Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population

SIMPLE SUMMARY: In this study, a genome-wide association study (GWAS) was conducted on 1518 Duroc × (Landrace × Yorkshire) commercial pigs to investigate the genetic basis of body conformation traits. The traits analyzed included body length, body height, chest circumference, abdominal circumference, and waist circumference. The researchers used two statistical models, a mixed linear model (MLM) and a fixed and random model circulating probability unification (FarmCPU), to identify significant genetic variants associated with these traits. A total of 60 significant single nucleotide polymorphisms (SNPs) were discovered in the crossbred pigs. Furthermore, the researchers identified a novel significant quantitative trait locus (QTL) on chromosome SSC7 (Sus scrofa chromosome 7) that was specifically associated with waist circumference. These findings contribute to our understanding of the genetic mechanisms underlying body conformation traits in crossbred commercial pigs. ABSTRACT: Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.