Zhang Ben, Hu Panyang, Wu Xiangzhe, Zheng Lixiang, Li Xiuling, Wang Kejun, Han Xuelei, Wang Yining, Hong Yuan, Qiao Ruimin
College of Animal Science, Henan Agricultural University, Zhengzhou, 450046, China.
College of Animal Science and Technology, FuJian Vocational College of Agriculture, FuZhou, 350119, China.
Sci Rep. 2025 Mar 21;15(1):9793. doi: 10.1038/s41598-025-88583-3.
To study the key genes that influence the body size of local pig breeds in China. Genome-wide SNP chip data from a total of 129 pigs from eight breeds, consisting of four large body size breeds (MZ, HT, ST, RC) and four small body size breeds (XI, BX, WZ, DN) were analyzed. Principal Component Analysis (PCA) was employed to assess the genetic clustering of the eight breeds. Fst and XP-CLR were used to detect selective signals between the large ans small body size breeds groups. The PCA results indicated a clear clustering of small breeds and a dispersion distribution among large breeds. Fst and XP-CLR identified 142 overlapping regions within a 500 kb up & down stream of significant loci. These regions encompassed 520 annotated genes, which were enriched in 34 biological pathways. Gene network analysis highlighted nine key genes, of which five (NPR3, TNFSF11, TBC1D7, FGF2, IGF1R) are known to be associated with bone growth and body size traits in animals. Additionally, four novel candidate genes (IKBKB, SFRP1, LRP6, SPRY1) were identified that might be related to pig body size. Our findings provide a theoretical basis for further revealing the genetic mechanism of pig body size traits.
为研究影响中国地方猪种体型大小的关键基因。分析了来自8个猪种共129头猪的全基因组SNP芯片数据，其中包括4个大体型猪种（民猪、淮猪、苏太猪、荣昌猪）和4个小体型猪种（香猪、八眉猪、五指山猪、滇南小耳猪）。采用主成分分析（PCA）评估这8个猪种的遗传聚类情况。利用Fst和XP-CLR检测大体型和小体型猪种组之间的选择信号。PCA结果表明小体型猪种明显聚类，大体型猪种呈分散分布。Fst和XP-CLR在显著位点上下游500 kb范围内鉴定出142个重叠区域。这些区域包含520个注释基因，富集于34条生物学通路。基因网络分析突出了9个关键基因，其中5个（NPR3、TNFSF11、TBC1D7、FGF2、IGF1R）已知与动物骨骼生长和体型性状相关。此外，还鉴定出4个可能与猪体型相关的新候选基因（IKBKB、SFRP1、LRP6、SPRY1）。我们的研究结果为进一步揭示猪体型性状的遗传机制提供了理论依据。
