Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing

文献类型： 外文期刊

第一作者： Li, Wenjun

作者： Li, Wenjun;Wu, Lingxiang;Meng, Xintong;Huo, Jinlong;Fu, Guowen;Zhao, Guiying;Wu, Xudong;Zhang, Wei;Xiang, Decai;Yin, Zongjun

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关键词： local breed; whole genome resequencing; runs of homozygosity; inbreeding coefficient; candidate gene

期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）

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年卷期： 2024 年 15 卷 2 期

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收录情况： SCI

摘要： Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 +/- 0.016, and the FPED, calculated based on the pedigree, was 0.027 +/- 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.

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