Int J Biol Sci 2012; 8(4):580-595. doi:10.7150/ijbs.3614

Research Paper

Genome-Wide Association Analysis of Meat Quality Traits in a Porcine Large White × Minzhu Intercross Population

Weizhen Luo1*, Duxue Cheng1*, Shaokang Chen2*, Ligang Wang1, Yong Li1, Xiaojun Ma1, Xin Song3, Xin Liu1, Wen Li1, Jing Liang1, Hua Yan1, Kebin Zhao1, Chuduan Wang2✉, Lixian Wang1✉, Longchao Zhang1✉

1. Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193 Beijing, China.
2. College of Animal Science and Technology and State Key Laboratory of Agrobiotechnology, China Agricultural University, 100193 Beijing, China.
3. College of Veterinary Medicine, Sichuan Agricultural University, 625014 Ya'an, China.
* These authors contributed equally to this work.

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) License. See for full terms and conditions.
Luo W, Cheng D, Chen S, Wang L, Li Y, Ma X, Song X, Liu X, Li W, Liang J, Yan H, Zhao K, Wang C, Wang L, Zhang L. Genome-Wide Association Analysis of Meat Quality Traits in a Porcine Large White × Minzhu Intercross Population. Int J Biol Sci 2012; 8(4):580-595. doi:10.7150/ijbs.3614. Available from

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Pork quality is an economically important trait and one of the main selection criteria for breeding in the swine industry. In this genome-wide association study (GWAS), 455 pigs from a porcine Large White × Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for intramuscular fat content (IMF), marbling, moisture, color L*, color a*, color b* and color score in the longissimus muscle (LM). Association tests between each trait and the 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 9. A total of 45 SNPs showed significant association with one or multiple meat quality traits. Of the 45 SNPs, 36 were located on SSC12. These significantly associated SNPs aligned to or were in close approximation to previously reported quantitative trait loci (QTL) and some were located within introns of previously reported candidate genes. Two haplotype blocks ASGA0100525-ASGA0055225-ALGA0067099-MARC0004712-DIAS0000861, and ASGA0085522-H3GA0056170 were detected in the significant region. The first block contained the genes MYH1, MYH2 and MYH4. A SNP (ASGA0094812) within an intron of the USP43 gene was significantly associated with five meat quality traits. The present results effectively narrowed down the associated regions compared to previous QTL studies and revealed haplotypes and candidate genes on SSC12 for meat quality traits in pigs.

Keywords: F2 design, genome-wide association study, meat quality trait, pig, SNP.