Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

A Single Nucleotide Polymorphism in LOC534614 as an Unknown Gene Associated with Body Weight and Cold Carcass Weight in Hanwoo (Korean Cattle)

  • Lee, Y.S. (Institution of Charmpoom Hanwoo) ;
  • Oh, D.Y. (School of Biotechnology, Yeungnam University) ;
  • Kim, J.J. (School of Biotechnology, Yeungnam University) ;
  • Lee, J.H. (Gyeongbuk Livestock Research Institution) ;
  • Park, H.S. (Korea Research Institute of Bioscience and Biotechnology) ;
  • Yeo, J.S. (School of Biotechnology, Yeungnam University)
  • Received : 2010.03.24
  • Accepted : 2010.06.16
  • Published : 2010.12.01
Download PDF
⟨ Previous Next ⟩

Abstract

A major aim of cattle genome research is to identify candidate genes associated with meat quantity and quality through QTL analysis for application in the livestock industry. Therefore, this study focused on discovery of useful SNPs within the LOC534614 gene, containing 12273_165 SNP which is located on the same site as the QTL on chromosome 6, and evaluation of the association between SNP and body weight and cold carcass weight in Hanwoo (Korean cattle) As a result of a BLAST search of the NCBI web site, we discovered that the mRNA sequence of the LOC534614 gene was similar to that of the coiled-coil domain containing 158 (CCDC158) for dog and human. According to the direct DNA sequence from the CCDC158 gene, we identified 19 polymorphic SNPs within exons and their flanking regions. Among them, 17 polymorphic SNPs were selected for genotyping in Hanwoo (n = 476) and seventeen marker haplotypes containing 12273_165 SNP (frequency >0.1) were identified. As a result of the association between 17 polymorphic SNPs and Hanwoo (n = 476), g.8778G>A SNP in exon 6 was found to be a non-synonymous SNP, and was significantly associated with body weight and cold carcass weight (p<0.05). We discovered 19 polymorphic SNPs in the CCDC158 gene on the QTL region of BTA 6 in Hanwoo and identified that the g.8778G>A SNP was significantly associated with body weight and cold carcass weight (p<0.05), which causes an amino acid variation from valine to methionine. Furthermore, statistical analysis demonstrated that the CCDC158 gene is strongly associated with body weight and cold carcass weight in Hanwoo. In this regard, the g.8778G>A SNP in the CCDC158 gene can be useful as a positional candidate for body weight and cold carcass weight for marker-assisted selection in Hanwoo.

Keywords

References

  1. Barendse, W., R. Bunch, M. Thomas, S. Armitage, S. Baud and N. Donaldson. 2004. The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle. Aust. J. Exp. Agric. 44:669-674. https://doi.org/10.1071/EA02156
  2. Barrett, J. C., B. Fry, J. Maller and M. J. Daly. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263-265. https://doi.org/10.1093/bioinformatics/bth457
  3. Casas, E., S. D. Shackelford, J. W. Keele, M. Koohmaraie, T. P. L. Smith and R. T Stone. 2003. Detection of quantitative trait loci for growth and carcass composition in cattle. J. Anim. Sci. 81:2976-2983.
  4. Casas, E., S. D. Shackelford, J. W. Keele, R. T. Stone, S. M. Kappes and M. Koohmaraie. 2000. Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. J. Anim. Sci. 78:560-569.
  5. Eberlein, A., A. Takasuga, K. Setoguchi, R. Pfuhl, K. Flisikowski, R. Fries, N. Klopp, R. Fürbass, R. Weikard and C. Kühn. 2009. Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene. Genetics 183:951-964. https://doi.org/10.1534/genetics.109.106476
  6. Fitzsimmons, C. J., S. M. Schmutz, R. D. Bergen and J. J. McKinnon. 1998. A potential association between the BM 1500 microsatellite and fat deposition in beef cattle. Mamm. Genome 6:432-434.
  7. Fitzsimmons, C. J. and S. M. Schmutz. 1999. A SNP in the leptin gene leads to a change in the amino acid sequence of the mature protein in cattle.: Plant and Animal Genome VII conference. San Diego. USA. pp. 17-21.
  8. Gabriel, S. B., S. F. Schaffner, H. Nguyen, J. M. Moore, J. Roy, B. Blumenstiel, J. Higgins, M. DeFelice, A. Lochner, M. Faggart, S. N. Liu-Cordero, C. Rotimi, A. Adeyemo, R. Cooper, R. Ward, E. S. Lander, M. J. Daly and D. Altshuler. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229. https://doi.org/10.1126/science.1069424
  9. Glover, J. N. and S. C. Harrison. 1995. Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA. Nature 373:257-261. https://doi.org/10.1038/373257a0
  10. Kim, J. W., S. I. Park and J. S. Yeo. 2003. Linkage mapping and QTL on chromosome 6 in Hanwoo(Korean Cattle). Asian-Aust. J. Anim. Sci. 16:1402-1405. https://doi.org/10.5713/ajas.2003.1402
  11. Kneeland, J., C. Li, J. Basarab, W. M. Snelling, B. Benkel, B. Murdoch, C. Hansen and S. S. Moore. 2004. Identification and fine mapping of quantitative trait loci for growth traits on bovine chromosomes 2, 6, 14, 19, 21, 23 within one commercial line of Bos taurus. J. Anim. Sci. 82:3405-3414.
  12. Lee, Y. S., J. H. Lee, J. Y. Lee, J. J. Kim, H. S. Park and J. S. Yeo. 2008. Identification of candidate SNP (Single Nucleotide Polymorphism) for growth and carcass traits related to QTL on chromosome 6 in Hanwoo (Korean Cattle). Asian-Aust. J. Anim. Sci. 21:1703-11709. https://doi.org/10.5713/ajas.2008.80223
  13. Mason, J. M. and K. M. Arndt. 2004. Coiled coil domain: stability, specificity and biological implications. Chembiochem 5:170-176. https://doi.org/10.1002/cbic.200300781
  14. Page, B. T., E. Casas, M. P. Heaton, N. G. Cullen, D. L. Hyndman, C. A. Morris, A. M. Crawford, T. L. Wheeler, M. Koohmaraie, J. W. Keele and T. P. L. Smith. 2002. Evaluation of singlenucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. J. Anim. Sci. 80:3077-3085.
  15. Primer3 software http://frodo.wi.mit.edu/cgi_bin/primer3/primer3_www.cgi
  16. Sambrook, J. and D. W. Russell. 2001. Molecular cloning: A laboratory manual. Vol. 1. 3rd edition.: Cold Spring Harbor. New York. pp. 6.4-6.12.
  17. Setoguchi, K., M. Furuta, T. Hirano, T. Nagao, T. Watanabe, Y. Sugimoto and A. Takasuga. 2009. Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate. BMC Genet. 10:43-54.
  18. Snelling, W. M., E. Casas, R. T. Stone, J. W. Keele, G. P. Harhay, G. L. Bennett and T. P. L. Smith. 2005. Linkage mapping bovine EST_based SNP. BMC. Genomics. 6:74-83. https://doi.org/10.1186/1471-2164-6-74
  19. Stephens, M., N. J. Smith and P. Donnelly. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68:978-989. https://doi.org/10.1086/319501
  20. Takasuga, A., T. Watanabe, Y. Mizoguchi, T. Hirano, N. Ihara, A. Takano, K. Yokouchi, A. Fujikawa, K. Chiba, N. Kobayashi, K. Tatsuda, T. Oe, M. Furukawa-Kuroiwa, A. Nishimura-Abe, T. Fujita, K. Inoue, K. Mizoshita, A. Ogino and Y. Sugimoto. 2007. Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-bydescent mapping. Mamm. Genome 18:125-136. https://doi.org/10.1007/s00335-006-0096-5
  21. Vreeland, W. N., R. J. Meagher and A. E. Barron. 2002. Multiplexed, highthroughput genotyping by single_base extension and endlabeled free_solution electrophoresis. Anal. Chem. 74:4328-4333. https://doi.org/10.1021/ac0258094

Cited by

  1. Identification of SNP(Single Nucleotide Polymorphism) from MC1R, MITF and TYRP1 associated with Feather Color in Chicken vol.41, pp.1, 2014, https://doi.org/10.5536/KJPS.2014.41.1.29
  2. Application of Linkage Disequilibrium Mapping Methods to Detect QTL for Carcass Quality on Chromosome 6 Using a High Density SNP Map in Hanwoo vol.24, pp.4, 2010, https://doi.org/10.5713/ajas.2011.11019
  3. Identification of Superior Single Nucleotide Polymorphisms (SNP) Combinations Related to Economic Traits by Genotype Matrix Mapping (GMM) in Hanwoo (Korean Cattle) vol.24, pp.11, 2010, https://doi.org/10.5713/ajas.2011.11112
  4. Determination of the effect of functional single-nucleotide polymorphisms associated with glycerolipid synthesis on intramuscular fat deposition in Korean cattle steer vol.64, pp.1, 2021, https://doi.org/10.5194/aab-64-27-2021