Browse > Article
http://dx.doi.org/10.5851/kosfa.2013.33.6.715

Whole Genome Resequencing of Heugu (Korean Black Cattle) for the Genome-Wide SNP Discovery  

Choi, Jung-Woo (Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph)
Chung, Won-Hyong (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
Lee, Kyung-Tai (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration)
Choi, Jae-Won (Chungcheong Buk-Do Institute of Livestock and Veterinary Research)
Jung, Kyoung-Sub (Chungcheong Buk-Do Institute of Livestock and Veterinary Research)
Cho, Yongmin (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration)
Kim, Namshin (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology)
Kim, Tae-Hun (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration)
Publication Information
Food Science of Animal Resources / v.33, no.6, 2013 , pp. 715-722 More about this Journal
Abstract
Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.
Keywords
Heugu; Korean Black Cattle; whole genome resequencing; single nucleotide polymorphisms;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 Abecasis, G. R., Auton, A., Brooks, L. D., DePristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T., and McVean, G. A. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65.   DOI   ScienceOn
2 Barendse, W., Harrison, B. E., Bunch, R. J., Thomas, M. B., and Turner, L. B. (2009) Genome wide signatures of positive selection: the comparison of independent samples and the identification of regions associated to traits. BMC Genomics 10, 178.   DOI   ScienceOn
3 Bolormaa, S., Hayes, B. J., Savin, K., Hawken, R., Barendse, W., Arthur, P. F., Herd, R. M., and Goddard, M. E. (2011) Genome-wide association studies for feedlot and growth traits in cattle. J. Anim. Sci. 89, 1684-1697.   DOI   ScienceOn
4 Canavez, F. C., Luche, D. D., Stothard, P., Leite, K. R., Sousa-Canavez, J. M., Plastow, G., Meidanis, J., Souza, M. A., Feijao, P., Moore, S. S., and Camara-Lopes, L. H. (2012) Genome sequence and assembly of Bos indicus. J. Hered. 103, 342-348.   DOI   ScienceOn
5 Casas, E., White, S. N., Wheeler, T. L., Shackelford, S. D., Koohmaraie, M., Riley, D. G., Chase, C. C., Jr., Johnson, D. D., and Smith, T. P. (2006) Effects of calpastatin and microcalpain markers in beef cattle on tenderness traits. J. Anim. Sci. 84, 520-525.
6 Casas, E., White, S. N., Shackelford, S. D., Wheeler, T. L., Koohmaraie, M., Bennett, G. L., and Smith, T. P. (2007) Assessing the association of single nucleotide polymorphisms at the thyroglobulin gene with carcass traits in beef cattle. J. Anim. Sci. 85, 2807-2814.   DOI   ScienceOn
7 Choi, T. J. (2009). Establishment of phylogenomic characteristics for Korean traditional cattle breeds (Hanwoo, Korean brindle and black). Doctoral Thesis. Jeon-buk National University, Republic of Korea.
8 Choi, S. B., Byun, M. J., Kim, Y. S., Kim, M. J., Choy, Y. H., Kim, D. H., Jeong, E. G., Kang, K. S., Kim, K. H., and Kim, J. H. (2012) National Management System for Conservation of Livestock Genetic Resources. Ann. Anim. Resour. Sci. 23, 142-148.   DOI
9 Choi, J. W., Lee, K. T., Liao, X., Stothard, P., An, H. S., Ahn, S., Lee, S., Lee, S. Y., Moore, S. S., and Kim, T. H. (2013) Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle. Mamm. Genome. 24, 151-163.   DOI   ScienceOn
10 Choi, J. W., Liao, X., Park, S., Jeon, H. J., Chung, W. H., Stothard, P., Park, Y. S., Lee, J. K., Lee, K. T., Kim, S. H., Oh, J. D., Kim, N., Kim, T. H., Lee, H. K., and Lee, S. J. (2013) Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels. Mol. Cells 36, 203-211.   DOI
11 Cingolani, P., Platts, A., Wang le, L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., and Ruden, D. M. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80-92.   DOI
12 Cingolani, P., Patel, V. M., Coon, M., Nguyen, T., Land, S. J., Ruden, D. M., and Lu, X. (2012) Using Drosophila melano-gaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift. Front. Genet. 3, 35.
13 Dekkers, J. C. (2004) Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons. J. Anim. Sci. 82 E-Suppl, E313-328.
14 DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., del Angel, G., Rivas, M. A., Hanna, M., McKenna, A., Fennell, T. J., Kernytsky, A. M., Sivachenko, A. Y., Cibulskis, K., Gabriel, S. B., Altshuler, D., and Daly, M. J. (2011) using next-generation DNA sequencing data. Nat. Genet. 43, 491-498.   DOI   ScienceOn
15 Dikeman, M. E., Pollak, E. J., Zhang, Z., Moser, D. W., Gill, C. A., and Dressler, E. A. (2005) Phenotypic ranges and relationships among carcass and meat palatability traits for fourteen cattle breeds, and heritabilities and expected progeny differences for Warner-Bratzler shear force in three beef cattle breeds. J. Anim. Sci. 83, 2461-2467.
16 Drinkwater, R., Li, Y., Lenane, I., Davis, G., Shorthose, R., Harrison, B., Richardson, K., Ferguson, D., Stevenson, R., and Renaud, J. (2006) Detecting quantitative trait loci affecting beef tenderness on bovine chromosome 7 near calpastatin and lysyl oxidase. Aust. J. Exp. Agric. 46, 159-164   DOI   ScienceOn
17 FAO (Food and Agriculture Organization). (2013) Domestic Animal Diversity Information Service (DAD-IS). http://dad.fao.org/ Accessed July 11, 2013.
18 Elsik, C. G., Tellam, R. L., Worley, K. C., Gibbs, R. A., Muzny, D. M., Weinstock, G. M., Adelson, D. L., Eichler, E. E., Elnitski, L., Guigo, R., Hamernik, D. L., Kappes, S. M., Lewin, H. A., Lynn, D. J., Nicholas, F. W., Reymond, A., Rijnkels, M., Skow, L. C., Zdobnov, E. M., Schook, L., Womack, J., Alioto, T., Antonarakis, S. E., Astashyn, A., Chapple, C. E., Chen, H. C., Chrast, J., Camara, F., Ermolaeva, O., Henrichsen, C. N., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Kokocinski, F., Landrum, M., Maglott, D., Pruitt, K., Sapojnikov, V., Searle, S. M., Solovyev, V., Souvorov, A., Ucla, C., Wyss, C., Anzola, J. M., Gerlach, D., Elhaik, E., Graur, D., Reese, J. T., Edgar, R. C., McEwan, J. C., Payne, G. M., Raison, J. M., Junier, T., Kriventseva, E. V., Eyras, E., Plass, M., Donthu, R., Larkin, D. M., Reecy, J., Yang, M. Q., Chen, L., Cheng, Z., Chitko-McKown, C. G., Liu, G. E., Matukumalli, L. K., Song, J., Zhu, B., Bradley, D. G., Brinkman, F. S., Lau, L. P., Whiteside, M. D., Walker, A., Wheeler, T. T., Casey, T., German, J. B., Lemay, D. G., Maqbool, N. J., Molenaar, A. J., Seo, S., Stothard, P., Baldwin, C. L., Baxter, R., Brinkmeyer-Langford, C. L., Brown, W. C., Childers, C. P., Connelley, T., Ellis, S. A., Fritz, K., Glass, E. J., Herzig, C. T., Iivanainen, A., Lahmers, K. K., Bennett, A. K., Dickens, C. M., Gilbert, J. G., Hagen, D. E., Salih, H., Aerts, J., Caetano, A. R., Dalrymple, B., Garcia, J. F., Gill, C. A., Hiendleder, S. G., Memili, E., Spurlock, D., Williams, J. L., Alexander, L., Brownstein, M. J., Guan, L., Holt, R. A., Jones, S. J., Marra, M. A., Moore, R., Moore, S. S., Roberts, A., Taniguchi, M., Waterman, R. C., Chacko, J., Chandrabose, M. M., Cree, A., Dao, M. D., Dinh, H. H., Gabisi, R. A., Hines, S., Hume, J., Jhangiani, S. N., Joshi, V., Kovar, C. L., Lewis, L. R., Liu, Y. S., Lopez, J., Morgan, M. B., Nguyen, N. B., Okwuonu, G. O., Ruiz, S. J., Santibanez, J., Wright, R. A., Buhay, C., Ding, Y., Dugan-Rocha, S., Herdandez, J., Holder, M., Sabo, A., Egan, A., Goodell, J., Wilczek-Boney, K., Fowler, G. R., Hitchens, M. E., Lozado, R. J., Moen, C., Steffen, D., Warren, J. T., Zhang, J., Chiu, R., Schein, J. E., Durbin, K. J., Havlak, P., Jiang, H., Liu, Y., Qin, X., Ren, Y., Shen, Y., Song, H., Bell, S. N., Davis, C., Johnson, A. J., Lee, S., Nazareth, L. V., Patel, B. M., Pu, L. L., Vattathil, S., Williams, R. L., Jr., Curry, S., Hamilton, C., Sodergren, E., Wheeler, D. A., Barris, W., Bennett, G. L., Eggen, A., Green, R. D., Harhay, G. P., Hobbs, M., Jann, O., Keele, J. W., Kent, M. P., Lien, S., McKay, S. D., McWilliam, S., Ratnakumar, A., Schnabel, R. D., Smith, T., Snelling, W. M., Sonstegard, T. S., Stone, R. T., Sugimoto, Y., Takasuga, A., Taylor, J. F., Van Tassell, C. P., Macneil, M. D., Abatepaulo, A. R., Abbey, C. A., Ahola, V., Almeida, I. G., Amadio, A. F., Anatriello, E., Bahadue, S. M., Biase, F. H., Boldt, C. R., Carroll, J. A., Carvalho, W. A., Cervelatti, E. P., Chacko, E., Chapin, J. E., Cheng, Y., Choi, J., Colley, A. J., de Campos, T. A., De Donato, M., Santos, I. K., de Oliveira, C. J., Deobald, H., Devinoy, E., Donohue, K. E., Dovc, P., Eberlein, A., Fitzsimmons, C. J., Franzin, A. M., Garcia, G. R., Genini, S., Gladney, C. J., Grant, J. R., Greaser, M. L., Green, J. A., Hadsell, D. L., Hakimov, H. A., Halgren, R., Harrow, J. L., Hart, E. A., Hastings, N., Hernandez, M., Hu, Z. L., Ingham, A., Iso-Touru, T., Jamis, C., Jensen, K., Kapetis, D., Kerr, T., Khalil, S. S., Khatib, H., Kolbehdari, D., Kumar, C. G., Kumar, D., Leach, R., Lee, J. C., Li, C., Logan, K. M., Malinverni, R., Marques, E., Martin, W. F., Martins, N. F., Maruyama, S. R., Mazza, R., McLean, K. L., Medrano, J. F., Moreno, B. T., More, D. D., Muntean, C. T., Nandakumar, H. P., Nogueira, M. F., Olsaker, I., Pant, S. D., Panzitta, F., Pastor, R. C., Poli, M. A., Poslusny, N., Rachagani, S., Ranganathan, S., Razpet, A., Riggs, P. K., Rincon, G., Rodriguez-Osorio, N., Rodriguez-Zas, S. L., Romero, N. E., Rosenwald, A., Sando, L., Schmutz, S. M., Shen, L., Sherman, L., Southey, B. R., Lutzow, Y. S., Sweedler, J. V., Tammen, I., Telugu, B. P., Urbanski, J. M., Utsunomiya, Y. T., Verschoor, C. P., Waardenberg, A. J., Wang, Z., Ward, R., Weikard, R., Welsh, T. H., Jr., White, S. N., Wilming, L. G., Wunderlich, K. R., Yang, J., and Zhao, F. Q. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324, 522-528.   DOI   ScienceOn
19 Jo, C., Cho, S. H., Chang, J., and Nam, K. C. (2012) Keys to production and processing of Hanwoo beef: A perspective of tradition and science. Anim. Frontiers 2, 32-38.
20 Kasprzyk, A. (2011) BioMart: driving a paradigm change in biological data management. Database, bar049.
21 Kawahara-Miki, R., Tsuda, K., Shiwa, Y., Arai-Kichise, Y., Matsumoto, T., Kanesaki, Y., Oda, S., Ebihara, S., Yajima, S., Yoshikawa, H., and Kono, T. (2011) Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics 12, 103.   DOI   ScienceOn
22 Koohmaraie, M. and Geesink, G. H. (2006) Contribution of postmortem muscle biochemistry to the delivery of consistent meat quality with particular focus on the calpain system. Meat Sci. 74, 34-43.   DOI   ScienceOn
23 Lee, K. T., Chung, W. H., Lee, S. Y., Choi, J. W., Kim, J., Lim, D., Lee, S., Jang, G. W., Kim, B., Choy, Y. H., Liao, X., Stothard, P., Moore, S. S., Lee, S. H., Ahn, S., Kim, N., and Kim, T. H. (2013) Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC genomics 14, 519.   DOI   ScienceOn
24 Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.   DOI   ScienceOn
25 McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., and DePristo, M. A. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303.   DOI   ScienceOn
26 NIAS (National Institute of Animal Science). (2012). The status of local livestock breeds in Korea, registered in DADIS. http://www.nias.go.kr/ Accessed July 12, 2013.
27 Qanbari, S., Gianola, D., Hayes, B., Schenkel, F., Miller, S., Moore, S., Thaller, G., and Simianer, H. (2011) Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 12, 318.   DOI
28 Schenkel, F. S., Miller, S. P., Jiang, Z., Mandell, I. B., Ye, X., Li, H., and Wilton, J. W. (2006) Association of a single nucleotide polymorphism in the calpastatin gene with carcass and meat quality traits of beef cattle. J. Anim. Sci. 84, 291-299.
29 Sherman, E. L., Nkrumah, J. D., and Moore, S. S. (2010) Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J. Anim. Sci. 88, 16-22.   DOI   ScienceOn
30 Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S., Abeysinghe, S., Krawczak, M., and Cooper, D. N. (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. 21, 577-581.   DOI   ScienceOn
31 Stothard, P., Choi, J. W., Basu, U., Sumner-Thomson, J. M., Meng, Y., Liao, X., and Moore, S. S. (2011). Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12, 559.   DOI
32 Zimin, A. V., Delcher, A. L., Florea, L., Kelley, D. R., Schatz, M. C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C. P., Sonstegard, T. S., Marcais, G., Roberts, M., Subramanian, P., Yorke, J. A., Salzberg, S. L. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 10, R42.   DOI   ScienceOn
33 Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., Lien, S., Matukumalli, L. K., McEwan, J. C., Nazareth, L. V., Schnabel, R. D., Weinstock, G. M., Wheeler, D. A., Ajmone-Marsan, P., Boettcher, P. J., Caetano, A. R., Garcia, J. F., Hanotte, O., Mariani, P., Skow, L. C., Sonstegard, T. S., Williams, J. L., Diallo, B., Hailemariam, L., Martinez, M. L., Morris, C. A., Silva, L. O., Spelman, R. J., Mulatu, W., Zhao, K., Abbey, C. A., Agaba, M., Araujo, F. R., Bunch, R. J., Burton, J., Gorni, C., Olivier, H., Harrison, B. E., Luff, B., Machado, M. A., Mwakaya, J., Plastow, G., Sim, W., Smith, T., Thomas, M. B., Valentini, A., Williams, P., Womack, J., Woolliams, J. A., Liu, Y., Qin, X., Worley, K. C., Gao, C., Jiang, H., Moore, S. S., Ren, Y., Song, X. Z., Bustamante, C. D., Hernandez, R. D., Muzny, D. M., Patil, S., San Lucas, A., Fu, Q., Kent, M. P., Vega, R., Matukumalli, A., McWilliam, S., Sclep, G., Bryc, K., Choi, J., Gao, H., Grefenstette, J. J., Murdoch, B., Stella, A., Villa-Angulo, R., Wright, M., Aerts, J., Jann, O., Negrini, R., Goddard, M. E., Hayes, B. J., Bradley, D. G., Barbosa da Silva, M., Lau, L. P., Liu, G. E., Lynn, D. J., Panzitta, F., and Dodds, K. G. (2009). Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528-532.   DOI   ScienceOn