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| Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population |
| LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian |
1、Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation, Ministry of Agriculture/Institute of Animal Science, Chinese
Academy of Agricultural Sciences, Beijing 100193, P.R.China
2、Jilin Academy of Agricultural Sciences, Changchun 130033, P.R.China |
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摘要 Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, specifically, backfat thickness (6-7 libs), carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study (GWAS) was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms (SNPs) (with the most significant SNP being MARC0033464, P value=6.80×10-13) were located in a 9.76-Mb (31.24-41.00 Mb) region on SSC7 and were found to be significantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most significant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in this candidate linkage disequilibrium (LD) interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.
Abstract Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large White×Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip and were phenotyped for 10 traits, specifically, backfat thickness (6-7 libs), carcass length, carcass weight, foot weight, head weight, heart weight, leaf fat weight, liver weight, lung weight and slaughter body weight. The genome-wide association study (GWAS) was assessed by Genome Wide Rapid Association using the mixed model and regression-genomic control approach. A total of 31 single nucleotide polymorphisms (SNPs) (with the most significant SNP being MARC0033464, P value=6.80×10-13) were located in a 9.76-Mb (31.24-41.00 Mb) region on SSC7 and were found to be significantly associated with one or more carcass traits and organ weights. High percentage of phenotypic variance explanation was observed for each trait ranging from 31.21 to 67.42%. Linkage analysis revealed one haplotype block of 495 kb, in which the most significant SNP being MARC0033464 was contained, on SSC7 at complete linkage disequilibrium. Annotation of the pig reference genome suggested 6 genes (GRM4, HMGA1, NUDT3, RPS10, SPDEF and PACSIN1) in this candidate linkage disequilibrium (LD) interval. Functional analysis indicated that the HMGA1 gene presents the prime biological candidate for carcass traits and organ weights in pig, with potential application in breeding programs.
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Received: 10 February 2014
Accepted:
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| Fund: This research was supported by the Agricultural Science and Technology Innovation Program, China (ASTIPIAS02), the National Key Technology R&D Program of China (2011BAD28B01), the National Natural Science Foundation of China (31201781), the Earmarked Fund for Modern Agroindustry Technology Research System, National Technology Program of China (2011ZX08006-003) and the Chinese Academy of Agricultural Sciences Foundation (2011cj-5, 2012ZL069 and 2014ywf-yb-8). |
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Corresponding Authors:
WANG Li-xian, Tel: +86-10-62816011, Fax: +86-10-62818771, E-mail: iaswlx@263.net; ZHANG Longchao,Tel: +86-10-62816011, E-mail: lczhang@iascaas.net.cn
E-mail: iaswlx@263.net; lczhang@iascaas.net.cn
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| About author: LIU Xin, E-mail: firstliuxin@163.com |
Cite this article:
LIU Xin, WANG Li-gang, LIANG Jing, YAN Hua, ZHAO Ke-bin, LI Na, ZHANG Long-chao, WANGLi-xian .
2014.
Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population. Journal of Integrative Agriculture, 13(12): 2721-2730.
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