Shi Liangyu, Wang Ligang, Liu Jiaxin, Deng Tianyu, Yan Hua, Zhang Longchao, Liu Xin, Gao Hongmei, Hou Xinhua, Wang Lixian, Zhao Fuping
Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China.
J Anim Sci Biotechnol. 2020 Apr 28;11:46. doi: 10.1186/s40104-020-00447-0. eCollection 2020.
Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs ( ), homozygosity ( ), genomic relationship matrix ( ) and pedigree ( ). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.
In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between and , while the lowest was - 0.083 between and . The correlations between and using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as , , and .
can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
纯合子片段（ROHs）是基因组中的纯合子区段，其中从父母遗传的两个单倍型是相同的。目前大量单核苷酸多态性（SNP）基因型的可得性使得对全基因组中ROHs的特征描述更加准确。在此，我们研究了3692头大白猪中ROHs的发生和分布情况，并比较了基于ROHs（ ）、纯合度（ ）、基因组关系矩阵（ ）和系谱计算的近交系数估计值。此外，我们确定了ROH频率高的基因组区域并注释了其候选基因。
总共从3569头动物中鉴定出176,182个ROHs，所有个体均显示至少一个长度超过1 Mb的ROH。鉴定出的ROHs在常染色体上分布不均。ROH对染色体（SSC）的最高和最低覆盖率分别在SSC14和SSC13上。不同近交系数估计值之间的最高成对相关性在 和 之间为0.95，而最低相关性在 和 之间为 -0.083。使用四类ROH长度时， 和 之间的相关性范围为0.18至0.37，并随ROH长度增加而增加，但ROH > 10 Mb除外。12个ROH岛位于四条染色体（SSC1、4、6和14）上。这些ROH岛含有与繁殖、肌肉发育、脂肪沉积和适应性相关的基因，如 、 、 和 。
与其他近交系数估计方法相比， 可用于准确评估个体的近交水平。在没有系谱记录的情况下， 可为近交估计提供一种替代方法。我们的研究结果不仅可用于通过适当管理近交率和最小化近交衰退的负面影响来有效提高选择反应，还可帮助检测对选择性状有影响的基因组区域。
