Genome-Wide Association Study for Somatic Skeletal Traits in Duroc × (Landrace × Yorkshire) Pigs.

Simple Summary: In China, soup is widely perceived as a nutritional tonic, and pig bones are a primary ingredient in its preparation. Consequently, the market price of pig bones, even when of equal weight, surpasses that of pork, particularly in southern China. Despite this economic significance, the trait of pig bone weight has not been a focus in pig breeding programs due to the inherent challenges associated with in vivo measurement. The genetic selection method stands out as an effective approach for targeting the trait of pig bone weight in pig breeding. Recognizing its significance, our research endeavors have delved into molecular genetics to gain insights into the genetic aspects of pig bone weight. In order to unravel the genetic underpinnings of specific traits, we employed bioinformatics methodologies to conduct an analysis on three-way hybrid commercial pigs. Our primary objective was to identify genetic markers and genes associated with four distinct bone weight traits. Utilizing genome-wide association studies (GWAS), we scrutinized a population comprising 571 three-way hybrid commercial pigs to pinpoint single nucleotide polymorphisms (SNPs) and genes linked to these traits. The results identified twelve genes, namely OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9, that were related to four bone weight traits. This comprehensive genetic insight provides valuable information on the mechanisms governing bone growth and weight in the context of pig breeding. The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits. [ABSTRACT FROM AUTHOR]