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) |
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 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. |