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Abstract：
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.
摘要：
保山猪（BS）是云南省的一种地方品种，由于其种群规模有限，可能面临近亲繁殖。为了准确评估BS猪群体的近亲繁殖水平，我们使用全基因组重测序来鉴定BS猪的纯合性（ROH）区域，根据谱系和ROH计算近交系数，并从ROH岛筛选出具有重要经济性状的候选基因。从BS猪的全基因组中总共获得了22,633,391个SNPS，经质量控制后，从532,450SNPS中检测到201ROHs。中等长度ROH（1-5Mb）的数量最高（98.43％），长ROH(>5Mb)的数量最低(1.57%)，BS猪的近亲繁殖主要发生在远缘世代。近交系数FROH,根据ROH计算，为0.018±0.016，FPED，根据血统计算，为0.027±0.028，呈正相关。确定了40个ROH岛，含有507个基因和891个QTLs。几个基因与生长和发育相关(IGFALS，PTN,DLX5,DKK1,WNT2),肉质性状(MC3R，ACSM3,ECI1,CD36,ROCK1,CACNA2D1),和生殖性状(NPW，TSHR,BMP7).本研究为BS猪的保护和利用提供参考。
