Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally considered more accurate than indexes based on other types of genomic or genealogical information. High frequencies of specific ROHs in a population can be used to identify selection signatures. The results of recent studies with ROHs in domestic animals have shown the efficiency of their use to characterize herds in a reliable and accessible way, using genomic information.

摘要：连续纯合子片段（Runs of Homozygosity, ROHs）是可通过分子标记识别的长段纯合基因组区域，可为精准估算种群特征、解析演化历史与种群统计信息、评估近交水平以及识别畜牧动物的选择印记提供基因组学数据支撑。本综述旨在系统梳理围绕ROHs在上述应用场景中应用效能的相关研究进展。遗传漂变、自然或人工选择、奠基者效应以及有效种群大小等因素，会直接影响ROHs在基因组上的长度与分布格局。单从个体层面而言，基于ROHs的基因组近交水平估算可通过FROH指数实现，该指数通常被认为比基于其他类型基因组或系谱信息的估算指数更为精准。种群中特定ROHs的高频率分布特征，可用于识别选择印记。近期针对家养动物开展的ROHs相关研究结果表明，借助基因组信息，利用ROHs能够可靠且便捷地表征畜群特征，其应用效能已得到充分验证。