title: Genomic regions affecting backfat thickness and cannon bone circumference identified by genome-wide association study in a Duroc pig population.
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.
authors.affiliation: JATAFF-Institute, Japan Association for Techno-Inovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan. okumura@jataff.jp
authors.forename: Naohiko
authors.initials: N
authors.lastname: Okumura
authors.forename: Toshimi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Takeshi
authors.initials: T
authors.lastname: Hayashi
authors.forename: Kensuke
authors.initials: K
authors.lastname: Hirose
authors.forename: Kazuo
authors.initials: K
authors.lastname: Fukawa
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Itou
authors.forename: Hirohide
authors.initials: H
authors.lastname: Uenishi
authors.forename: Satoshi
authors.initials: S
authors.lastname: Mikawa
authors.forename: Takashi
authors.initials: T
authors.lastname: Awata
mesh_terms: D000273:Adipose Tissue / Q000254:growth & development; D000818:Animals; D001947:Breeding; D002874:Chromosome Mapping / Q000662:veterinary; D020869:Gene Expression Profiling / Q000662:veterinary; D005819:Genetic Markers; D016678:Genome / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000662:veterinary*; D006239:Haplotypes; D007867:Leg Bones / Q000254:growth & development; D016014:Linear Models; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000662:veterinary; D013552:Swine / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D005819:Genetic Markers
keywords: SSC6; SSC7; closed nucleus herd of Duroc; nine traits; porcineSNP60 BeadChip