DOI QR코드

DOI QR Code

BcSNPdb: Bovine Coding Region Single Nucleotide Polymorphisms Located Proximal to Quantitative Trait Loci

  • Moon, Sun-Jin (Laboratory of Bioinformatics and Population Genetics, School of Agricultural Biotechnology, Seoul National University) ;
  • Shin, Hyoung-Doo (Department of Genetic Epidemiology, SNP Genetics Inc.) ;
  • Cheong, Hyun-Sub (Department of Genetic Epidemiology, SNP Genetics Inc.) ;
  • Cho, Hye-Young (Department of Genetic Epidemiology, SNP Genetics Inc.) ;
  • NamGoong, Sohg (Department of Genetic Epidemiology, SNP Genetics Inc.) ;
  • Kim, Eun-Mi (Department of Genetic Epidemiology, SNP Genetics Inc.) ;
  • Han, Chang-Su (Department of Genetic Epidemiology, SNP Genetics Inc.) ;
  • Sung, Sam-Sun (Laboratory of Bioinformatics and Population Genetics, School of Agricultural Biotechnology, Seoul National University) ;
  • Kim, Hee-Bal (Laboratory of Bioinformatics and Population Genetics, School of Agricultural Biotechnology, Seoul National University)
  • Published : 2007.01.31

Abstract

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

Keywords

References

  1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402. https://doi.org/10.1093/nar/25.17.3389
  2. Cohen-Zinder, M., Seroussi, E., Larkin, D. M., Loor, J. J., Evertsvan der Wind, A., Lee, J. H., Drackley, J. K., Band, M. R., Hernandez, A. G., Shani, M., Lewin, H. A., Weller, J. I. and Ron, M. (2005) Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Res. 15, 936-944. https://doi.org/10.1101/gr.3806705
  3. Day, I. N., Chen, X. H., Gaunt, T. R., King, T. H., Voropanov, A., Ye, S., Rodriguez, S., Syddall, H. E., Sayer, A. A., Dennison, E. M., Tabassum, F., Barker, D. J., Cooper, C. and Phillips, D. I. (2004) Late life metabolic syndrome, early growth, and common polymorphism in the growth hormone and placental lactogen gene cluster. J. Clin. Endocrinol. Metab. 89, 5569-5576. https://doi.org/10.1210/jc.2004-0152
  4. Fahrenkrug, S. C., Freking, B. A., Smith, T. P., Rohrer, G. A. and Keele, J. W. (2002) Single nucleotide polymorphism (SNP) discovery in porcine expressed genes. Anim. Genet. 33, 186-195. https://doi.org/10.1046/j.1365-2052.2002.00846.x
  5. Hawken, R. J., Barris, W. C., McWilliam, S. M. and Dalrymple, B. P. (2004) An interactive bovine in silico SNP database (IBISS). Mamm. Genome 15, 819-827. https://doi.org/10.1007/s00335-004-2382-4
  6. Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. and Cox, D. R. (2005) Whole-Genome Patterns of Common DNA Variation in Three Human Populations. Science 307, 1072-1079. https://doi.org/10.1126/science.1105436
  7. Hirschhorn, J. N. (2005) Genetic approaches to studying common diseases and complex traits. Pediatr. Res. 57, 74-77. https://doi.org/10.1203/01.PDR.0000159574.98964.87
  8. Innan, H. and Kim, Y. (2004) Pattern of polymorphism after strong artificial selection in a domestication event. PNAS 101, 10667-10672. https://doi.org/10.1073/pnas.0401720101
  9. Iseli, C., Jongeneel, C. V. and Bucher, P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 138-48.
  10. Kent, W. J. (2002) BLAT--the BLAST-like alignment tool. Genome Res. 12, 656-664. https://doi.org/10.1101/gr.229202.ArticlepublishedonlinebeforeMarch2002
  11. Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., 3rd, Zody, M. C., et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803-819. https://doi.org/10.1038/nature04338
  12. Mendrzyk, F., Korshunov, A., Toedt, G., Schwarz, F., Korn, B., Joos, S., Hochhaus, A., Schoch, C., Lichter, P. and Radlwimmer, B. (2006) Isochromosome breakpoints on 17p in medulloblastoma are flanked by different classes of DNA sequence repeats. Genes Chromosomes Cancer 45, 401-410. https://doi.org/10.1002/gcc.20304
  13. Nagaki, K., Cheng, Z., Ouyang, S., Talbert, P. B., Kim, M., Jones, K. M., Henikoff, S., Buell, C. R. and Jiang, J. (2004) Sequencing of a rice centromere uncovers active genes. Nat. Genet. 36, 138-145. https://doi.org/10.1038/ng1289
  14. Nickerson, D. A., Tobe, V. O. and Taylor, S. L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745-2751. https://doi.org/10.1093/nar/25.14.2745
  15. Ramensky, V., Bork, P. and Sunyaev, S. (2002) Human nonsynonymous SNPs: server and survey. Nucleic Acids Res. 30, 3894-3900. https://doi.org/10.1093/nar/gkf493
  16. Sachidanandam, R., Weissman, D., Schmidt, S. C., Kakol, J. M., Stein, L. D., Marth, G., Sherry, S., Mullikin, J. C., Mortimore, B. J., Willey, D. L., et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933. https://doi.org/10.1038/35057149
  17. She, X., Horvath, J. E., Jiang, Z., Liu, G., Furey, T. S., Christ, L., Clark, R., Graves, T., Gulden, C. L., Alkan, C., Bailey, J. A., Sahinalp, C., Rocchi, M., Haussler, D., Wilson, R. K., Miller, W., Schwartz, S. and Eichler, E. E. (2004) The structure and evolution of centromeric transition regions within the human genome. Nature 430, 857-864. https://doi.org/10.1038/nature02806
  18. Stone, R. T., Casas, E., Smith, T. P., Keele, J. W., Harhay, G., Bennett, G. L., Koohmaraie, M., Wheeler, T. L., Shackelford, S. D. and Snelling, W. M. (2005) Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: development of a low-density single nucleotide polymorphism map. J. Anim. Sci. 83, 2280-2288. https://doi.org/10.2527/2005.83102280x
  19. Stone, R. T., Grosse, W. M., Casas, E., Smith, T. P., Keele, J. W. and Bennett, G. L. (2002) Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers. Mamm. Genome 13, 211-215. https://doi.org/10.1007/s00335-001-2124-9
  20. Wade, C. M., Kulbokas, E. J., 3rd, Kirby, A. W., Zody, M. C., Mullikin, J. C., Lander, E. S., Lindblad-Toh, K. and Daly, M. J. (2002) The mosaic structure of variation in the laboratory mouse genome. Nature 420, 574-578. https://doi.org/10.1038/nature01252
  21. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., Helmberg, W., et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33, 39-45.
  22. Wright, S. I., Bi, I. V., Schroeder, S. G., Yamasaki, M., Doebley, J. F., McMullen, M. D. and Gaut, B. S. (2005) The effects of artificial selection on the maize genome. Science 308, 1310-1314. https://doi.org/10.1126/science.1107891

Cited by

  1. Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence vol.39, pp.2, 2008, https://doi.org/10.1111/j.1365-2052.2007.01686.x