- Volume 24 Issue 11
DOI QR Code
Identification of Superior Single Nucleotide Polymorphisms (SNP) Combinations Related to Economic Traits by Genotype Matrix Mapping (GMM) in Hanwoo (Korean Cattle)
- Lee, Yoon-Seok (Charmpoom Hanwoo Research Institution) ;
- Oh, Dong-Yep (School of Biotechnology, Yeungnam University) ;
- Lee, Yong-Won (Department of Statistics, Yeungnam University) ;
- Yeo, Jung-Sou (School of Biotechnology, Yeungnam University) ;
- Lee, Jea-Young (Department of Statistics, Yeungnam University)
- Received : 2011.04.15
- Accepted : 2011.08.19
- Published : 2011.11.01
It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.
- Casas, E., S. N. White, T. L. Wheeler, S. D. Shackelford, M. Koohmaraie, D. G. Riley, C. C. Chase, Jr., D. D. Johnson and T. P. L. Smith. 2006. Effect of calpastatin and u-calpain markers in beef cattle on tenderness traits. J. Anim. Sci. 84:520-525.
- Chung, Y. J., S. Y. Lee and T. S. Park. 2006. Multifactor dimensionality reduction in the presence of missing observations. Journal of Korea Statistical Society, Proceedings of the Autumn Conference, Korea. pp. 31-36.
- Churchill, G. A. and R. W. Deorge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.
- Efron, B. and R. Tibshirani. 1993. An Introduction to the bootstrap. Champman & Hall/CRC.
- Good, P. 2000. Permutation test: a practical guide to resampling method for testing hypotheses. Springer-Verlag Berlin and Heidelberg GmbH & Co., New York.
- Henderson, C. R. 1976. A Simple method for computing the inverse of a numerator relationship matrix used in predicting of breeding values. Biometrics 32:69-83. https://doi.org/10.2307/2529339
- Lee, J. Y., J. C. Kwon and J. J. Kim. 2008. Multifactor dimensionality reduction (MDR) analysis to detect single nucleotide polymorphisms associated with a carcass trait in a Hanwoo population. Asian- Aust. J. Anim. Sci. 21(6):784-788. https://doi.org/10.5713/ajas.2008.70645
- Lee, J. Y. and J. Y. Goh. 2009. Selection of the principal genotype with genetic algorithm. Journal of the Korean Data & Information Science Society. 20(4):639-647.
- Lee, J. Y. and H. G. Lee. 2009. Multifactor dimensionality reduction (MDR) analysis by dummy variables. The Korean Journal of Applied Statistics. 22(2):435-442. https://doi.org/10.5351/KJAS.2009.22.2.435
- Lee, J. Y., Y. W. Lee and J. S. Yeo. 2007. Bootstrapping of Hanwoo chromosome17 based on BMS1167 microsatellite locus. Journal of the Korean Data & Information Science Society. 18(1):175-184.
- Lee, Y. S. 2009. Study on the identification of candidate genes and their haplotypes that are associated with growth and carcass traits in the QTL region of BTA6 in a Hanwoo population, Ph. D. Thesis, University of Yeungnam, Gyeongbuk, Korea.
- Lee, Y. S., J. H. Lee, J. Y. Lee, J. J. Kim, H. S. Park and J. S. Yeo. 2008. Identification of candidate SNP (single nucleotide polymorphism) for growth and carcass traits related to QTL on chromosome 6 in Hanwoo (Korean cattle). Asian-Aust. J. Anim. Sci. 21(12):1703-1709. https://doi.org/10.5713/ajas.2008.80223
- Lee, Y. S., D. Y. Oh, J. J. Kim, J. H. Lee, H. S. Park and J. S. Yeo. 2010. A single nucleotide polymorphism in LOC534614 as an unknown gene associated with body weight and cold carcass weight in Hanwoo (Korean cattle). Asian-Aust. J. Anim. Sci. 23(12):1543-1551. https://doi.org/10.5713/ajas.2010.10113
- Ritchie, M. D., L. W. Hahn, N. Roodi, L. R. Bailey, W. D. Dupont, F. F. Parl and J. H. Moore. 2001. Multifactor-dimensionality reduction reveals high-order interactions among estrogenmetabolism genes in sporadic breast cancer. Am. J. Hum. Genet. 69(1):138-147. https://doi.org/10.1086/321276
- Sachiko, I., N. Akihiro and T. Satoshi. 2007. Genotype matrix mapping:searching for quantitative trait loci interactions in genetic variation in complex trait. DNA Res. 14:217-225. https://doi.org/10.1093/dnares/dsm020
- Sambrook, J. and D. W. Russell. 2001. Molecular cloning: A laboratory manual. Vol. 1. 3rd edition: Cold Spring Harbor. New York. pp. 6.4-6.12.
- Snelling, W. M., E. Casas, R. T. Stone, J. W. Keele, G. P. Harhay, G. L. Benett and T. P. L. Smith. 2005. Linkage mapping bovine EST-based SNP. BMC Genomics 6(1):74-84. https://doi.org/10.1186/1471-2164-6-74
- Vreeland, W. N., R. J. Meagher and A. E. Barron. 2002. Multiplexed, highthroughput genotyping by single base extension and end labeled free solution electrophoresis. Anal. Chem. 74:4328-4333. https://doi.org/10.1021/ac0258094