Restricted partition method and gene-gene interaction analysis with Hanwoo economic traits

제한된 분할방법과 한우 경제형질에서 유전자들간의 상호작용

  • Published : 2009.01.31

Abstract

In order to make the high quality Korean cattle, it has been identified the gene which influence to various economic characters. In this paper, we introduce Restricted Partition Method for gene-gene interaction analysis. Further, economic traits, longissimus muscle dorsi area (LMA), carcass cold weight (CWT) and average daily gain (ADG) are applied with Restricted Partition Method (RPM). The SNP (19_1)$^*$SNP (28_2) was selected and was best marker on Single nucleotide polymorphisms (SNPs). It also influenced SNP (19_1)$^*$SNP (28_2) was an very important marker for economic character and to make the thing know it became.

제한된 분할방법은 어떤 개체의 표현형을 가장 많이 설명할 수 있는 multilocus 유전자형들의 분할된 그룹을 찾는 것이며 연속형 데이터에 적합하다. 또한 이 방법은 인간의 여러 질병에 영향을 주는 유전자를 찾는 방법으로 주로 이용된다. 그러나 본 연구에서는 제한된 분할 방법을 인간의 질병뿐만 아니라 가축의 경제형질에도 적용할 수 있는 것을 보이기 위해 한우의 여러 경제형질인 등심단면적, 도체중과 일당증체량에 영향을 주는 유전자를 규명해 보았다. 그 결과 모든 경제형질에 영향을 주는 유전자로는 SNP (19_1)$^*$SNP (28_2)의 상호작용이 가장 좋은 SNP로 선정되었다. 따라서 이 유전자 SNP (19_1)$^*$SNP (28_2)가 한우의 경제형질에 가장 많은 영향을 준다는 것을 규명하였으며 제한된 분할 방법이 가축의 경제형질에도 적용할 수 있다는 것을 보였다.

Keywords

References

  1. Barendse W., Bunch R., Thomas M., Armitage S., Baud S. and Donaldson N. (2004). The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle. Australian Journal of Experimental Agriculture, 44, 669-674. https://doi.org/10.1071/EA02156
  2. Boerwinkle, E. and sing, C.f. (1986). Bias of the contribution of single-locus effects to the variance of a quantitative trait. American Journal of Human Genetics, 39, 137-144.
  3. Chung, Y., Lee, S., Park, T. (2005). Multifactor dimensionality reduction in the presence of missing observations. Journal of Korea Statistical Society, Proceedings of the Autumn Conference, 1, 31-36.
  4. Comtet, L. (1974). Advanced combinatorics: The art of infinite expansions. Reidel, Boston.
  5. Culverhouse Robert, Tsvika Klein and William Shannon. (2004) Detecting epistatic interactions contributing to quantitative traits. Genetic Epidemiology, 27, 141-152. https://doi.org/10.1002/gepi.20006
  6. Hahn, L. W., Ritchie, M. D. and Moore, J. H. (2003). Multifactor dimensionality reduction software for detecting gene-gene and gene- environment interactions. Bioinformatics, 19, 376-382. https://doi.org/10.1093/bioinformatics/btf869
  7. Kim, J. W., Park, S. I. and Yeo, J. S. (2003). Linkage mapping and QTL on chromosome 6 in Hanwoo (Korean Cattle). Asian-Australasian Journal of Animal Sciences. 16, 1402-1405. https://doi.org/10.5713/ajas.2003.1402
  8. Lee, J. Y., Kwon, J. C., Choi, Y. M. (2006). DNA marker traceability in Korean Cattle. Journal of the Korean Data & Information Science Society, Proceedings of the Autumn Conference, 155-159.
  9. Lee, J. Y. (2007). Multifactor dimensionality reduction (MDR) analysis for SNP detection in a Hanwoo population. Journal of the Korean Data & Information Science Society, Proceedings of the Autumn Conference, 77-83.
  10. Lee, J. Y. and Kim, D. C. (2008a). Important SNPs identification from the various economic characters for the high quality Koran cattle. Journal of Korea statistical Society, submitted.
  11. Lee, Y. S., Bae, J. H., Lee, J. Y., Park, H. S. and Yeo J. S. (2008). Identification of candidate SNP for economic traits on chromosome 6 in Korean cattle. Animal Genetics, (to appear).
  12. Lee, J. Y. and Kim, D. C. (2008b). RPM (restricted partition method) analysis for SNP detection in a Hanwoo cattle. Journal of Korea Statistical Society, Proceedings of the Spring Conference, 70.
  13. Nelson MR, Kardia SL, Ferrell RE, Sing CF. (2001). A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res, 11, 458-470. https://doi.org/10.1101/gr.172901
  14. Page B. T., Casas E., Quaas R. L., Thallman R. M., Wheeler T. L., Shackelford S.D., Koohmaraie M., White S. N., Bennett G. L., Keele J. W., Dikeman M. E. and Smith T. P. L. (2004). Association of markers in the bovine CAPNI gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science, 82, 3474-3481. https://doi.org/10.2527/2004.82123474x
  15. Ritchie, M. D., Hahn, L. W., and Moore, J. H. (2003) Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genetic Epidemiology, 24, 150-157. https://doi.org/10.1002/gepi.10218
  16. Snelling, W. M., Casas E., Stone, R. T., Keele, J. W., Harhay G. P., Benett G. L. and Smith T. PL. (2005). Linkage mapping bovine EST-based SNP. BMC Genomics, 6, 74-84. https://doi.org/10.1186/1471-2164-6-74