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Genomic regions affecting backfat thickness and cannon bone circumference identified by genome‐wide association study in a D uroc pig population
Author(s) -
Okumura Naohiko,
Matsumoto Toshimi,
Hayashi Takeshi,
Hirose Kensuke,
Fukawa Kazuo,
Itou Tetsuya,
Uenishi Hirohide,
Mikawa Satoshi,
Awata Takashi
Publication year - 2013
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12018
Subject(s) - biology , single nucleotide polymorphism , genetics , circumference , snp , quantitative trait locus , population , bonferroni correction , genome wide association study , haplotype , genetic association , gene , genotype , statistics , mathematics , geometry , demography , sociology
Summary We performed a genome‐wide association study using the porcine 60 K SNP array to detect QTL regions for nine traits in a three‐generational D uroc 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 SSC 6 for backfat thickness ( BFT ) and on SSC 7 for cannon bone circumference ( CANNON ), with a genome‐wide significance of P < 0.01 after B onferroni 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 SNP s, 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 SSC 7 region with strong LD can be used to select for the CANNON trait in our resource family.