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. (Key Words : Single Nucleotide Polymorphism, Whole Genome Association, Carcass Traits, Hanwoo)
Highlights
Quantitative trait loci (QTL) mapping studies have been extensively performed and more than two thousand QTL for traits of economic importance have previously been reported in cattle
The number of reports and of the QTL for growth and carcass quality traits that have been detected in Hanwoo in the last two decades have been very limited, i.e. less than 20 QTL for a trait in the 20 publications because most of the QTL mapping approaches were based on candidate genes such that the categories of QTL to be detected were restricted within pre-chosen candidate genes with given physiological functions
SNPs in 29 The steers from Gyeongbuk produced heavier, fatter, autosomes were chosen, and any SNP was removed based and more marbled carcasses with larger muscle area, on the following criteria: i) the number of genotype group is because the steers were fed more than six months longer one or none, ii) than those in Seosan
Summary
Quantitative trait loci (QTL) mapping studies have been extensively performed and more than two thousand QTL for traits of economic importance have previously been reported in cattle (www.animalgenome.org). High throughput technologies such as the development of bovine SNP chips enabled the genotyping of large amount of SNPs, e.g. the bovine 50k Illumina Infinium assay, which would enable genome-wide association (WGA) mapping to detect many QTL with high mapping resolution up to 1 or 2 Mb confidence region for a QTL position (Sellner et al, 2007; van Tassell et al, 2008; Sherman et al, 2010) This WGA method would take the place of the conventional QTL mapping approach based on linkage mapping using microsatellite markers, which is characterized as a mapping method with low mapping density and limited power for QTL detection (Sellner et al, 2007). The number of reports and of the QTL for growth and carcass quality traits that have been detected in Hanwoo in the last two decades have been very limited, i.e. less than 20 QTL for a trait in the 20 publications (data not shown) because most of the QTL mapping approaches were based on candidate genes such that the categories of QTL to be detected were restricted within pre-chosen candidate genes with given physiological functions
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