Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China.
Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China.
Anim Genet. 2022 Dec;53(6):867-871. doi: 10.1111/age.13250. Epub 2022 Sep 9.
Inbreeding and loss of genetic diversity are serious problems in local Chinese pig breeds. Runs of homozygosity (ROHs) are contiguous lengths of homozygous genotypes that can provide information on inbreeding levels, mating schemes, selection pressure, and genetic events. The Anqing six-end-white (AQ) pig, an important autochthonous pig breed bred in the Anhui province of China, plays a key role in the local pig industry. In recent decades, AQ pigs have become a closed breed with a small population size in conservation farms, raising the issue of inbreeding decline. In this study, we used 10× resequencing to detect the whole genome of 24 AQ pigs and six Asian wild boars (AWBs). We used the Plink software to analyze the homozygosity of the genome and the distribution of ROHs in the genome based on the resequencing data. We obtained 935.04 Gb of raw data from the resequencing results and more than 45 822 239 SNPs. Additionally, we identified 28 702 ROHs. Compared with AWB, AQ pigs had higher ROH numbers, longer ROH rates, and higher F values, which revealed that artificial selection influenced ROH distribution and genome inbreeding level. A total of 307 and 205 ROH islands were identified in the AQ pigs and AWBs respectively. The genes of ROH islands in AQ pigs were mainly enriched in immune biological processes. Our findings provide a useful reference for developing breeding programs to maintain genetic diversity and germplasm resources in AQ pigs.
近交和遗传多样性的丧失是中国地方猪种面临的严重问题。纯合子连续区（ROH）是纯合基因型的连续区域，可提供关于近交水平、交配方案、选择压力和遗传事件的信息。安庆六端白猪（AQ）是中国安徽省培育的一种重要的本地猪种，在中国本地猪产业中起着关键作用。近几十年来，AQ 猪在保护农场中已成为一个种群规模较小的封闭品种，这引发了近交衰退的问题。在这项研究中，我们使用 10×重测序技术检测了 24 头 AQ 猪和 6 头亚洲野猪（AWB）的全基因组。我们使用 Plink 软件根据重测序数据分析基因组的同质性和 ROH 在基因组中的分布。我们从重测序结果中获得了 935.04 Gb 的原始数据和超过 45822299 个 SNP。此外，我们还鉴定了 28702 个 ROH。与 AWB 相比，AQ 猪的 ROH 数量更多、ROH 率更长、F 值更高，这表明人工选择影响了 ROH 分布和基因组的近交水平。在 AQ 猪和 AWB 中分别鉴定出 307 个和 205 个 ROH 岛。AQ 猪 ROH 岛的基因主要富集在免疫生物学过程中。我们的研究结果为制定保持 AQ 猪遗传多样性和种质资源的选育计划提供了有益的参考。
