title: A SNP Harvester Analysis to Better Detect SNPs of CCDC158 Gene That Are Associated with Carcass Quality Traits in Hanwoo.
abstract: The purpose of this study was to investigate interaction effects of genes using a Harvester method. A sample of Korean cattle, Hanwoo (n = 476) was chosen from the National Livestock Research Institute of Korea that were sired by 50 Korean proven bulls. The steers were born between the spring of 1998 and the autumn of 2002 and reared under a progeny-testing program at the Daekwanryeong and Namwon branches of NLRI. The steers were slaughtered at approximately 24 months of age and carcass quality traits were measured. A SNP Harvester method was applied with a support vector machine (SVM) to detect significant SNPs in the CCDC158 gene and interaction effects between the SNPs that were associated with average daily gains, cold carcass weight, longissimus dorsi muscle area, and marbling scores. The statistical significance of the major SNP combinations was evaluated with x (2)-statistics. The genotype combinations of three SNPs, g.34425+102 A>T(AA), g.4102636T>G(GT), and g.11614+19G>T(GG) had a greater effect than the rest of SNP combinations, e.g. 0.82 vs. 0.75 kg, 343 vs. 314 kg, 80.4 vs 74.7 cm(2), and 7.35 vs. 5.01, for the four respective traits (p<0.001). Also, the estimates were greater compared with single SNPs analyzed (the greatest estimates were 0.76 kg, 320 kg, 75.5 cm(2), and 5.31, respectively). This result suggests that the SNP Harvester method is a good option when multiple SNPs and interaction effects are tested. The significant SNPs could be applied to improve meat quality of Hanwoo via marker-assisted selection.
authors: School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea.
authors: Jea-Young
authors: JY
authors: Lee
authors: School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea.
authors: Jong-Hyeong
authors: JH
authors: Lee
authors: School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea.
authors: Jung-Sou
authors: JS
authors: Yeo
authors: School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Korea.
authors: Jong-Joo
authors: JJ
authors: Kim
keywords: CCDC158 Gene; Hanwoo; Harvester Method; Single Nucleotide Polymorphisms