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

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.

Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)

“…Wu et al measured 29 body conformation traits of 1 314 Chinese Holstein cattle and discovered 59 genome-wide significant SNPs and several candidate genes (DARC, GAS1, MTPN, HTR2A, ZNF521, PDIA6, and TMEM130) [47]. In pigs, 60 significant genetic variants on chromosome 7 and their annotated genes (such as INTS10, KIRREL3, SOX21, BMP2, and MAP4K3) were associated with body conformation traits [48]. Zhang et al identified 82 SNPs and candidate genes such as BMP2, TNFAIP3, KDM4C, and HSPG2, which were significantly associated with body conformation traits due to their role in growth and bone development [49].…”