Journal
JOURNAL OF INTEGRATIVE AGRICULTURE
Volume 13, Issue 12, Pages 2721-2730Publisher
ELSEVIER SCI LTD
DOI: 10.1016/S2095-3119(14)60787-5
Keywords
genome-wide association study (GWAS); carcass trait; HMGA1 gene; organ weight; pig
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Funding
- Agricultural Science and Technology Innovation Program, China [ASTIP-IAS02]
- National Key Technology R&D Program of China [2011BAD28B01]
- National Natural Science Foundation of China [31201781]
- Earmarked Fund for Modem Agro-industry Technology Research System, National Technology Program of China [2011ZX08006-003]
- Chinese Academy of Agricultural Sciences Foundation [2011cj-5, 2012ZL069, 2014ywf-yb-8]
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Porcine carcass traits and organ weights have important economic roles in the swine industry. A total of 576 animals from a Large WhitexMinzhu 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=6.80x10(-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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