genome-wide association study identifies loci for body composition and structural soundness traits in pigs全基因组关联研究识别位点在猪的身体成分和结构稳定性特征.pdfVIP

Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs 1,2 1 1 1 1 1 Bin Fan , Suneel K. Onteru , Zhi-Qiang Du , Dorian J. Garrick , Kenneth J. Stalder , Max F. Rothschild * 1 Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America, 2 Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People’s Republic of China Abstract Background: The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs. Methodology/Principal Findings: Using Illumina’s PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body si