Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
Int J Mol Sci. 2023 Aug 18;24(16):12914. doi: 10.3390/ijms241612914.
Large White pigs are extensively utilized in China for their remarkable characteristics of rapid growth and the high proportion of lean meat. The economic traits of pigs, comprising reproductive and meat quality traits, play a vital role in swine production. In this study, 2295 individuals, representing three different genetic backgrounds Large White pig populations were used: 500 from the Canadian line, 295 from the Danish line, and 1500 from the American line. The GeneSeek 50K GGP porcine HD array was employed to genotype the three pig populations. Firstly, genomic selective signature regions were identified using the pairwise fixation index (F) and locus-specific branch length (LSBL). By applying a top 1% threshold for both parameters, a total of 888 candidate selective windows were identified, harbouring 1571 genes. Secondly, the investigation of regions of homozygosity (ROH) was performed utilizing the PLINK software. In total, 25 genomic regions exhibiting a high frequency of ROHs were detected, leading to the identification of 1216 genes. Finally, the identified potential functional genes from candidate genomic regions were annotated, and several important candidate genes associated with reproductive traits (, , , , , , , ) and meat quality traits (, , , , , , , , , ) were identified. The findings of this study provide valuable insights into the genetic basis of economic traits in Large White pigs and may have potential use in future pig breeding programs.
大白猪在中国被广泛用于其生长迅速和瘦肉比例高的显著特点。猪的经济性状，包括繁殖和肉质性状，在生猪生产中起着至关重要的作用。本研究以三个不同遗传背景的大白猪群体（500 头加拿大系、295 头丹麦系和 1500 头美系）的 2295 个个体为研究对象，采用 GeneSeek 50K GGP 猪 HD 基因芯片对三个猪群体进行基因分型。首先，利用成对固定指数（F）和基因座特异性分支长度（LSBL）识别基因组选择特征区域。通过对两个参数应用 1%的阈值，共鉴定出 888 个候选选择窗口，包含 1571 个基因。其次，利用 PLINK 软件对同源区域（ROH）进行了调查。共检测到 25 个具有高 ROH 频率的基因组区域，鉴定出 1216 个基因。最后，对候选基因组区域的潜在功能基因进行注释，鉴定出几个与繁殖性状（、、、、、、）和肉质性状（、、、、、、、、、）相关的重要候选基因。本研究为大白猪经济性状的遗传基础提供了有价值的见解，可能对未来的猪育种计划具有潜在的应用价值。
