首页|Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population

Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population

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  • 国家科技期刊平台
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Rib eye muscle area (REMA) is an economicaly important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Ilumina PorcineSNP60 BeadChip containing 62163 single nucleotide polymorphisms (SNPs) was used to genotype 557 pigs from a porcine Large White×Minzhu intercross population. The REMA (at the 5th–6th, 10th–11th and the last ribs) was measured after slaughtered at the age of (240±7) d for each animal. Association tests between REMA trait and SNPs were performedvia the Genome-Wide Rapid Asso-ciation using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented usingSus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed signiifcant association with REMA at the last rib at the chromosome-wide signiifcance level. None of the SNPs of REMA at the 5th–6th rib and only a few numbers of the SNPs of REMA at the 10th–11th ribs were found in this study. The Haploview V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with REMA at the last rib. A linkage analysis revealed that 4 haplotype blocks contained 4, 4, 2, and 4 SNPs, respectively. Annotations from pig reference genome suggested 2 genes (NOS2,NLK) in block 1 (266 kb), one gene (TMIGD1) in block 2 (348 kb), and one gene (MAP2K4) in block 3 (453 kb). A functional analysis indicated thatMYH3andMYH13 genes are the potential genes controling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred thatNOS2 and NLK genes maybe the main genes of REMA at the last ribs.

genome-wide association studyrib eye muscle areapigSNP

GUO Yun-yan、ZHANG Long-chao、WANG Li-xian、LIU Wen-zhong

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Colege of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, P.R.China

Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China

This research was supported by the Agricultural Science and Technology Innovation Program, ChinaNational Key Technology R&D Program of ChinaNational Natural Science Foundation of ChinaNational High Technology Re-search and Development Program of ChinaEarmarked Fund for Modern Agro-industry Tech-nology Research System of ChinaChinese Academy of Agricultural Sciences Foundation

ASTIP-IAS022011BAD28B01312017812011ZX08006-0032011cj-5

2015

10.1016/S2095-3119(14)60981-3

农业科学学报(英文)
中国农业科学院农业信息研究所

农业科学学报(英文)

CSTPCDCSCDSCI
影响因子：0.576
ISSN：2095-3119
年,卷(期)：2015.(12)
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