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Identification of Recently Selected Mutations Driven by Artificial Selection in Hanwoo (Korean Cattle)

  • Lim, Dajeong ;
  • Gondro, Cedric ;
  • Park, Hye Sun ;
  • Cho, Yong Min ;
  • Chai, Han Ha ;
  • Seong, Hwan Hoo ;
  • Yang, Bo Suk ;
  • Hong, Seong Koo ;
  • Chang, Won Kyung ;
  • Lee, Seung Hwan
  • Received : 2012.08.20
  • Accepted : 2012.10.24
  • Published : 2013.05.01

Abstract

Hanwoo have been subjected over the last seventy years to intensive artificial selection with the aim of improving meat production traits such as marbling and carcass weight. In this study, we performed a signature of selection analysis to identify recent positive selected regions driven by a long-term artificial selection process called a breeding program using whole genome SNP data. In order to investigate homozygous regions across the genome, we estimated iES (integrated Extended Haplotype Homozygosity SNP) for the each SNPs. As a result, we identified two highly homozygous regions that seem to be strong and/or recent positive selection. Five genes (DPH5, OLFM3, S1PR1, LRRN1 and CRBN) were included in this region. To go further in the interpretation of the observed signatures of selection, we subsequently concentrated on the annotation of differentiated genes defined according to the iES value of SNPs localized close or within them. We also described the detection of the adaptive evolution at the molecular level for the genes of interest. As a result, this analysis also led to the identification of OLFM3 as having a strong signal of selection in bovine lineage. The results of this study indicate that artificial selection which might have targeted most of these genes was mainly oriented towards improvement of meat production.

Keywords

Hanwoo;Signatures of Selection;SNP

References

  1. Weir, B. S., L. R. Cardon, A. D. Anderson, D. M. Nielsen and W. G. Hill. 2005. Measures of human population structure show heterogeneity among genomic regions. Genome Res. 15:1468-1476. https://doi.org/10.1101/gr.4398405
  2. Yamada. T., S. Sasaki, S. Sukegawa, T. Miyake, T. Fujita, H. Kose, M. Morita, Y. Takahagi, H. Murakami and F. Morimatsu et al.. 2010. Novel SNP in 5' flanking region of EDG1 associated with marbling in Japanese Black beef cattle. Anim. Sci. J. 80:486-489.
  3. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
  4. Yang, Z. and J. P. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15:496-503. https://doi.org/10.1016/S0169-5347(00)01994-7
  5. Yoon, D., Y. S. Kwon, K. Y. Lee, W. Y. Jung, S. Sasazaki, H. Mannen, J. T. Jeon and J. H. Lee. 2008. Discrimination of Korean cattle (Hanwoo) using DNA markers derived from SNPs in bovine mitochondrial and SRY genes. Asian Australas. J. Anim. Sci. 21:25-28. https://doi.org/10.5713/ajas.2008.70209
  6. Lynn, D. J., A. R. Freeman, C. Murray and D. G. Bradley. 2005. A genomics approach to the detection of positive selection in cattle: adaptive evolution of the T-cell and natural killer cell-surface protein CD2. Genetics 170:1189-1196. https://doi.org/10.1534/genetics.104.039040
  7. MacEachern, S., B. Hayes, J. McEwan and M. Goddard. 2009. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics 10:181. https://doi.org/10.1186/1471-2164-10-181
  8. Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter, S. F. Schaffner, S. B. Gabriel, J. V. Platko, N. J. Patterson and G. J. McDonald, et al.. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837. https://doi.org/10.1038/nature01140
  9. Sasaki, Y., K. Nagai, Y. Nagata, K. Doronbekov, S. Nishimura, S. Yoshioka, T. Fujita, K. Shiga, T. Miyake, Y. Taniguchi and T. Yamada. 2006. Exploration of genes showing intramuscular fat deposition-associated expression changes in musculus longissimus muscle. Anim. Genet. 37:40-46. https://doi.org/10.1111/j.1365-2052.2005.01380.x
  10. Sharma, N. K., S. K. Das, A. K. Mondal, O. G. Hackney, W. S. Chu, P. A. Kern, N. Rasouli, H. J. Spencer, A. Yao-Borengasser and S. C. Elbein. 2008. Endoplasmic reticulum stress markers are associated with obesity in nondiabetic subjects. J. Clin. Endocrinol. Metab. 93:4532-4541. https://doi.org/10.1210/jc.2008-1001
  11. Sharon, D., G. Glusman, Y. Pilpel, M. Khen, F. Gruetzner, T. Haaf and D. Lancet. 1999. Primate evolution of an olfactory receptor cluster: diversification by gene conversion and recent emergence of pseudogenes. Genomics 61:24-36. https://doi.org/10.1006/geno.1999.5900
  12. Stone, E. M., J. H. Fingert, W. L. Alward, T. D. Nguyen, J. R. Polansky, S. L. Sunden, D. Nishimura, A. F. Clark, A. Nystuen and B. E. Nichols. 1997. Identification of a gene that causes primary open angle glaucoma. Science 275:668-670. https://doi.org/10.1126/science.275.5300.668
  13. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
  14. Tang. K, K. R. Thornton, M. Stoneking. 2007. A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5:e171. https://doi.org/10.1371/journal.pbio.0050171
  15. Tang, S., J. P. Kerry, D. Sheehan, D. J. Buckley and P. A. Morrissey. 2001. Antioxidative effect of added tea catechins on susceptibility of cooked red meat, poultry and fish patties to lipid oxidation. Food Res. Int. 34:651-657. https://doi.org/10.1016/S0963-9969(00)00190-3
  16. Torrado, M., R. Trivedi, R. Zinovieva, I. Karavanova and S. I. Tomarev. 2002. Optimedin: a novel olfactomedin-related protein that interacts with myocilin. Hum. Mol. Genet. 11:1291-1301. https://doi.org/10.1093/hmg/11.11.1291
  17. Voight, B. F., S. Kudaravalli, X. Wen and J. K. Pritchard. 2006. A map of recent positive selection in the human genome. PLoS Biol. 4:e72. https://doi.org/10.1371/journal.pbio.0040072
  18. Wei, Y., D. Wang and M. J. Pagliassotti. 2007. Saturated fatty acid-mediated endoplasmic reticulum stress and apoptosis are augmented by trans-10, cis-12-conjugated linoleic acid in liver cells. Mol. Cell Biochem. 303:105-113. https://doi.org/10.1007/s11010-007-9461-2
  19. Bradley, D. G. and E. P. Cunningham. 1999. Genetic aspects of domestication. In: The genetics of cattle (Ed. R. Fries and A. Ruvinsky) pp. 15-31. CABI Publishing, Wallingford.
  20. Clark, A. G., S. Glanowski, R. Nielsen, P. D. Thomas, A. Kejariwal, M. A. Todd, D. M. Tanenbaum, D. Civello, F. Lu, B. Murphy, et al. 2003. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302:1960-1963. https://doi.org/10.1126/science.1088821
  21. Fay, J. C. and C. I. Wu. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
  22. Flicek, P., B. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham and T. Cutts. 2008. Ensembl 2008. Nucleic Acids Res. 36 (Suppl 1):D707.
  23. Goldman, N. and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
  24. Hannun, Y. A. and L. M. Obeid. 2008. Principles of bioactive lipid signalling: lessons from sphingolipids. Nat. Rev. Mol. Cell Biol. 9:139-150. https://doi.org/10.1038/nrm2329
  25. Hayes, B. J., A. J. Chamberlain, S. Maceachern, K. Savin, H. McPartlan, I. MacLeod, L. Sethuraman and M. E. Goddard. 2009. A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Anim. Genet. 40:176-184. https://doi.org/10.1111/j.1365-2052.2008.01815.x
  26. Kim, Y. and R. Nielsen. 2004. Linkage disequilibrium as a signature of selective sweeps. Genetics 167:1513-1524. https://doi.org/10.1534/genetics.103.025387
  27. Kim, Y. and W. Stephan. 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160:765-777.
  28. Kimura, T., K. Sato, E. Malchinkhuu, H. Tomura, K. Tamama, A. Kuwabara, M. Murakami and F. Okajima. 2003. High-density lipoprotein stimulates endothelial cell migration and survival through sphingosine 1-phosphate and its receptors. Arterioscler Thromb. Vasc. Biol. 23:1283-1288. https://doi.org/10.1161/01.ATV.0000079011.67194.5A
  29. Lee, K. M., S. Jo, H. Kim, J. Lee and C. S. Park. 2011. Functional modulation of AMP-activated protein kinase by cereblon. Biochim. Biophys. Acta. 1813:448-455. https://doi.org/10.1016/j.bbamcr.2011.01.005
  30. Lee, S. H ., J. H. van der Werf, N. K. Kim , S. H. Lee , C. Gondro, E. W. Park , S. J. Oh , J. P. Gibson and J. M. Thompson . 2011. QTL and gene expression analyses identify genes affecting carcass weight and marbling on BTA14 in Hanwoo (Korean Cattle). Mamm. Genome 22:589-601. https://doi.org/10.1007/s00335-011-9331-9
  31. Lee, W. J., M. Kim, H. S. Park, H. S. Kim, M. J. Jeon, K. S. Oh, E. H. Koh, J. C. Won, M. S. Kim and G. T. Oh. 2006. AMPK activation increases fatty acid oxidation in skeletal muscle by activating PPAR and PGC-1. Biochem. Biophys. Res. Commun. 340:291-295. https://doi.org/10.1016/j.bbrc.2005.12.011
  32. Andreae, L. C., D. Peukert, A. Lumsden and J. D. Gilthorpe. 2007. Analysis of Lrrn1 expression and its relationship to neuromeric boundaries during chick neural development. Neural. Dev. 2:22. https://doi.org/10.1186/1749-8104-2-22
  33. Bluher, M., L. Wilson-Fritch, J. Leszyk, P. G. Laustsen, S. Corvera and C. R. Kahn . 2004. Role of insulin action and cell size on protein expression patterns in adipocytes. J. Biol. Chem. 279:31902-31909. https://doi.org/10.1074/jbc.M404570200

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