Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
권호 표지
DOI QR코드

DOI QR Code

The 3rd Generation Genome Map of the Korean Cattle (Hanwoo)

제3세대 한우유전체지도작성

  • Lee, Yong-Seok (Department of Parasitology, College of Medicine, Inje University) ;
  • Choi, In-Ho (Busan and School of Biotechnology, Yeungnam University)
  • 이용석 (인제대학교 의과대학 기생충학교실) ;
  • 최인호 (영남대학교 생명공학부)
  • Received : 2009.01.19
  • Accepted : 2009.04.16
  • Published : 2009.04.01
Download PDF
⟨ Previous Next ⟩

Abstract

Recently, the $2^{nd}$ generation genome map of the Korean cattle (Hanwoo) has been constructed by comparison of the nucleotide sequence of the Korean cattle BAC clones with whole genome sequence of the bovine data-base (B_tau 2.1 build). The objective of this study was to update the $2^{nd}$ generation genome map of the Korean cattle using the similar approach. The nucleotide sequence of the Korean cattle BAC clones utilized in the construction of the $2^{nd}$ generation map was compared with the newly released bovine data-base (B_tau 3.1 build) to generate the $3^{rd}$ generation map. While, 5,105 BAC clones were localized on bovine chromosome in the $2^{nd}$ generation map, a total of 9,595 BAC clones, which spans about 37.27% of the bovine chromosome after eliminating the overlapping sequence among the clones, have been mapped on the bovine chromosome in the $3^{rd}$ generation map. Further analysis of the nucleotide sequence of the BAC clones will allow us to develop map and facilitate to pinpoint the genes that are important for the improvement of the performance in this cattle breed.

최근 한우의 유전체 연구의 핵심 소재인 박테리아인공염색체(BAC; Bacterial Artificial Chromosome) 클론이 제작되었고 이에 대한 염기서열의 해독과 이를 NCBI (National Center for Biotechnology Information)의 소 유전체 데이터(B_tau 2.1)와 비교 분석하여 한우의 유전체지도 초안(제2 세대 한우유전체지도)이 제작되었다. 본 연구에서는 기존에 확보한 한우의 박테리아인공염색체 클론의 염기서열을 최근에 공개된 소유전체 데이터(B-tau 3.1)와 비교 분석하여 한우 유전체 지도를 최신화하기 위해 실시하였다. 제2 세대 한우유전체지도에서 총 5,105개의 클론에 대한 염색체상 위치가 결정된 반면에 제3세대 한우유전체지도에서는 총 9,595개의 클론에 대한 염색체 위치가 결정되어 약 2배 정도로 향상되었다. 또한 겹치는 부분을 제외했을 때 제3세대 한우유전체지도에 사용된 클론은 소 전체 염색체의 약 37.27%에 해당되는 부분을 커버하는 것으로 나타났다. 앞으로 추가적인 한우 클론의 염기서열 해독을 통해 얻어진 데이터를 확보한다면 한우염색체 정밀 지도의 완성과 이를 이용한 한우 개량에 유용한 유전자 발굴에 활용될 수 있을 것으로 판단되다.

Keywords

References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. andLipman, D. J. 1990. Basic local alignment search tool. J MolBiol. 215:403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  2. Band, M. R., Larson, J. H., Rebeiz, M., Green, C. A., Heyen,D. W., Donovan, J., Windish, R., Steining, C., Mahyuddin, P.,Womack, J. E. and Lewin, H. A. 2000. An orderedcomparative map of the cattle and human genomes. GenomeRes. 10:1359-1368. https://doi.org/10.1101/gr.145900
  3. Barendse, W., Vaiman, D., Kemp, S. J., Sugimoto, Y.,Armitage, S. M., Williams, J. L., Sun, H. S., Eggen, A.,Agaba, M., Aleyasin, S. A., Band, M., Bishop, M. D.,Buitkamp, J., Byrne, K., Collins, F., Cooper, L., Coppettiers,W., Denys, B., Drinkwater, R. D., Easterday, K., Elduque, C.,Ennis, S., Erhardt, G., Ferretti, L., Flavin, N., Gao, Q.,Georges, M., Gurung, R., Harlizius, B., Hawkins, G., Hetzel,J., Hirano, T., Hulme, D., Jorgensen, C., Kessler, M.,Kirkpatrick, B. W., Konfortov, B., Kostia, S., Kuhn, C.,Lenstra, J. A., Leveziel, H., Lewin, H. A., Leyhe, B., Lil, L.,Burriel, I. M., McGraw, R. A., Miller, J. R., Moody, D. E.,Moore, S. S., Nakane, S., Nijman, I. J., Olsaker, I., Pomp, D.,Rando, A., Ron, M., Shalom, A., Teale, A. J., Thieven, U.,Urquhart, B. G. D., Vage, D.-I., Weghe, A. V. d., Varvio, S.,Velmala, R., Vilkki, J., Weikard, R., Woodside, C., Womack,J. E., Zanotti, M. and Zaragoza, P. 1997. A medium-densitygenetic linkage map of the bovine genome MammalianGenome. 8:21-28. https://doi.org/10.1007/s003359900340
  4. Birnboim, H. C. and Doly, J. 1979. A rapid alkaline extractionprocedure for screening recombinant plasmid DNA. NucleicAcids Res. 7:1513-1523. https://doi.org/10.1093/nar/7.6.1513
  5. Chae, S. H., Kim, J. W., Choi, J., Larkin, D. M., Everts-VanDer Wind, A., Park, H. S., Yeo, J. S. and Choi, I. 2007.Chromosomal localization of Korean cattle (Hanwoo) BACclones via BAC end sequence analysis. Asian-australasianjournal of animal sciences. 20:316-327. https://doi.org/10.5713/ajas.2007.316
  6. Choi, J. M., Chae, S. H., S. W., K., Choi, D. S., Lee, Y. S.,Park, H. S., Yeo, J. S. and Choi, I. 2007. Localization of the5,105 Hanwoo (Korean cattle) BAC clones on BovineChromosome by Analyzing BAC End Sequences (BESs) of the21,024 clones. Asian-australasian journal of animal sciences.20:1636-1650. https://doi.org/10.5713/ajas.2007.1636
  7. Choi, S. H., Kim, I. C., Kim, D. S., Kim, D. W., Chae, S.H., Choi, H. H., Choi, I., Yeo, J. S., Song, M. N. and Park,H. S. 2006. Comparative genomic organization of the humanand bovine PRNP locus. Genomics. 87:598-607. https://doi.org/10.1016/j.ygeno.2005.12.012
  8. Everts-van der Wind, A., Kata, S. R., Band, M. R., Rebeiz,M., Larkin, D. M., Everts, R. E., Green, C. A., Liu, L.,Natarajan, S., Goldammer, T., Lee, J. H., McKay, S.,Womack, J. E. and Lewin, H. A. 2004. A 1463 gene cattle-humancomparative map with anchor points defined by humangenome sequence coordinates. Genome Res. 14:1424-1437. https://doi.org/10.1101/gr.2554404
  9. Ewing, B. and Green, P. 1998. Base-calling of automatedsequencer traces using phred. II. Error probabilities. GenomeRes. 8:186-194. https://doi.org/10.1101/gr.8.3.186
  10. Ewing, B., Hillier, L., Wendl, M. C. and Green, P. 1998.Base-calling of automated sequencer traces using phred. I.Accuracy assessment. Genome Res. 8:175-185. https://doi.org/10.1101/gr.8.3.175
  11. Ihara, N., Takasuga, A., Mizoshita, K., Takeda, H., Sugimoto,M., Mizoguchi, Y., Hirano, T., Itoh, T., Watanabe, T., Reed,K. M., Snelling, W. M., Kappes, S. M., Beattie, C. W.,Bennett, G. L. and Sugimoto, Y. 2004. A comprehensive geneticmap of the cattle genome based on 3802 microsatellites.Genome Res. 14:1987-1998. https://doi.org/10.1101/gr.2741704
  12. Itoh, T., Watanabe, T., Ihara, N., Mariani, P., Beattie, C. W.,Sugimoto, Y. and Takasuga, A. 2005. A comprehensiveradiation hybrid map of the bovine genome comprising 5593loci. Genomics. 85:413-424. https://doi.org/10.1016/j.ygeno.2004.12.007
  13. Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P.,Kohany, O. and Walichiewicz, J. 2005. Repbase Update, adatabase of eukaryotic repetitive elements. Cytogenet GenomeRes. 110:462-467. https://doi.org/10.1159/000084979
  14. Kelley, J. M., Field, C. E., Craven, M. B., Bocskai, D., Kim,U. J., Rounsley, S. D. and Adams, M. D. 1999. Highthroughput direct end sequencing of BAC clones. NucleicAcids Res. 27:1539-1546. https://doi.org/10.1093/nar/27.6.1539
  15. Kim, U. J., W., B. B., T., S., V., M., C., B., L., K. H., I., S.M. and H., S. 1996. Construction and characterization of ahuman bacterial artificial chromosome library. Genomics. 34-2:213-218.
  16. Larkin, D. M., Everts-van der Wind, A., Rebeiz, M., Schweitzer,P. A., Bachman, S., Green, C., Wright, C. L., Campos, E. J.,Benson, L. D., Edwards, J., Liu, L., Osoegawa, K., Womack,J. E., de Jong, P. J. and Lewin, H. A. 2003. A cattle-humancomparative map built with cattle BAC-ends and humangenome sequence. Genome Res. 13:1966-1972.
  17. Womack, J. E., Johnson, J. S., Owens, E. K., Rexroad, C. E.,3rd, Schlapfer, J. and Yang, Y. P. 1997. A whole-genomeradiation hybrid panel for bovine gene mapping. MammGenome. 8:854-856. https://doi.org/10.1007/s003359900593
  18. Yu, S. L., Kim, J. E., Chung, H. J., Jung, K. C., Lee, Y. J.,Yoon, D. H., Lee, S. H., Choi, I., Bottema, C. D., Sang, B.C. and Lee, J. H. 2005. Molecular cloning and characterizationof bovine PRKAG3 gene: structure, expression and singlenucleotide polymorphism detection. J. Anim Breed Genet. 122:294-301. https://doi.org/10.1111/j.1439-0388.2005.00545.x