DOI QR코드

DOI QR Code

Prediction of genomic breeding values of carcass traits using whole genome SNP data in Hanwoo (Korean cattle)

한우에 있어서 유전체 육종가 추정

  • Received : 2012.08.09
  • Accepted : 2012.09.22
  • Published : 2012.09.30

Abstract

Genomic breeding value (GEBV) has recently become available in the beef cattle industry. Genomic selection methods are exceptionally valuable for selecting traits, such as marbling, that are difficult to measure until later in life. One method to utilize information from sparse marker panels is the Bayesian model selection method with RJMCMC. The accuracy of prediction varies between a multiple SNP model with RJMCMC (0.47 to 0.73) and a least squares method (0.11 to 0.41) when using SNP information, while the accuracy of prediction increases in the multiple SNP (0.56 to 0.90) and least square methods (0.21 to 0.63) when including a polygenic effect. In the multiple SNP model with RJMCMC model selection method, the accuracy ($r^2$) of GEBV for marbling predicted based only on SNP effects was 0.47, while the $r^2$ of GEBV predicted by SNP plus polygenic effect was 0.56. The accuracies of GEBV predicted using only SNP information were 0.62, 0.68 and 0.73 for CWT, EMA and BF, respectively. However, when polygenic effects were included, the accuracies of GEBV were increased to 0.89, 0.90 and 0.89 for CWT, EMA and BF, respectively. Our data demonstrate that SNP information alone is missing genetic variation information that contributes to phenotypes for carcass traits, and that polygenic effects compensate genetic variation that whole genome SNP data do not explain. Overall, the multiple SNP model with the RJMCMC model selection method provides a better prediction of GEBV than does the least squares method (single marker regression).

Keywords

References

  1. Fernando RL, Grossman M. 1989. Marker assisted selection using best linear unbiased prediction. Genetic Selection Evolution 21: 467-477. https://doi.org/10.1186/1297-9686-21-4-467
  2. Fernando RL, Garrick, DJ. 2008. GenSel-User manual for a portfolio of genomic selection related analyses. Animal Breeding and Genetics, Iowa State University, Ames. http://taurus.ansci.iastate.edu/gensel Accessed Apr. 21, 2009.
  3. Goddard ME, Hayes, BJ. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programs. Nature Review Genetics 10:381-391 https://doi.org/10.1038/nrg2575
  4. Grapes L, Dekkers JCM, Rothschild MF, Fernando RL. 2004. Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci. Genetics 166:1561-1570. https://doi.org/10.1534/genetics.166.3.1561
  5. Habier D, Fernando RL, Dekkers JCM. 2007 The impact of genetic relationship information on genome-assisted breeding values. Genetics 177: 2389-2397.
  6. Hayes BJ, Chamberlain AC, McPartlan H, McLeod I, Sethuraman L, Goddard ME. 2007. Accuracy of marker assisted selection with single markers and marker haplotypes in cattle. Genetical Research 89: 215-220.
  7. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. 2009. Invited review: Genomic selection in dairy cattle: Progress and challenges. Journal of Diary Science 92:433-443. https://doi.org/10.3168/jds.2008-1646
  8. Lande R, Thompson, R. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124, 743-756.
  9. Lee SH, Van der Werf JHJ, Hayes BJ, Goddard ME, Visscher PM. 2008. Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data. PLoS Genetics 4: e1000231. https://doi.org/10.1371/journal.pgen.1000231
  10. Meuwissen THE, Hayes BJ, Goddard ME. 2001. Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. Genetics 157: 1819-1829.
  11. VanRaden PM, Van Tassel CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, Schenkel FS. 2009. Invited Review: Reliability of genomic predictions for North American Holstein bulls. Journal of Dairy Science 92:16-24. https://doi.org/10.3168/jds.2008-1514
  12. Zhao HH, Fernando RL, Dekkers JCM. 2007. Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci. Genetics 175: 1975-1986. https://doi.org/10.1534/genetics.106.066480

Cited by

  1. Accuracy of Genomic Estimated Breeding Value with Hanwoo Cows in the Commercial Farms vol.52, pp.2, 2018, https://doi.org/10.14397/jals.2018.52.2.91