Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
Novogene Bioinformatics Institute, Beijing 100015, China.
Genes (Basel). 2023 Jun 1;14(6):1211. doi: 10.3390/genes14061211.
In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (, , and ), muscle development ( and ), positive regulation of heart rate and heart contraction ( and ), regulation of insulin secretion (, , and ), and spermatogenesis (, , and ). Our findings provide insight into horse breed characteristics and future breeding strategies.
在二倍体生物的基因组中，纯合子连续区（ROH）是连续的纯合区域。ROH 可用于评估无系谱数据个体的近交情况，并通过 ROH 岛检测选择信号。我们对 97 匹马的全基因组测序数据进行了测序和分析，研究了全基因组 ROH 模式的分布，并计算了来自世界各地 16 个代表性马品种的基于 ROH 的近交系数。我们的研究结果表明，古代和近代的近交事件对各种马品种都有不同程度的影响。然而，近代的近交事件并不常见，尤其是在本地马品种中。因此，基于 ROH 的基因组近交系数可以帮助监测近交水平。使用纯血马种群作为案例研究，我们发现了 24 个含有 72 个与人工选择性状相关的候选基因的 ROH 岛。我们发现，纯血马中的候选基因参与了神经递质传递（、和）、肌肉发育（和）、心率和心脏收缩的正调控（和）、胰岛素分泌的调控（、、和）以及精子发生（、、和）。我们的研究结果为马的品种特征和未来的繁殖策略提供了参考。
