Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

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.

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations

“…With the development of DNA sequencing technology and the reduction in the cost of sequencing and genotyping, whole-genome molecular markers provide powerful tools for studying animal genomes. Tens of thousands of single nucleotide polymorphism (SNP) markers covering the whole pig genome have facilitated the use of molecular breeding strategies such as genomic selection (GS) ( Uemoto et al, 2017 ) and genome-wide association study (GWAS) ( Zhang et al, 2021 ), which has rapidly improved the breeding process of Duroc pigs. In addition, genomic data was utilized to explore selection signatures and reveal potential genetic mechanisms underlying the domestication and evolution of Duroc pigs ( Kim et al, 2015 ; Zhang et al, 2020 ).…”

Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs

“…Association tests in FarmCPU are validated by FEM with the same computing efficiency as GLM, while the statistical power surpasses that of MLM at the same level of type I errors. In much research, FarmCPU could detect more significant signals than MLM and GLM could in our research [ 4 , 17 , 30 ].…”

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

“…Furthermore, we identified one novel QTL, which was located in a 7.10-Mb region (25.22–32.32 Mb) on SSC7 significantly associated with BL ( Table S7 ). In several previous studies, some significant SNPs associated with BL were also found in the 7.10-Mb region in different pig populations [ 2 , 13 , 16 , 47 ]. Among all SNPs detected, 18 SNPs were located in previously reported QTL regions for growth traits in pigs.…”

“…Pork is a popular form of animal protein and is now one of the main sources of human dietary protein. Growth and body size traits, including live backfat thickness (LBT), average daily gain (ADG), body length (BL), body height (BH), back height (BAH), chest circumference (CC), chest depth (CD), and rump circumference (RC), are vital economic traits in the swine industry and have a crucial effect on pig production [ 1 , 2 , 3 ]. Among them, LBT and ADG in different stages are vital indicators of the growth rate of pigs due to their significant impact on production efficiency [ 1 ].…”