Journal of Life Science (생명과학회지)

Korean Society of Life Science (한국생명과학회)
권호 표지
DOI QR코드

DOI QR Code

Estimation of Linkage Disequilibrium and Effective Population Size using Whole Genome Single Nucleotide Polymorphisms in Hanwoo

한우에서 전장의 유전체 정보를 활용한 연관불평형 및 유효집단크기 추정에 관한 연구

  • Cho, Chung-Il (National Institute of Animal Science, RDA) ;
  • Lee, Joon-Ho (Department of Animal Life and Environment Science, Hankyong National Univerisity) ;
  • Lee, Deuk-Hwan (Department of Animal Life and Environment Science, Hankyong National Univerisity)
  • 조충일 (농촌진흥청 축산과학원) ;
  • 이준호 (국립한경대학교 동물생명환경과학과) ;
  • 이득환 (국립한경대학교 동물생명환경과학과)
  • Received : 2011.12.09
  • Accepted : 2012.03.09
  • Published : 2012.03.30
Download PDF
⟨ Previous Next ⟩

Abstract

This study was conducted to estimate the extent of linkage disequilibrium (LD) and effective population size using whole genomic single nucleotide polymorphisms (SNP) genotyped by DNA chip in Hanwoo. Using the blood samples of 35 young bulls born from 2005 to 2008 and their progenies (N=253) in a Hanwoo nucleus population collected from Hanwoo Improvement Center, 51,582 SNPs were genotyped using Bovine SNP50 chips. A total of 40,851 SNPs were used in this study after elimination of SNPs with a missing genotyping rate of over 10 percent and monomorphic SNPs (10,730 SNPs). The total autosomal genome length, measured as the sum of the longest syntenic pairs of SNPs by chromosome, was 2,541.6 Mb (Mega base pairs). The average distances of all adjacent pairs by each BTA ranged from 0.55 to 0.74 cM. Decay of LD showed an exponential trend with physical distance. The means of LD ($r^2$) among syntenic SNP pairs were 0.136 at a range of 0-0.1 Mb in physical distance and 0.06 at a range of 0.1-0.2 Mb. When these results were used for Luo's formula, about 2,000 phenotypic records were found to be required to achieve power > 0.9 to detect 5% QTL in the population of Hanwoo. As a result of estimating effective population size by generation in Hanwoo, the estimated effective population size for the current status was 84 heads and the estimate of effective population size for 50 generations of ancestors was 1,150 heads. The average decreasing rates of effective population size by generation were 9.0% at about five generations and 17.3% at the current generation. The main cause of the rapid decrease in effective population size was considered to be the intensive use of a few prominent sires since the application of artificial insemination technology in Korea. To increase and/or sustain the effective population size, the selection of various proven bulls and mating systems that consider genetic diversity are needed.

본 연구는 한우 유전체 전장에 존재하는 고밀도 단일염기다형을 DNA chip을 이용하여 각각의 유전자형을 구명하고, 동일염색체 내에 존재하는 각 표지인자쌍의 연관불평형을 성 염색체를 제외한 모든 상염색체에서 추정하여 물리적 거리별 연관불평형의 정도를 확인하고 이러한 결과를 이용하여 한우 집단의 유효집단 크기를 추정하기 위하여 실시하였다. 한우개량사업소에서 2005년부터 2008년까지 후대검정에 공시된 후보종모우 및 후대 검정우 288두에 대해 혈액을 채취하고 Bovine SNP 50 DNA Chip을 이용하여 유전자형을 분석하였으며, 총 51,582 표지인자 중 결측률이 10% 이상인 표지인자 1개 및 다형성이 없는 표지인자 10,730개에 대해 사전제거를 실시하고 남은 40,851개의 SNP표지인자를 본 분석에 활용하였다. 연구 결과, 성 염색체를 제외한 상 염색체의 총 SNP표지인자의 길이는 2,541.6 Mb였으며, 염색체별 평균 SNP표지인자간 거리는 0.55에서 0.74로 분포하였으며, EM알고리즘을 이용하여 염색체별 연관불평형을 추정해 보았을 때, 기존의 보고된 연구와 유사하게 표지인자간 거리가 짧을수록 높게 나타나는 지수형태의 그래프를 나타냈으며, SNP표지인자간 거리에 따른 $r^2$를 보면, 0 Mb에서 0.1 Mb일 때 0.136, 0.1-0.2 Mb에서 0.06로 나타났다. Luo (1998)의 연구결과를 한우에 적용시켰을 때, 전체분산의 5%이상 설명하는 양적형질좌위 발굴을 위해서 약 2,000두의 표현형 자료가 필요할 것으로 사료되었다. 또한 한우의 세대별 유효집단 크기에 대해 추정해 본 결과, 현재 한우의 유효집단크기는 84두로 추정되었고, 지금으로부터 약 50세대 이전의 유효집단 크기는 1,150두로 추정되었다. 가축에서 인공수정이 도입(1960년대)된 이 후 개량의 가속화로 인해 한우의 유효집단 크기가 급격히 감소한 것으로 사료되었다.

Keywords

References

  1. Dadi, H., Kim, J. J., Yoon, D. H. and Kim, K. S. 2012. Evaluation of Single Nucleotide Polymorphisms (SNPs) Genotyped by the Illumina Bovine SNP50K in Cattle Focusing on Hanwoo Breed. Asian-Aust. J. Anim. Sci. 1, 28-32.
  2. Du, F. X., Clutter, A. C. and Lohuis, M. M. 2007. Charaterizing Linkage Disequilibrium in Pig Populations. Int. J. Biol. Sci. 3, 166-178.
  3. Excoffier, L. and Slatkin, M. 1995. Maximum-likelihood-estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12, 921-927.
  4. Hayes, B. J. 2008. Course Notes 'QTL Mapping, Mas, and Genomic Selection'.
  5. Hayes, B. J., Bowman, P. J., Chamberlain, A. C., Verbyla, K. and Goddard, M. E. 2008. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genetic Selection Evolution 2009, 41-51.
  6. Hayes, B. J., Bowman, P. J., Chamberlain, A. J. and Goddard, M. E. 2009. Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92, 433-443. https://doi.org/10.3168/jds.2008-1646
  7. Hayes, B. J. and Goddard, M. E. 2001. The distribution of the effects of genes affecting quantitative traits in livestock. Genetics Selection Evolution 33, 209-229. https://doi.org/10.1186/1297-9686-33-3-209
  8. Hayes, B. J., Visscher, P. E., McPartlan, H. and Goddard, M. E. 2003. A novel multi-locus measure of linkage disequilibrium and it use to estimate past effective population size. Genome Research 13, 635-643. https://doi.org/10.1101/gr.387103
  9. Hill, W. G. and Robertson, A. 1968. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38, 226-231. https://doi.org/10.1007/BF01245622
  10. Lee, S. H., Cho, Y. M., Lim. D., Kim, H. C., Choi, B. H., Park, H. S., Kim, O. H., Kim, S., Kim, T. H., Yoon, D. and Hong, S. K. 2011. Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle. Asian-Aust. J. Anim. Sci. 12, 1660-1665.
  11. Lewontin, R. C. 1964. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 49-67.
  12. Luo, Z. W. 1998. Linkage diseuilibrium in a two-locus model. Heredity 80, 198-208. https://doi.org/10.1046/j.1365-2540.1998.00275.x
  13. McKay, S. D., Schnabel, R. D., Murdoch, B. M., Matukumalli, L. K., Aerts, J., Coppieters, W., Crews, D., Dias Neto, E., Gill, C. A., Gao, C., Mannen, H., Stothard, P., Wang, Z., Van Tassell, C. P., Williams, J. L., Taylor, J. F. and Moore, S. S. 2007. Whole genome linkage disequilibrium maps in cattle. BMC Genet. 2007, 8-74.
  14. McRae, A. F., McEwan, J. C., Dodds, K. G., Wilson, T., Crawford, A. M. and Slate, J. 2002. Linkage disequilibrium in domestic sheep. Genetics 160, 113-1122.
  15. Pritchard, J. K. and Przeworski, M. 2001. Likage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69, 1-14. https://doi.org/10.1086/321275
  16. Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R. and Simianer, H. 2010. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. Aug. 41, 346-356.
  17. Sargolzaei, M., Schenkel, F. S., Jansen, G. B. and Schaeffer, L. R. 2008. Extent of Linkage Disequilibrium in Holstein Cattle in North America. J. Dairy Sci. 91, 2106-2117. https://doi.org/10.3168/jds.2007-0553
  18. Scheet, P. and Stephens, M. 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78, 629-644. https://doi.org/10.1086/502802
  19. Su, G., Guldbrandtsen, B., Gregersen, V. R. and Lund, M. S. 2010. Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population. J. Dairy Sci. 93, 1175-1183. https://doi.org/10.3168/jds.2009-2192
  20. Sved, J. A. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite population. Theor. Popul. Biol. 2, 125-141. https://doi.org/10.1016/0040-5809(71)90011-6
  21. Thevenon, S., Dayo, G. K., Sylla, S., Sidibe, I., Berthier, D., Legros, H., Boichard, D., Eggen, A. and Gautier, M. 2007. The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Anim. Genet. 38, 277-286. https://doi.org/10.1111/j.1365-2052.2007.01601.x
  22. Toosi, A., Ferando, R. L. and Dekkers, J. C. M. 2010. Genomic selection in admixed and crossbred populations. J. Anim. Sci. 88, 32-46. https://doi.org/10.2527/jas.2009-1975
  23. Uimari, P. and Tapio, M. 2011. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. J. Anim. Sci. 89, 609-614. https://doi.org/10.2527/jas.2010-3249
  24. VanRaden, P. M., Van Tassell, C. P., Wiggans, G. R., Sonstegard, T. S., Schnabel, R. D., Taylor, J. F. and Schenkel, F. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92, 16-24. https://doi.org/10.3168/jds.2008-1514

Cited by

  1. The Analysis of Pedigree Structure and Inbreeding Coefficient in Hanwoo Cows vol.48, pp.4, 2014, https://doi.org/10.14397/jals.2014.48.4.187