Hostname: page-component-78c5997874-g7gxr Total loading time: 0 Render date: 2024-11-14T15:16:11.817Z Has data issue: false hasContentIssue false
  • English
  • Français

Prospection of genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line

Published online by Cambridge University Press:  17 July 2014

C. T. Meira ,
R. A. Curi ,
M. M. Farah ,
H. N. de Oliveira ,
N. A. R. Béltran ,
J. A. II V. Silva  and
M. D. S. da Mota
C. T. Meira*
Affiliation:
Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Access Route Paulo Donato Castellane, 14884-900 Jaboticabal, São Paulo, Brazil
R. A. Curi
Affiliation:
Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, 18618-970 Botucatu, São Paulo, Brazil
M. M. Farah
Affiliation:
Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Access Route Paulo Donato Castellane, 14884-900 Jaboticabal, São Paulo, Brazil
H. N. de Oliveira
Affiliation:
Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Access Route Paulo Donato Castellane, 14884-900 Jaboticabal, São Paulo, Brazil
N. A. R. Béltran
Affiliation:
Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Access Route Paulo Donato Castellane, 14884-900 Jaboticabal, São Paulo, Brazil
J. A. II V. Silva
Affiliation:
Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, 18618-970 Botucatu, São Paulo, Brazil
M. D. S. da Mota
Affiliation:
Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, 18618-970 Botucatu, São Paulo, Brazil
*
† E-mail: [email protected]
Get access

Abstract

Selection of Quarter Horses for different purposes has led to the formation of lines, including racing and cutting horses. The objective of this study was to identify genomic regions divergently selected in racing line of Quarter Horses in relation to cutting line applying relative extended haplotype homozygosity (REHH) analysis, an extension of extended haplotype homozygosity (EHH) analysis, and the fixation index (F ST) statistic. A total of 188 horses of both sexes, born between 1985 and 2009 and registered at the Brazilian Association of Quarter Horse Breeders, including 120 of the racing line and 68 of the cutting line, were genotyped using single nucleotide polymorphism arrays. On the basis of 27 genomic regions identified as selection signatures by REHH and F ST statistics, functional annotations of genes were made in order to identify those that could have been important during formation of the racing line and that could be used subsequently for the development of selection tools. Genes involved in muscle growth (n=8), skeletal growth (n=10), muscle energy metabolism (n=15), cardiovascular system (n=14) and nervous system (n=23) were identified, including the FKTN, INSR, GYS1, CLCN1, MYLK, SYK, ANG, CNTFR and HTR2B.

Keywords

equinefixation indexextended haplotype homozygosityselection signatureSNP array
Type
Research Article
Information
animal , Volume 8 , Issue 11 , November 2014 , pp. 1754 - 1764
Copyright
© The Animal Consortium 2014 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Aberle, KS and Distl, O 2004. Domestication of the horse: results based on microsatellite and mitochondrial DNA markers. Archiv Tierzucht 47, 517–535.Google Scholar
Akaike, H 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control 19, 716–723.CrossRefGoogle Scholar
Akey, JM, Zhang, G, Zhang, K, Jin, L and Shriver, MD 2002. Interrogating a high density SNP map for signatures of natural selection. Genome Research 12, 1805–1814.Google Scholar
Aleman, M 2008. A review of equine muscle disorders. Neuromuscular Disorder 18, 277–287.Google Scholar
Barrey, E 2010. Genetics and genomics in equine exercise physiology: an overview of the new applications of molecular biology as positive and negative markers of performance and health. Equine Veterinary Journal 42, 561–568.CrossRefGoogle Scholar
Bernardo, JM and Smith, AFM 1994. Bayesian theory. Wiley, Chichester, UK.CrossRefGoogle Scholar
Bevilacqua, L, Doly, S, Kaprio, J, Yuan, Q, Tikkanen, R, Paunio, T, Zhou, Z, Wedenoja, J, Maroteaux, L, Diaz, S, Belmer, A, Hodgkinson, CA, Dell’Osso, L, Suvisaari, J, Coccaro, E, Rose, RJ, Peltonen, L, Virkkunen, M and Goldman, D 2010. A population-specific HTR2B stop codon predisposes to severe impulsivity. Nature 468, 1061–1066.CrossRefGoogle ScholarPubMed
Bray, MS, Hagberg, JM, Pérusse, L, Rankinen, T, Roth, SM, Wolfarth, B and Bouchard, C 2009. The human gene map for performance and health-related fitness phenotypes: the 2006–2007 update. Medicine and Science in Sports and Exercise 41, 35–73.Google Scholar
Clarkson, PM, Hoffman, EP, Zambraski, E, Gordish-Dressman, H, Kearns, A, Hubal, M, Harmon, B and Devaney, JM 2005. ACTN3 and MLCK genotype associations with exertional muscle damage. Journal of Applied Physiology 99, 564–569.CrossRefGoogle ScholarPubMed
De Mars, G, Windelinckx, A, Beunen, G, Delecluse, C, Lefevre, J and Thomis, MA 2007. Polymorphisms in the CNTF and CNTF receptor genes are associated with muscle strength in men and women. Journal of Applied Physiology 102, 1824–1831.CrossRefGoogle ScholarPubMed
Evans, JW 1996. Horses: a guide to selection, care and enjoyment. Freeman and Company, New York, USA.Google Scholar
Evans, DL 2007. Physiology of equine performance and associated tests of function. Equine Veterinary Journal 39, 373–383.Google Scholar
Fernandez-Santiago, R, Hoenig, S, Lichtner, P, Sperfeld, AD, Sharma, M, Sperfeld, AD, Sharma, M, Berg, D, Weichenrieder, O, Illig, T, Eger, K, Meyer, T, Anneser, J, Münch, C, Zierz, S, Gasser, T and Ludolph, A 2009. Identification of novel angiogenin (ANG) gene missense variants in German patients with amyotrophic lateral sclerosis. Journal of Neurology 256, 1337–1342.Google Scholar
Freeman, DW 2013. Physical conditioning of horses. Oklahoma State University: Division of Agricultural Sciences and Natural Resources. ANSI-3983, 1–6. Retrieved June 2, 2013, from http://pods.dasnr.okstate.edu/docushare/dsweb/View/Collection-305 Google Scholar
Gabriel, SB, Schaffner, SF, Nguyen, H, Moore, JM, Roy, J, Blumenstiel, B, Higgins, J, DeFelice, M, Lochner, A, Faggart, M, Liu-Cordero, SN, Rotimi, C, Adeyemo, A, Cooper, R, Ward, R, Lander, ES, Daly, MJ and Altshuler, D 2002. The structure of haplotype blocks in the human genome. Science 296, 2225–2229.Google Scholar
Gianola, D, Simianer, H and Qanbari, S 2010. A two-step method for detecting selection signatures using genetic markers. Genetics Research Cambridge 92, 141–155.Google Scholar
Glick, G, Shirak, A, Uliel, S, Zeron, Y, Ezra, E, Seroussi, E, Ron, M and Weller, JI 2012. Signatures of contemporary selection in the Israeli Holstein dairy cattle. Animal Genetics 43, 45–55.Google Scholar
Gunn, HM 1989. Heart weight and running ability. Journal of Anatomy 167, 225–233.Google Scholar
Henckel, P 1983. Training and growth induced changes in the middle gluteal muscle of young Standardbred trotters. Equine Veterinary Journal 14, 134–140.Google Scholar
Kazerounian, S, Duquette, M, Reyes, MA, Lawler, JT, Song, K, Perruzzi, C, Primo, L, Khosravi-Far, R, Bussolino, F, Rabinovitz, I and Lawler, J 2011. Priming of the vascular endothelial growth factor signaling pathway by thrombospondin-1, CD36, and spleen tyrosine kinase. Blood 117, 4658–4666.Google Scholar
Kim, D, Cho, SY, Yeau, SH, Park, SW, Sohn, YB, Kwon, MJ, Kim, JY, Ki, CS and Jin, DK 2012. Two novel insulin receptor gene mutations in a patient with Rabson–Mendenhall syndrome: the first Korean case confirmed by biochemical, and molecular evidence. Journal of Korean Medical Science 27, 565–568.Google Scholar
Leisch, F 2004. FlexMix: a general framework for finite mixture models and latent class regression in R. Journal of Statistical Software 11, 1–18.Google Scholar
McCoy, AM, Schaefer, R, Petersen, JL, Morrell, PL, Slamka, MA, Mickelson, JR, Valberg, SJ and McCue, ME 2014. Evidence of positive selection for a glycogen synthase (GYS1) mutation in domestic horse populations. Journal of Heredity 105, 163–172.Google Scholar
McCue, ME, Valberg, SJ, Miller, MB, Wade, C, DiMauro, S, Akman, HO and Mickelson, JR 2008. Glycogen synthase (GYS1) mutation causes a novel skeletal muscle glycogenosis. Genomics 91, 458–466.Google Scholar
Meira, CT, Curi, RA, JAIIV, Silva, Corrêa, MJM, Oliveira, HN and Mota, MDS 2013. Morphological and genomic differences between cutting and racing lines of Quarter Horses. Journal of Equine Veterinary Science 13, 244–249.Google Scholar
Mills, DS 1998. Personality and individual differences in the horse, their significance, use and measurement. Equine Veterinary Journal 30 (suppl. 27), 10–13.Google Scholar
Murakami, T, Hayashi, YK, Noguchi, S, Ogawa, M, Nonaka, I, Tanabe, Y, Ogino, M, Takada, F, Eriguchi, M, Kotooka, N, Campbell, KP, Osawa, M and Nishino, I 2006. Fukutin gene mutations cause dilated cardiomyopathy with minimal muscle weakness. Annals of Neurology 60, 597–602.CrossRefGoogle ScholarPubMed
Myles, S, Tang, K, Somel, M, Green, RE, Kelso, J and Stoneking, M 2008. Identification and analysis of genomic regions with large between-population differentiation in humans. Annals of Human Genetics 72, 99–110.Google Scholar
National Center for Biotechnology Information (NCBI) 2013. National Center for Biotechnology Information. Retrieved May 1, 2013, from http://www.ncbi.nlm.nih.gov Google Scholar
Nollet, H and Deprez, P 2005. Hereditary skeletal muscle diseases in the horse: a review. The Veterinary Quarterly 27, 65–75.Google Scholar
Petersen, JL, Mickelson, JR, Cleary, KD and McCue, ME 2014. The American Quarter Horse: population structure and relationship to the Thoroughbred. Journal of Heredity 105, 148–162.CrossRefGoogle Scholar
Qanbari, S, Pimentel, ECG, Tetens, J, Thaller, G, Lichtner, P, Sharifi, AR and Simianer, H 2010. A genome-wide scan for signatures of recent selection in Holstein cattle. Animal Genetics 41, 377–389.Google Scholar
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 12, 318.CrossRefGoogle ScholarPubMed
Sabeti, PC, Reich, DE, Higgins, JM, Levine, HZP, Richter, DJ, Schaffner, SF, Gabriel, SB, Platko, JV, Patterson, NJ, McDonald, GJ, Ackerman, HC, Campbell, SJ, Altshuler, D, Cooperk, R, Kwiatkowski, D, Ward, R and Lander, ES 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832–837.CrossRefGoogle ScholarPubMed
Schröder, W, Klostermann, A and Distl, O 2011. Candidate genes for physical performance in the horse. The Veterinary Journal 190, 39–48.Google Scholar
Scott, M 2008. Musculoskeletal injuries in nonracing Quarter Horses. Veterinary Clinics Equine Practice 24, 133–152.Google Scholar
Stanley, RL, McCue, ME, Valberg, SJ, Mickelson, JR, Mayhew, IG, Mcgowan, C, Hahn, CN, Patterson-Kane, JC and Piercy, RJ 2009. A glycogen synthase 1 mutation associated with equine polysaccharide storage myopathy and exertional rhabdomyolysis occurs in a variety of UK breeds. Equine Veterinary Journal 41, 597–601.Google Scholar
Suagee, JK, Corl, BA, Wearn, JG, Crisman, MV, Hulver, MW, Geor, RJ and McCutcheon, LJ 2011. Effects of the insulin-sensitizing drug pioglitazone and lipopolysaccharide administration on insulin sensitivity in horses. Journal of Veterinary Internal Medicine 25, 356–364.CrossRefGoogle ScholarPubMed
Walsh, B 2010. Tests for molecular signatures of selection, Institute on Statistical Genetics, Beijing, China, August.Google Scholar
Wijnberg, ID, Owczarek-Lipska, M, Sacchetto, R, Mascarello, F, Pascoli, F, Grunberg, W, van der Kolk, JH and Drogemuller, C 2012. A missense mutation in the skeletal muscle chloride channel 1 (CLCN1) as candidate causal mutation for congenital myotonia in a New Forest pony. Neuromuscular Disorders 22, 361–367.Google Scholar
Yanagi, S, Inatome, R, Ding, J, Kitaguchi, H, Tybulewicz, VL and Yamamura, H 2001. SYK expression in endothelial cells and their morphologic defects in embryonic SYK-deficient mice. Blood 98, 2869–2871.Google Scholar