Browse > Article
http://dx.doi.org/10.5713/ajas.14.0696

A Genome-wide Scan for Selective Sweeps in Racing Horses  

Moon, Sunjin (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Lee, Jin Woo (Horse Registry, Korea Racing Authority (KRA))
Shin, Donghyun (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Shin, Kwang-Yun (Institute for Livestock Promotion)
Kim, Jun (Institute for Livestock Promotion)
Choi, Ik-Young (Genome analysis center, National Instrumentation and Environmental Management (NICEM), Seoul National University)
Kim, Jaemin (Interdisciplinary Program in Bioinformatics, Seoul National University)
Kim, Heebal (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.28, no.11, 2015 , pp. 1525-1531 More about this Journal
Abstract
Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.
Keywords
Single Nucleotide Polymorphism; Racehorse; Selective Sweep; Quantitative Trait Loci;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 Nei, M. and W. H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. 76:5269-5273.   DOI   ScienceOn
2 Orlando, L., A. Ginolhac, G. Zhang, D. Froese, A. Albrechtsen, M. Stiller, M. Schubert, E. Cappellini, B. Petersen, and I. Moltke et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499:74-78.   DOI   ScienceOn
3 Park, K. D., H. Kim, J. Y. Hwang, C. K. Lee, K. T. Do, H. S. Kim, Y. M. Yang, Y. J. Kwon, J. Kim, H. J. Kim, K. D. Song, J. D. Oh, H. Kim, B. W. Cho, S. Cho, and H. K. Lee. 2014. Copy number deletion has little impact on gene expression levels in racehorses. Asian Australas. J. Anim. Sci. 27:1345-1354.   DOI   ScienceOn
4 Petersen, J. L., J. R. Mickelson, E. G. Cothran, L. S. Andersson, J. Axelsson, E. Bailey, D. Bannasch, M. M. Binns, A. S. Borges, and P. Brama et al. 2013. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One 8(1):e54997.   DOI
5 Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. W. de Bakker, M. J. Daly, and P. C. Sham. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81:559-575.   DOI   ScienceOn
6 Qanbari, S., H. Pausch, S. Jansen, M. Somel, T. M. Strom, R. Fries, R. Nielsen, and H. Simianer. 2014. Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genet. 10(2):e1004148.   DOI
7 Riquetl, I., A. Schoeberleinl, S. Dunnerz, F. Menissier, and I. Massabanda. 1997. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nat. Genet. 17:71-71.   DOI   ScienceOn
8 Suzuki, J., Y. Yamazaki, L. Guang, Y. Kaziro, and H. Koide. 2000. Involvement of Ras and Ral in chemotactic migration of skeletal myoblasts. Mol. Cell. Biol. 20:4658-4665.   DOI
9 Thomas, P. D., M. J. Campbell, A. Kejariwal, H. Mi, B. Karlak, R. Daverman, K. Diemer, A. Muruganujan, and A. Narechania. 2003. PANTHER: A library of protein families and subfamilies indexed by function. Genome Res. 13:2129-2141.   DOI   ScienceOn
10 Tozaki, T., T. Miyake, H. Kakoi, H. Gawahara, S. Sugita, T. Hasegawa, N. Ishida, K. Hirota, and Y. Nakano. 2010. A genome.wide association study for racing performances in Thoroughbreds clarifies a candidate region near the MSTN gene. Anim. Genet. 41:28-35.   DOI   ScienceOn
11 Vaysse, A., A. Ratnakumar, T. Derrien, E. Axelsson, G. Rosengren Pielberg, S. Sigurdsson, T. Fall, E. H. Seppala, M. S. Hansen, and C. T. Lawley et al. 2011. Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet. 7(10):e1002316.   DOI
12 Williamson, S. A. and R. G. Beilharz. 1998. The inheritance of speed, stamina and other racing performance characters in the Australian Thoroughbred. J. Anim. Breed. Genet. 115:1-16.   DOI   ScienceOn
13 Willing, E. M., C. Dreyer, and C. van Oosterhout. 2012. Estimates of genetic differentiation measured by $F_ST$ do not necessarily require large sample sizes when using many SNP markers. PLoS One 7(8):e42649.   DOI
14 Excoffier, L., T. Hofer, and M. Foll. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103:285-298.   DOI   ScienceOn
15 Anisimova, M. and C. Kosiol. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol. Biol. Evol. 26:255-271.   DOI   ScienceOn
16 Binns, M., D. A. Boehler, and D. H. Lambert. 2010. Identification of the myostatin locus (MSTN) as having a major effect on optimum racing distance in the Thoroughbred horse in the USA. Anim. Genet. 41:154-158.   DOI   ScienceOn
17 Browning, S. R. and B. L. Browning. 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81:1084-1097.   DOI   ScienceOn
18 Cunningham, E. P., J. J. Dooley, R. K. Splan, and D. G. Bradley. 2001. Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses. Anim. Genet. 32:360-364.   DOI   ScienceOn
19 Duggal, P., E. M. Gillanders, T. N. Holmes, and J. E. Bailey-Wilson. 2008. Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies. BMC Genomics 9:516.   DOI   ScienceOn
20 Excoffier, L. and H. E. L. Lischer. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10:564-567.   DOI   ScienceOn
21 Gilmour, A. R., B. J. Gogel, B. R. Cullis, R. Thompson, D. Butler, M. Cherry, D. Collins, G. Dutkowski, S. A. Harding, and K. Haskard. 2009. ASReml User Guide Release 3.0. VSN International Ltd., UK. http://www.vsni.co.uk275.
22 Grobet, L., D. Pirottin, F. Farnir, D. Poncelet, L. J. Royo, B. Brouwers, E. Christians, D. Desmecht, F. Coignoul, R. Kahn, and M. Georges. 2003. Modulating skeletal muscle mass by postnatal, muscle-specific inactivation of the myostatin gene. Genesis 35:227-238.   DOI   ScienceOn
23 Gu, J., N. Orr, S. D. Park, L. M. Katz, G. Sulimova, D. E. MacHugh, and E. W. Hill. 2009. A genome scan for positive selection in thoroughbred horses. PLoS One 4(6):e5767-e5767.   DOI   ScienceOn
24 Jacob, J., R. Storm, D. S. Castro, C. Milton, P. Pla, F. Guillemot, C. Birchmeier, and J. Briscoe. 2009. Insm1 (IA-1) is an essential component of the regulatory network that specifies monoaminergic neuronal phenotypes in the vertebrate hindbrain. Development 136:2477-2485.   DOI   ScienceOn
25 Hill, E. W., D. G. Bradley, M. Al Barody, O. Ertugrul, R. Splan, I. Zakharov, and E. P. Cunningham. 2002. History and integrity of thoroughbred dam lines revealed in equine mtDNA variation. Anim. Genet. 33:287-294.   DOI   ScienceOn
26 Hill, E. W., J. Gu, S. S. Eivers, R. G. Fonseca, B. A. McGivney, P. Govindarajan, N. Orr, L. M. Katz, and D. MacHugh. 2010. A sequence polymorphism in MSTN predicts sprinting ability and racing stamina in Thoroughbred horses. PLoS One 5(1):e8645.   DOI   ScienceOn
27 Innan, H. and Y. Kim. 2008. Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179:1713-1720.   DOI   ScienceOn
28 Jansen, T., P. Forster, M. A. Levine, H. Oelke, M. Hurles, C. Renfrew, J. Weber, and K. Olek. 2002. Mitochondrial DNA and the origins of the domestic horse. Proc. Natl. Acad. Sci. USA 99:10905-10910.   DOI   ScienceOn
29 Kalashnikova, E., R. A. Lorca, I. Kaur, G. A. Barisone, B. Li, T. Ishimaru, J. S. Trimmer, D. P. Mohapatra, and E. Diaz. 2010. SynDIG1: An activity-regulated, AMPA-receptor-interacting transmembrane protein that regulates excitatory synapse development. Neuron 65:80-93.   DOI   ScienceOn
30 Kambadur, R., M. Sharma, T. P. L. Smith, and J. J. Bass. 1997. Mutations in myostatin (GDF8) in double-muscled Belgian Blue and Piedmontese cattle. Genome Res. 7:910-915.   DOI
31 Lindgren, G., N. Backstrom, J. Swinburne, L. Hellborg, A. Einarsson, K. Sandberg, G. Cothran, C. Vila, M. Binns, and H. Ellegren. 2004 Limited number of patrilines in horse domestication. Nat. Genet. 36:335-336.   DOI   ScienceOn
32 Kim, K. I., Y. H. Yang, S. S. Lee, C. Park, R. Ma, J. L. Bouzat, and H. A. Lewin. 1999. Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism. Anim. Genet. 30:102-108.   DOI   ScienceOn
33 Lee, S. J. 2007. Sprinting without myostatin: A genetic determinant of athletic prowess. Trends Genet. 23:475-477.   DOI   ScienceOn
34 Li, H. and R. Durbin. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.   DOI   ScienceOn
35 McGivney, B. A., J. A. Browne, R. G. Fonseca, L. M. Katz, D. E. MacHugh, R. Whiston, and E. W. Hill. 2012. MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance. Anim. Genet. 43:810-812.   DOI   ScienceOn
36 McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M. A. DePristo. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-1303.   DOI   ScienceOn
37 McPherron, A. C. and S. J. Lee. 1997. Double muscling in cattle due to mutations in the myostatin gene. Proc. Natl. Acad. Sci. USA 94:12457-12461.   DOI
38 Nam, D. Y. 1969. Horse production in Cheju during Lee dynasty. Studies on Korean History 4:131-131.
39 Nei, M. 1987. Molecular evolutionary genetics. Columbia Univ. Press, New York, NY, USA.