Ma Xuejian, Chen Zitao, Zhang Zhenyang, Liu Shengqiang, Wang Meng, Zhang Xiaowei, Shi Jinhu, Gao Hui, Gu Jiamin, Han He, Pan Yuchun, Wang Qishan
Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya, China.
Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou, China.
Anim Genet. 2025 Feb;56(1):e13502. doi: 10.1111/age.13502.
The Beigang pig was recently identified as one of the endangered breeds during a Chinese indigenous pig genetic resource survey. The Beigang breed is notable for its remarkable roughage tolerance and high reproductive capacity according to historical records. Morphologically, the Beigang pig resembles many indigenous pigs in eastern China, especially in its large ears. This makes the Beigang pig a valuable reference for studying the genetic mechanisms on large ear size in pigs. However, there is currently a lack of clear understanding regarding the genetic structure and inbreeding levels of the Beigang pig population. This study used whole-genome sequencing data from Beigang pig (N = 145 pigs) and integrated genetic information from commercial pigs and indigenous pigs in eastern China to conduct a comprehensive analysis of the Beigang pig's genetic structure. Three selection signal detection methods-runs of homozygosity, fixation index, and integrated haplotype score-were employed to explore the differences in genomic selection signatures between Beigang pig and other pig populations. Additionally, we used a public project for regulatory variants discovery and molecular phenotype prediction in farm animal species called FarmGtex to explore the expression of three genes (WIF1, LEMD3, and MSRB3) related to ear size in Beigang pig. This research identified five homozygous variant sites in the WIF1 gene as important candidate loci potentially influencing ear size in Beigang pig. The results indicate that the Beigang pig holds a unique status among Chinese indigenous pigs, characterized by high genetic diversity and low levels of inbreeding. The study also revealed that WIF1 may play a significant role in influencing ear size in this breed. These findings contribute to a deeper understanding of the population structure and genetic characteristics of Beigang pig.
在一次中国地方猪遗传资源调查中，北港猪最近被确定为濒危品种之一。根据历史记录，北港猪以其显著的耐粗饲能力和高繁殖能力而闻名。在形态上，北港猪与中国东部的许多地方猪相似，尤其是耳朵较大。这使得北港猪成为研究猪大耳尺寸遗传机制的宝贵参考。然而，目前对北港猪种群的遗传结构和近亲繁殖水平缺乏清晰的了解。本研究使用了北港猪（N = 145头猪）的全基因组测序数据，并整合了中国东部商业猪和地方猪的遗传信息，对北港猪的遗传结构进行了全面分析。采用了三种选择信号检测方法——纯合子连续片段、固定指数和综合单倍型得分——来探索北港猪与其他猪种群之间基因组选择特征的差异。此外，我们利用一个名为FarmGtex的家畜物种调控变异发现和分子表型预测的公共项目，来探索北港猪中与耳朵大小相关的三个基因（WIF1、LEMD3和MSRB3）的表达。本研究确定了WIF1基因中的五个纯合变异位点为可能影响北港猪耳朵大小的重要候选基因座。结果表明，北港猪在中国地方猪中具有独特的地位，其特点是遗传多样性高和近亲繁殖水平低。该研究还表明，WIF1可能在影响该品种耳朵大小方面发挥重要作用。这些发现有助于更深入地了解北港猪的种群结构和遗传特征。
