A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations

Title
A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations
Author(s)
이윤미[이윤미]한찬명리이이중재[이중재]김령호[김령호]김진호[김진호]김덕임[김덕임]이성수[이성수]박병래[박병래]신형두[신형두]김관석[김관석]김내수[김내수]김종주
Keywords
BOS-TAURUS; CATTLE; LOCI; GROWTH; IDENTIFICATION; DISCOVERY; EVOLUTION
Issue Date
201004
Publisher
ASIAN-AUSTRALASIAN ASSOC ANIMAL PRODUCTION SOC
Citation
ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, v.23, no.4, pp.417 - 424
Abstract
The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.
URI
http://hdl.handle.net/YU.REPOSITORY/22647
ISSN
1011-2367
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공과대학 > 컴퓨터공학과 > Articles
생명공학부 > 생명공학부 > Articles
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