Identification of candidate genes associated with carcass component weights in commercial crossbred pigs through a combined GWAS approach

Abstract

In the pork industry chain, carcass cutting is crucial for enhancing the commercial value of pork carcasses. However, the genetic mechanisms underlying carcass component weights remain poorly understood. Here, we used a combined genome-wide association study (GWAS) approach that integrated single- and multi-locus models to map genetic markers and genes associated with the weights of seven carcass components in Duroc × Landrace × Yorkshire (DLY) pigs. As multi-locus GWAS captures more single nucleotide polymorphisms (SNPs) with large effects than single-locus GWAS, the combined GWAS approach detected more SNPs than using the single-locus model alone. We identified 177 nonredundant SNPs associated with these traits in 526 DLY pigs, including boneless butt shoulder (BBS), boneless picnic shoulder (BPS), boneless leg (BL), belly (BELLY), front fat (FF), rear fat (RF) and skin-on whole loin (SLOIN). Using single-locus GWAS, we identified a quantitative trait locus (QTL) for SLOIN on Sus scrofa chromosome 15 (SSC15). Notably, a single SNP (ASGA0069883) in the proximity of this QTL was consistently detected by all GWAS models (one single-locus and four multi-locus models) and explained more than 4% of the phenotypic variance. Our findings suggest that the involved gene, MYO3B, is proposed to be a strong candidate for SLOIN. Further analysis also identified several candidate genes related to BBS (PPP3CA and CPEB4), BPS (ECH1), FF (CACNB2 and ZNF217), BELLY (FGFRL1), BL (CHST11), and RF (LRRK2). The identified SNPs can be used as molecular markers for the genetic improvement of pork carcasses in the molecular-guided breeding of modern commercial pigs.

Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle

“…However, the quantitative traits of beef cattle are co-regulated by multiple genes, which are harder to find. GWAS provides a good example of screening for dominant genes associated with quantitative traits in livestock and poultry, such as pigs [24,25], chickens [26][27][28], ducks [29], sheep [30,31], beef cattle [32,33], and cows [34][35][36]. Moreover, GWASs of beef cattle mainly assess growth traits [37], reproductive traits [38,39], and meat quality traits [40,41].…”

Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS

“…Carcass segmentation enables the separate sale of distinct parts, thereby enhancing the overall market value of the carcass and providing better economic benefits and market competitiveness for pork production [3,4]. In the Chinese market, tenderloin represents the highest-priced fresh meat [5,6], and customers particularly appreciate tenderloin for its attributes such as juiciness, low fat content, and high protein content [7,8].…”