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| Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population |
| GUO Yun-yan, ZHANG Long-chao, WANG Li-xian, LIU Wen-zhong |
1、College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, P.R.China
2、Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China |
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摘要 Rib eye muscle area (REMA) is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Illumina PorcineSNP60 BeadChip containing 62 163 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 performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance 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 that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.
Abstract Rib eye muscle area (REMA) is an economically important trait and one of the main selection criteria for breeding in the swine industry. In the genome-wide association study (GWAS), the Illumina PorcineSNP60 BeadChip containing 62 163 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 performed via the Genome-Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. From the Ensembl porcine database, SNP annotation was implemented using Sus scrofa Build 10.2. Thirty-three SNPs on SSC12 and 3 SNPs on SSC2 showed significant association with REMA at the last rib at the chromosome-wide significance 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 that MYH3 and MYH13 genes are the potential genes controlling REMA at the last rib. We screened several candidate intervals and genes based on the SNPs location and the gene function, and inferred that NOS2 and NLK genes maybe the main genes of REMA at the last ribs.
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Received: 31 December 2014
Accepted:
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| Fund: This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIP-IAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundationand Development Program of China (2011ZX08006- 003), the Earmarked Fund for Modern Agro-industry Technology Research System of China, and Chinese Academy of Agricultural Sciences Foundation (2011cj-5). |
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Corresponding Authors:
WANG Li-xian, E-mail: iaswlx@263.net;LIU Wen-zhong, E-mail: tglwzyc@163.com
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| About author: GUO Yun-yan, E-mail: xmsyxbg@163.com; |
Cite this article:
GUO Yun-yan, ZHANG Long-chao, WANG Li-xian, LIU Wen-zhong.
2015.
Genome-wide association study for rib eye muscle area in a Large White×Minzhu F2 pig resource population. Journal of Integrative Agriculture, 14(12): 2590-2597.
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