A Restricted Partition Method to Detect Single Nucleotide Polymorphisms for a Carcass Trait in Hanwoo

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Lee, Ji-Hong;Kim, Dong-Chul;Kim, Jong-Joo;Lee, Jea-Young

  • 투고 : 2011.05.26
  • 심사 : 2011.08.19
  • 발행 : 2011.11.01

초록

The purpose of this study was to detect SNPs that were responsible for a carcass trait in Hanwoo populations. A non-parametric model applying a restricted partition method (RPM) was used, which exploited a partitioning algorithm considering statistical criteria for multiple comparison testing. Phenotypic and genotypic data were obtained from the Hanwoo Improvement Center, National Agricultural Cooperation Federation, Korea, in which the pedigree structure comprised 229 steers from 16 paternal half-sib proven sires that were born in Namwon or Daegwanryong livestock testing station between spring of 2002 and fall of 2003. A carcass trait, longissimus dorsi muscle area for each steer was measured after slaughter at approximately 722 days. Three SNPs (19_1, 18_4 and 28_2) near the microsatellite marker ILSTS035 on BTA6, around which the quantitative trait loci (QTL) for meat quality were previously detected, were used in this study. The RPM analyses resulted in two significant interaction effects between SNPs (19_1 and 18_4) and (19_1 and 28_2) at ${\alpha}$ = 0.05 level. However, under a general linear (parametric) model no interaction effect between any pair of the three SNPs was detected, while only one main effect for SNP19_1 was found for the trait. Also, under another non-parametric model using a multifactor dimensionality reduction (MDR) method, only one interaction effect of the two SNPs (19_1 and 28_2) explained the trait significantly better than the parametric model with the main effect of SNP19_1. Our results suggest that RPM is a good alternative to model choices that can find associations of the interaction effects of multiple SNPs for quantitative traits in livestock species.

키워드

SNP;Hanwoo;Carcass Trait;Restricted Partition Method

참고문헌

  1. Alam, M., Y. M. Lee, B.-L. Park, J.-H. Kim, S.-S. Lee, H.-D. Shin, K.-S. Kim, N.-S. Kim and J.-J. Kim. 2011. A whole genome association study to detect single nucleotide polymorphisms for body conformation traits in a Hanwoo population. Asian-Aust. J. Anim. Sci. 24(3):322-329. https://doi.org/10.5713/ajas.2011.11012
  2. Barendse, W., A. Reverter, R. J. Bunch, B. E. Harrison, W. Barris and M. B. Thomas. 2007. A validated whole-genome association study of efficient food conversion in cattle. Genetics 176:1893-1905. https://doi.org/10.1534/genetics.107.072637
  3. Bastone, L., M. Reilly, D. J. Rader and A. S. Foulkes. 2004. MDR and PRP: a comparison of methods for high-order genotypephenotype associations. Hum. Hered. 58:82-92. https://doi.org/10.1159/000083029
  4. Culverhouse, R., T. Klein and W. Shannon. 2004. Detecting epistatic interactions contributing to quantitative traits. Genet. Epidemiol. 27:141-152. https://doi.org/10.1002/gepi.20006
  5. Games, P. A. and J. F. Howell. 1976. Pairwise multiple comparison procedures with unequal n's and/or variances. J. Educ. Behav. Stat. 1:113-125. https://doi.org/10.3102/10769986001002113
  6. Goddard, M. E. and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programs. Nat. Rev. Genet. 10:381-391. https://doi.org/10.1038/nrg2575
  7. Good, P. 1994. Permutation test: a practical guide to resampling for testing hypotheses. Springer, New York.
  8. 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
  9. Lee, J.-Y., J. C. Kwon and J.-J. Kim. 2008a. Multifactor dimensionality reduction (MDR) analysis to detect single nucleotide polymorphism 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
  10. Lee, Y. S., J. H. Lee, J. Y. Lee, J. J. Kim, H. S. Park and J. S. Yeo. 2008b. Identification of candidate SNP 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
  11. Lee, Y.-M., C.-M. Han, Y. Li, J.-J. Lee, L. H. Kim, J.-H. Kim, D.-I. Kim, S.-S. Lee, B.-L. Park, H.-D. Shin, K.-S. Kim, N.-S. Kim and J.-J. Kim. 2010. A whole genome association study to detect single nucleotide polymorphism for carcass traits in Hanwoo population. Asian-Aust. J. Anim. Sci. 23(4):417-424. https://doi.org/10.5713/ajas.2010.10019
  12. Ritchie, M. D., L. Hahn, W. 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
  13. Yeo, J. S., J. Y. Lee and J. W. Kim. 2004. DNN marker mining of ILST035 microsatellite locus on chromosome 6 of Hanwoo cattle. J. Genet. 83:245-250. https://doi.org/10.1007/BF02717893