Abstract
The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.
Highlights
In recent decades, pork has made up a large share of total worldwide meat production to accommodate growing human consumption
We identified 82 singlenucleotide polymorphism (SNP) associated with seven body conformation traits in DLY pigs using GEMMA-based genome-wide association study (GWAS) and FarmCPU-based GWAS
We identified three genomic regions and several genes related to body conformation traits in pigs
Summary
Pork has made up a large share of total worldwide meat production to accommodate growing human consumption. Growth and body conformation traits (such as body height and length) are economic traits which are moderately to highly important in pig production. Body height (BH) and body length (BL) are associated with meat production and were typical polygenic quantitative traits. An SNP (EU169095: g.40395T > G) within the PPARδ gene was found to be associated with the carcass length in a Large White × Meishan resource pig population (Xu et al, 2013). The number of thoracolumbar vertebrae can affect carcass length, which is an economically important trait in pig production. Rohrer and Keele (1998) (Rohrer and Keele, 1998) and Wada et al (2000) (Wada et al, 2000) reported QTL for carcass length and vertebra number on the corresponding region of SSC 1. Previous findings have provided a certain number of molecular markers to help elucidate the genetic basis of swine body conformation traits, inadequacies and challenges remain when elucidating the biological mechanisms of the complex traits
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