Genome-wide scan for runs of homozygosity in Asian wild boars and Anqing six-end-white pigs.
Genome-wide scan for runs of homozygosity in Asian wild boars and Anqing six-end-white pigs.
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DOI：
10.1111/age.13250
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发表时间：
2022-09
期刊：
影响因子：
2.4
通讯作者：
Xudong Wu;Ren-chao Zhou;Yuanlang Wang;Wei Zhang;Xianrui Zheng;Guiying Zhao;Xiaodong Zhang;Z. Yin;Yueyun Ding
中科院分区：
文献类型：
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作者：
Xudong Wu;Ren-chao Zhou;Yuanlang Wang;Wei Zhang;Xianrui Zheng;Guiying Zhao;Xiaodong Zhang;Z. Yin;Yueyun Ding
近交和遗传多样性丧失是中国地方猪种面临的严重问题。纯合子序列（ROHs）是纯合子基因型的连续长度，可以提供近交水平、交配方案、选择压力和遗传事件的信息。安庆六端白猪是安徽省重要的地方生猪品种，在当地养猪业中占有重要地位。在最近的几十年里，AQ猪已经成为一个封闭的品种，在保护农场的人口规模很小，提出了近亲繁殖减少的问题。本研究采用10倍重测序技术对24头AQ猪和6头亚洲野猪进行全基因组检测。基于重测序数据，我们使用Plink软件分析了基因组的纯合性和ROHs在基因组中的分布。我们从重测序结果中获得935.04 Gb的原始数据，超过45 822 239个snp。此外，我们确定了28702种ROHs。与AWB猪相比，AQ猪的ROH数、ROH率和FROH值较高，说明人工选择影响了ROH的分布和基因组近交水平。在AQ猪和awb猪中分别鉴定出307个和205个ROH岛。AQ猪的ROH岛基因主要富集在免疫生物学过程中。研究结果可为AQ猪的遗传多样性和种质资源保护提供参考。
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 FROH 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.