Cai Jiarui, Yang Liu, Gao Yahui, Liu George E, Da Yang, Ma Li
Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture, Beltsville, MD 20705, USA.
Animals (Basel). 2025 Jul 31;15(15):2247. doi: 10.3390/ani15152247.
A unique line of Holstein cattle has been maintained without selection in Minnesota since 1964. After many generations, unselected cattle produce less milk, but have better reproductive performance and health traits when compared with contemporary cows. Comparisons between this line of unselected Holstein and those under selection provide useful insights that connect selection and complex traits in cattle. Utilizing these unique resources and sequence data, we sought to identify genome changes due to selection. We sequenced 30 unselected and 54 selected Holstein cattle and compared their sequence variants to identify selection signatures. After many years, the two populations showed completely different patterns in their genome-level population structures and linkage disequilibrium. By integrating signals from five different detection methods, we detected consensus selection signatures from at least four methods covering 14,533 SNPs and 155 protein-coding genes. An integrated analysis of selection signatures with gene annotation, pathways, and the cattle QTL database demonstrated that the genomic regions under selection are related to milk productivity, health, and reproductive efficiency. The polygenic nature of these complex traits is evident from hundreds of selection signatures and candidate genes, suggesting that long-term artificial selection has acted on the whole genome rather than a few major genes. In summary, our study identified candidate selection signatures underlying phenotypic differences between unselected and selected Holstein cows and revealed insights into the genetic basis of complex traits in cattle.
自1964年以来，明尼苏达州一直维持着一个未经选育的荷斯坦奶牛独特品系。经过许多代之后，未经选育的奶牛产奶量减少，但与当代奶牛相比，具有更好的繁殖性能和健康性状。将这个未经选育的荷斯坦奶牛品系与经过选育的品系进行比较，能提供有用的见解，将选育与奶牛的复杂性状联系起来。利用这些独特的资源和序列数据，我们试图确定因选育而产生的基因组变化。我们对30头未经选育的和54头经过选育的荷斯坦奶牛进行了测序，并比较它们的序列变异以识别选择特征。多年后，这两个群体在基因组水平的群体结构和连锁不平衡方面呈现出完全不同的模式。通过整合来自五种不同检测方法的信号，我们检测到至少四种方法的一致选择特征，涵盖14,533个单核苷酸多态性（SNP）和155个蛋白质编码基因。对选择特征与基因注释、通路和奶牛数量性状位点（QTL）数据库的综合分析表明，被选择的基因组区域与产奶量、健康和繁殖效率有关。从数百个选择特征和候选基因可以明显看出这些复杂性状的多基因性质，这表明长期的人工选择作用于整个基因组而非少数几个主要基因。总之，我们的研究确定了未经选育和经过选育的荷斯坦奶牛之间表型差异潜在的候选选择特征，并揭示了奶牛复杂性状遗传基础的相关见解。
