Mining of candidate genes related to body size in Chinese native pig breeds based on public data

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.