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.

中文翻译：

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纯合子的全基因组模式和 Piétrain 猪种群结构的相关特征

研究家畜的纯合性、连锁不平衡、有效种群规模和近交系数的模式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 来识别纯合性 (ROH) 的运行并估计整个基因组的连锁不平衡 (LD)，然后预测有效种群大小。此外，我们在305头Piétrain猪中计算了基于ROH的近交系数，并将其效果与通过不同计算方法获得的其他两种近交系数进行了比较。共检测到 23,434 个 ROH，每个个体的 ROH 平均长度约为 507.27 Mb。这些纯合子在基因组中的分布没有规律性。不同类别的比较表明，长ROH的形成可能与最近的近交事件有关。虽然位于ROH核心区域的基因密度低于其他基因组区域，但大部分与肉质等Piétrain商业性状有关。总体而言，结果提供了对 ROH 产生方式的深入了解，并且确定的 ROH 核心区域可用于绘制与家畜商业性状相关的基因。