Journal of Life Science (생명과학회지)

Korean Society of Life Science (한국생명과학회)
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Association of SNP Markers on Chromosomes 3 and 9 with Body Weight in Jeju Horses

제주마에서 3번 및 9번 염색체상의 단일염기변이와 생체중과의 관련성 연구

  • Kim, Nam Young (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Yang, Young Hoon (Faculty of Animal Biotechnology, Jeju National University) ;
  • Park, Nam Geon (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Yang, Byoung Chul (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Son, Jun Kyu (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Shin, Sang Min (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Woo, Jae Hoon (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Shin, Moon Cheol (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Yoo, Ji Hyun (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Hong, Hyun Ju (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A) ;
  • Park, Hee Bok (Subtropical Livestock Research Institute, National Institute of Animal Science, R.D.A)
  • 김남영 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 양영훈 (제주대학교 생명공학부 동물생명공학전공) ;
  • 박남건 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 양병철 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 손준규 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 신상민 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 우제훈 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 신문철 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 유지현 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 홍현주 (농촌진흥청 국립축산과학원 난지축산연구소) ;
  • 박희복 (농촌진흥청 국립축산과학원 난지축산연구소)
  • Received : 2018.04.16
  • Accepted : 2018.06.05
  • Published : 2018.07.30
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Abstract

This study was conducted to investigate the association of single nucleotide polymorphism (SNP) markers on equine chromosomes (ECA) 3 and 9 with body weight in Jeju horses. We used DNA samples and body weight data of 320 horses provided by the Livestock Promotion Agency, Jeju Special Self-Governing Province, and the Korean Racing Association, respectively. We genotyped all the experimental animals using nine SNP markers located on ECA 3 (BIEC2-808466, BIEC2-808543, BIEC2-808967, and BIEC2-809370) and ECA 9 (BIEC2-1105370, BIEC2-1105372, BIEC2-1105377, BIEC21105505, and BIEC2-1105840). These markers were selected due to their effects on body conformation traits in horses. The joint effect of the genotypes of the two SNP markers (BIEC2-808467 and BIEC2-1105377) regarding body weight were also evaluated. The estimated breeding value (EBV) of body weight was obtained as the dependent variable for association analyses using a linear mixed model. Significant associations were detected between SNP markers (BIEC2-808543, BIEC2-808967, BIEC2-809370, BIEC2-1105370, BIEC2-1105372, and BIEC2-1105377) and the body weight EBV. In addition, the joint genotype effect of the BIEC2-808467 and BIEC2-1105377 on the body weight EBV was significant. These results indicate that the SNP markers, which showed their significant effects on body conformation, can be used as genetic markers to improve the efficiency of the selective breeding program for the body weight traits in Jeju horses.

본 연구는 제주마 체중 형질과 말의 3번 및 9번 염색체 단일염기변이마커간의 관련성을 분석하기 위해 수행되었다. 본 연구에 사용된 DNA 샘플은 제주특별자치도 축산진흥원에서 등록관리 중인 제주마 320두를 제공받았고, 생체중 자료는 한국마사회에서 시행한 경마에 출주한 제주마의 체중자료를 이용하였다. 기존에 말의 체형관련형질과의관련성이 보고된 바 있는 말의 3번 염색체상에 위치한 BIEC2-808466, BIEC2-808543, BIEC2-808967, BIEC2-809370 단일염기변이마커와 9번 염색체상에 위치한 BIEC2-1105370, BIEC2-1105372, BIEC2-1105377, BIEC2-1105505 and BIEC2-1105840 유전자형을 분석하였다. 관련성 분석을 위한 종속변수는 선형혼합모형을 이용해서 추정한 생체중 육종가를 이용하였다. 관련성 분석결과 6개의 마커(BIEC2-808543, BIEC2-808967, BIEC2-809370, BIEC2-1105370, BIEC2-1105372, and BIEC2-1105377)와 생체중 추정육종가간의 유의성이 인정되었다. 또한, BIEC2-808967과 BIEC2-1105377의 유전자형조합을 구성하여 생체중 추정육종가에 대한 효과를 분석한 결과, 두 마커의 유전자 조합은 생체중 변이에 유의한 효과가 있었다. 본 연구에서 유의성이 인정된 단일염기변이마커들은 제주마의 체중 개량을 위한 선발육종체계의 효율성을 높일 수 있는데 사용될 수 있을 것으로 사료되지만, 이 들 마커효과의 좀더 정확한 추정을 위한 추가의 연구가 필요할 것으로 생각된다.

Keywords

References

  1. Al-Mamun, H. A., Kwan, P., Clark, S. A., Ferdosi, M. H., Tellam, R. and Gondro, C. 2015. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genet. Sel. Evol. 47, 66. https://doi.org/10.1186/s12711-015-0142-4
  2. Balding, D. J. 2006. A tutorial on statistical methods for population association studies. Nat. Rev. Genet. 7, 781-791. https://doi.org/10.1038/nrg1916
  3. Bene, S., Kecskes, S. B., Polgar, J. P. and Szabo, F. 2014. Comparison of live weight and body measurements of adult brood mares from different genotypes in Hungary. J. Cent. Eur. Agric. 15, 1-11.
  4. Carlborg, O. and Haley, C. S. 2004. Epistasis: too often neglected in complex trait studies? Nat. Rev. Genet. 5, 618-625. https://doi.org/10.1038/nrg1407
  5. Falconer, D. S. and Mackay, T. F. C. 1996. Introduction to Quantitative Genetics. Addison Wesley Longman, Harlow, UK.
  6. Gu, X., Feng, C., Ma, L., Song, C., Wang, Y., Da, Y., Li, H., Chen, K., Ye, S., Ge, C., Hu, X. and Li, N. 2011. Genome-wide association study of body weight in chicken F2 resource population. PLoS One 6, e21872. https://doi.org/10.1371/journal.pone.0021872
  7. Gunderson, K. L., Steemers, F. J., Lee, G., Mendoza, L. G. and Chee, M. S. 2005. A genome-wide scalable SNP genotyping assay using microarray technology. Nat. Genet. 37, 549-554. https://doi.org/10.1038/ng1547
  8. He, S., Zhang, L., Li, W. and Liu, M. 2015. BIEC2-808543 SNP in the LCORL gene is associated with body conformation in the Yili Horse. Anim. Biotechnol. 26, 289-291. https://doi.org/10.1080/10495398.2014.995303
  9. Horikoshi, M., Beaumont, R. N., Day, F. R., Warrington, N. M., Kooijman, M. N. and Fernandez-Tajes, J. et al. 2016. Genome-wide associations for birth weight and correlations with adult disease. Nature 538, 248-252. https://doi.org/10.1038/nature19806
  10. Jung, E. J., Park, H. B., Lee, J. B., Yoo, C. K., Kim, B. M., Kim, H. I., Kim, B. W. and Lim, H. T. 2014. Genome-wide association analysis identifies quantitative trait loci for growth in a Landrace purebred population. Anim. Genet. 45, 442-444. https://doi.org/10.1111/age.12117
  11. Makvandi-Nejad, S., Hoffman, G. E., Allen, J. J., Chu, E., Gu, E., Chandler, A. M., Loredo, A. I., Bellone, R. R., Mezey, J. G., Brooks, S. A. and Sutter, N. B. 2012. Four loci explain 83% of size variation in the horse. PLoS One 7, e39929. https://doi.org/10.1371/journal.pone.0039929
  12. Ronaghi, M., Uhlen, M. and Nyren, P. 1998. A sequencing method based on real-time pyrophosphate. Science 281, 363-365. https://doi.org/10.1126/science.281.5375.363
  13. SAS Institute Inc., SAS 9.1. Help and Documentation, Cary, NC: SAS Institute Inc., 2002-2004
  14. Signer-Hasler, H., Flury, C., Haase, B., Burger, D., Simianer, H., Leeb, T. and Rieder, S. 2012. A genome-wide association study reveals loci influencing height and other conformation traits in horses. PLoS One 7, e37282. https://doi.org/10.1371/journal.pone.0037282
  15. Tetens, J., Widmann, P., Kuhn, C. and Thaller, G. 2013. A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in German Warmblood horses. Anim. Genet. 44, 467-471. https://doi.org/10.1111/age.12031
  16. Wood, A. R., Esko, T., Yang, J., Vedantam, S., Pers, T. H. and Gustafsson, S. et al. 2014. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 46, 1173-1186. https://doi.org/10.1038/ng.3097
  17. Wu, Y., Fan, H., Wang, Y., Zhang, L., Gao, X., Chen, Y., Li, J., Ren, H. and Gao, H. 2014. Genome-wide association studies using haplotypes and individual SNPs in Simmental cattle. PLoS One 9, e109330. https://doi.org/10.1371/journal.pone.0109330