Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
Genes (Basel). 2020 May 21;11(5):577. doi: 10.3390/genes11050577.
Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.
研究家畜的同型合子模式、连锁不平衡、有效种群大小和近交系数有助于我们了解遗传多样性和进化历史。在这里，我们使用 Illumina PorcineSNP50 Bead Chip 来识别整个基因组的同型合子区（ROH）并估计连锁不平衡（LD），然后预测有效种群大小。此外，我们根据 305 头皮特兰猪的 ROH 计算了近交系数，并将其与通过不同计算方法获得的另外两种近交系数进行了比较。共检测到 23434 个 ROH，每个个体的 ROH 平均长度约为 507.27Mb。ROH 在基因组中的分布没有规律。不同类别之间的比较表明，长 ROH 的形成可能与近期的近交事件有关。尽管位于 ROH 核心区域的基因密度低于其他基因组区域，但它们中的大多数与皮特兰商业性状有关，如肉质。总的来说，这些结果深入了解了 ROH 的产生方式，并且所识别的 ROH 核心区域可用于对与家畜商业性状相关的基因进行定位。
