AUTHOR=Zhang Hui , Zhuang Zhanwei , Yang Ming , Ding Rongrong , Quan Jianping , Zhou Shenping , Gu Ting , Xu Zheng , Zheng Enqin , Cai Gengyuan , Yang Jie , Wu Zhenfang 

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

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.664343

DOI=10.3389/fgene.2021.664343

ISSN=1664-8021

ABSTRACT=<p>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 BMI<sub>CL</sub>, BMI<sub>BL</sub>, and BMI<sub>BH</sub>, 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 <italic>TNFAIP3</italic>, <italic>KDM4C</italic>, <italic>HSPG2</italic>, <italic>BMP2</italic>, <italic>PLCB4</italic>, and <italic>GRM5</italic>) were found to be associated with body weight and body conformation traits in pigs. Notably, the <italic>BMP2</italic> gene had pleiotropic effects on CL, BL, BH, BMI<sub>CL</sub>, and BMI<sub>BL</sub> 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.</p>