影响QH群体性能的更好理解。
