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Anim Genet. 2013 Aug;44(4):454-7. doi: 10.1111/age.12018. Epub 2012 Dec 12.

Genomic regions affecting backfat thickness and cannon bone circumference identified by genome-wide association study in a Duroc pig population.

Author information

1
JATAFF-Institute, Japan Association for Techno-Inovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan. okumura@jataff.jp

Abstract

We performed a genome-wide association study using the porcine 60K SNP array to detect QTL regions for nine traits in a three-generational Duroc samples (n = 651), viz. generations 1, 2 and 3 from a population selected over five generations using a closed nucleus breeding scheme. We applied a linear mixed model for association mapping to detect SNP effects, adjusting for fixed effects (sex and season) and random polygenic effects (reflecting genetic relatedness), and derived a likelihood ratio statistic for each SNP using the efficient mixed-model association method. We detected a region on SSC6 for backfat thickness (BFT) and on SSC7 for cannon bone circumference (CANNON), with a genome-wide significance of P < 0.01 after Bonferroni correction. These regions had been detected previously in other pig populations. Six genes are located in the BFT-associated region, while the CANNON-associated region includes 66 genes. In the future, significantly associated SNPs, derived by sequencing the coding regions of the six genes in the BFT region, can be used in marker-assisted selection of BFT, whereas haplotypes constructed from the SSC7 region with strong LD can be used to select for the CANNON trait in our resource family.

KEYWORDS:

SSC6; SSC7; closed nucleus herd of Duroc; nine traits; porcineSNP60 BeadChip

PMID:
23777416
DOI:
10.1111/age.12018
[Indexed for MEDLINE]

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