Genomic Scan of Selective Signature in Kurd Horse

Document Type : Genetic

Authors

1 Animal Science Department, Gonbad-e-Kavous University, Gonbad-e-Kavos, Iran, P.O.Box: 163

2 Animal Science Department, Agricultural Sciences and Natural Resources University of Sari, Sari, Iran, POBox: 5780

3 Department of Animal Science, Campus of Tehran University, Karaj, Iran, POBox: 4111

4 Department of Animal Science, Faculty of Agriculture, Zanjan University, Zanjan, Iran, POBox: 313

Abstract

The selection of useful mutations in some populations will leave footprints at the genome level. Because of the link between these regions and important economic traits, genomics is one of the important issues in animal genetic research. The aim of this research is to identify regions of the genome which carrier signature of selection in Kurd horse using 70kb SNP markers. 28 horses selected from the different area of Kurdistan and Kermanshah, after collected sample, DNA extracted, they were genotyping. To detect footprint of signal selection, extended haplotype homozygosity (EHH) and integrated Haplotype Score (iHS) was used. The using of iHS statistics, 9 genomic regions on chromosomes 5,7,11 and 15 as regions candidate of footprint selection, identified. For the detect effect of selection on this region, used of EHH as well as investigate of bifurcation diagram of haplotype and LD. In order to evaluate the possible genes and QTLs in selected candidate regions, used of the horse SNP databases (HSDB) and the QTL of the animals. The regions on 7 and 11 chromosomes were observed as candidate positive selection while in other regions (chromosomes 5 and 15), notwithstanding allele frequency, it wasn’t affected positive selection so these alleles were the common and old alleles. In these regions, a number of genes and QTLs were identified that are active in the muscle, immune system and intracellular activity. Therefore, these genomic regions of Kurd horse, probability were targeted positive selection.

Keywords


  1. Akey, J.M., 2009. Constructing genomic maps of positive selection in humans. Where do we go from here? Genome Research. Vol. 19, pp: 711-722.
  2. Bahbahani, H.; Clifford, H.; Wragg, D.; Mbole-Kariuki, M.N.; Tassell, C.V.; Sonstegard, T.; woolhouse, M. and Hanotte, O., 2015. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis. Scientific Reports. Vol. 5, pp: 1-13.
  3. Barrett, R.D.H. and Schluter, D., 2007. Adaptation from standing genetic variation. Trends in Ecology and Evolution. Vol. 23, pp: 38-44.
  4. Biswas, S. and Akey, J.M., 2006. Genomic insights into positive selection. Trends in Genetics. Vol. 22, pp: 437-436.
  5. Charlesworth, B., 2007. A hitch-hiking guide to the genome: A commentary on 'The hitch-hiking effect of a favourable gene' by John Maynard Smith and John Haigh. Genetic Research. Vol. 89, pp: 389-390.
  6. Diamond, J., 2002. Evolution, consequences and future of plant and animal domestication. Nature. Vol. 418,
    pp:700-707.
  7. Emmeline, W.H.; Beatrice, A.M.; Jingjing, G.U.; Ronan, W. and David, E.M., 2010. A genome-wide SNP-association study onfirms a sequence variant (g.66493737C>T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC genetics. Vol. 11, pp: 1-10.
  8. Flory, L.; Fritz, S.; Jaffrézic, F.; Boussaha, M.; Gut, I.; Heath, S.; Foulley, J.L. and Gautier, M., 2009. The genome response to artificial selection: A case study in dairy cattle. PLOS One. Vol. 4, pp: 6595.
  9. Gautier, M. and Renaud, V., 2012. Rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics. Vol. 28, pp: 1176-1177.
  10. Harris, E.E. and Meyer, D., 2006. The molecular signature of selection underlying human adaptations. American Journal of Physical Anthropology. Vol. 131, pp: 89-130.
  11. Hayes, B.; Lien, S.; Nilsen, H.; Olsen, H.G.; Berg, P.; MacEachern, S.; Potter, S. and Meuwissen, T.H.E., 2008. The origin of selection signatures on bovine chromosome six. Animal Genetics. Vol. 39,
    pp: 105-111.
  12. Jessica Petersen, J.L.; Mickelson, J.R.; Cothran, E.G.; L.S. and Andersson, J.A., 2013. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLOS ONE. Vol. 8, No. 1, pp: 54997.
  13. Kaplan, N.L.; Hudson, R.R. and Langley, C.H., 1989. The Hitchhiking Effect revisited. Genetics. Vol. 123,
    pp: 887-899. 
  14. Kim, Y. and Stephan, W., 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics. Vol. 160, pp: 765-777. 
  15. Kimura, M., 1989. The neutral theory of molecular evolution and the world view of neutralists. Genome.
    Vol. 31, pp: 24-31.
  16. Maynard-Smith, J. and Haigh, J., 1974. The hitch-hiking effect of a favorable gene. Genetic Research. Vol. 23,
    pp: 23-35.
  17.  Miller, S.A.; Dykes, D.D. and Pole sky, H.F., 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research. Vol. 16, 1215 p.
  18. Nielsen, R., 2001. Statistical tests of selective neutrality in the age of genomics. Heredity. Vol. 86, pp: 641-647.
  19. Nielsen, R., 2005. Molecular signatures of natural selection. Annual Review of Genetics. Vol. 39, pp:197-218. 
  20. Purcell, S.; Neale, B.; Todd-Brown, K.; Thomas, L.; Ferreira, M.A.; Bender, D.; Maller, J.; Sklar, P.; Bakker, P.I. and Daly, M.J., 2007. PLINK: a tool set for whole genome association and population-based linkage analyses. The American Journal of Human Genetics. Vol. 81, pp: 559-575.
  21. 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. Vol. 16, pp: 12-318.
  22. Qanbari, S.; Pausch, H.; Janse, S.; Somel, M.; Strom, T.M.; Fries, R.; Nielsen, R. and Simianer, H., 2014. Classic selective sweeps revealed by massive sequencing in cattle. PLOS Genet. Vol. 10, pp:1004148.
  23. Sabeti, P.; Reich, D.E.; Higgins, J.M.; Levine, H.Z.; Richter,  D.J.; Schaffner, S.F.; Gabriel, S.B.; Platko, J.V.; Patterson, N.J.; McDonald, G.J.; Ackerman, H.J.; Campbell, S.J.; Altshuler, D.;   Cooper, R.; Kwiatkowski,  D.; Ward, R. and  Lander, E.S., 2002.  Detecting recent positive selection in the human genome from haplotype structure. Nature. Vol. 419, pp:832-837.
  24. Sabeti, P.; Schaffner, S.F.; Fry, B.; Lohmueller, J.; Varilly, P.; Shamovsky, O.; Palma, A.; Mikkelsen, T.S.; Altshuler, D. and Lande, E.S., 2006. Positive natural selection in the human lineage. Science. Vol. 3129,
    pp: 1614-1620.
  25. Scheet, P. and Stephens, M., 2006. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. The American Journal of Human Genetics. Vol. 78, pp: 629-644.
  26. Schurink, A.; Ducro, B.J.; Bastiaansen, J.W.M.; Frankena, K. and van Arendonk, J.A.M., 2012. Genome wide association study of insect bite hypersensitivity in Dutch Shetland pony marses. Animal genetics. Vol. 44,
    pp: 44-52.
  27. Teo, Y.Y.; Fry, A.E.; Clark, T.G.; Tai, E.S. and Seielstad, M., 2007. On the Usage of HWE for identifying genotyping errors. Annals of Human Genetics. Vol. 71, pp: 701-703.
  28. Voight, B.F.; Kudaravalli, S.; Wen, X. and Pritchard. J.K., 2006. A map of recent positive selection in the human genome. PLOS Biology. Vol. 4, pp: 72.
  29. Yun Young, G.O.; Ernest, B.;   Deborah, G.; Cook, J.; Stephen, J.; Coleman, J.; James, N.;  MacLeod, N.; Kuey-Chu, C.; Peter, J.; Timoney, J. and  Udeni Balasuriya, B.R., 2011. Genome-wide association study among four horse breeds identifies a common haplotype associated with in vitro CD3+ T cell susceptibility/resistance to equine arteritis virus infection. Journal of Virology. Vol. 24, pp:13174-13184.
  30. Zola, H.; Swart, B.; Banham, A.; Barry, S.; Beare, A.; Bensussan, A.; Boumsell, L.; Buckley, D.; Bühring, H.J.; Clark, G.; Engel, P.; Fox, D.; Jin, B.Q.; Macardle, P.J.; Malavasi, F.; Mason, D.; Stockinger, H. and Yang, X., 2007. CD molecules -human cell differentiation molecules. Journal Immunology Methods. Vol. 319,
    pp: 1-5.