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1. Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Author

Jessica L Petersen, James R Mickelson, Aaron K Rendahl, Stephanie J Valberg, Lisa S Andersson, Jeanette Axelsson, Ernie Bailey, Danika Bannasch, Matthew M Binns, Alexandre S Borges, Pieter Brama, Artur da Câmara Machado, Stefano Capomaccio, Katia Cappelli, E Gus Cothran, Ottmar Distl, Laura Fox-Clipsham, Kathryn T Graves, Gérard Guérin, Bianca Haase, Telhisa Hasegawa, Karin Hemmann, Emmeline W Hill, Tosso Leeb, Gabriella Lindgren, Hannes Lohi, Maria Susana Lopes, Beatrice A McGivney, Sofia Mikko, Nicholas Orr, M Cecilia T Penedo, Richard J Piercy, Marja Raekallio, Stefan Rieder, Knut H Røed, June Swinburne, Teruaki Tozaki, Mark Vaudin, Claire M Wade, and Molly E McCue

Subjects
Genetics, QH426-470
Abstract

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Published
2013
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2. Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

Author

Gérard Guérin, Pieter A.J. Brama, M. Cecilia T. Penedo, Teruaki Tozaki, M. S. Lopes, Tosso Leeb, Emmeline W. Hill, Ottmar Distl, Knut Røed, Stefan Rieder, Claire M. Wade, Hannes Lohi, Stephanie J. Valberg, Molly E. McCue, E. Gus Cothran, Laura Y Fox-Clipsham, Jeanette Axelsson, Jessica L. Petersen, K. T. Graves, Katia Cappelli, Stefano Capomaccio, Sofia Mikko, James R. Mickelson, Karin Hemmann, Artur da Câmara Machado, Aaron Rendahl, Mark Vaudin, Danika L. Bannasch, June E Swinburne, Marja Raekallio, E. Bailey, Gabriella Lindgren, Lisa S. Andersson, Matthew M. Binns, Beatrice A. McGivney, Nick Orr, Alexandre Secorun Borges, Richard J. Piercy, Telhisa Hasegawa, Bianca Haase, College of Veterinary Medicine, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, School of Statistics, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Department of Veterinary Science, University of Kentucky, School of Veterinary Medicine, University of California, Department of Veterinary Clinical Science, University Estadual Paulista, Department of Agriculture, University of the Azores, Faculty of Veterinary Medicine, Università degli Studi di Perugia (UNIPG), College of Veterinary Medicine and Biomedical Science, Texas A&M University [College Station], Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Faculty of Veterinary Science, The University of Sydney, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin [Dublin] (UCD), Institute of Genetics, University of Bern, Breakthrough Breast Cancer Research Centre, Institute of cancer research, Comparative Neuromuscular Diseases Laboratory, Royal Veterinary College, Agroscope Liebefeld- Posieux Research Station, Swiss National Stud Farm, Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Department of Molecular Genetics, Laboratory of Racing Chemistry, This work was supported by National Research Initiative Competitive Grants 2008-35205-18766, 2009-55205-05254, and 2012-67015-19432 from the USDA-NIFA, Foundation for the Advancement of the Tennessee Walking Show Horse and Tennessee Walking Horse Foundation, NIH-NAIMS grant 1K08AR055713-01A2 (MEM salary support) and 2T32AR007612 (JLP salary support), American Quarter Horse Foundation grant 'Selective Breeding Practices in the American Quarter Horse: Impact on Health and Disease 2011-2012', Morris Animal Foundation Grant D07EQ-500, The Swedish Research Council FORMAS (Contract 221-2009-1631 and 2008-617), The Swedish-Norwegian Foundation for Equine Research (Contract H0847211 and H0947256), The Carl Tryggers Stiftelse (Contract CTS 08:29), support to IBB-CBA-UAç (University of the Azores) by FCT and DRCT, and to MSL by FRCT/2011/317/005, Science Foundation Ireland Award (04/Y11/B539) to EWH, Volkswagen Stiftung und Niedersächsisches Ministerium für Wissenschaft und Kultur, Germany (VWZN2012)., University of Minnesota [Twin Cities] (UMN), Department of Animal Bredding and Genetics, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Petersen, Jessica L, Departments of Faculty of Veterinary Medicine, Veterinary Biosciences, Equine and Small Animal Medicine, Research Centre for Animal Welfare, Teachers' Academy, University of Minnesota, Swedish University of Agricultural Sciences, University of California Davis, Equine Analysis, Universidade Estadual Paulista (Unesp), University College Dublin, University of Perugia, Texas AandM University, Animal Health Trust, French National Institute for Agricultural Research, University of Sydney, Nihon Bioresource College, University of Helsinki, Institute of Cancer Research, Agroscope Liebefeld-Posieux Research Station, and Animal DNA Diagnostics

Subjects
POSITIVE SELECTION, genetic association, Genome-wide association study, Breeding, 413 Veterinary science, Genome Evolution, 0303 health sciences, education.field_of_study, 630 Agriculture, 1184 Genetics, developmental biology, physiology, Genomics, MYOSTATIN GENE, muscle cell, Biological Evolution, horse, SNP genotyping, gluteus maximus muscle, 590 Animals (Zoology), genetic trait, muscle biopsy, FIBER-TYPE COMPOSITION, BODY-COMPOSITION, breed, Genotype, phenotype, education, biology.animal_breed, Locus (genetics), Single-nucleotide polymorphism, gene sequence, gait, histology, 03 medical and health sciences, MISSENSE MUTATION, Genetic Mutation, Genetics, Horses, genome, Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Genetic Drift, Haplotype, 0402 animal and dairy science, 040201 dairy & animal science, domestic animal, genetic selection, Mutational Hypotheses, Mutation, Population Genetics, SILVER COAT COLOR, Evolutionary Genetics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, haplotype, Cancer Research, Candidate gene, DMRT3 gene, DMRT2 gene, single nucleotide polymorphism, genetic variability, SEQUENCE VARIANTS, Natural Selection, Genetics (clinical), biology, 04 agricultural and veterinary sciences, sample size, Phenotype, SKELETAL-MUSCLE, THOROUGHBRED HORSES, Research Article, gene locus, intron, lcsh:QH426-470, Population, RACING PERFORMANCE, Polymorphism, Single Nucleotide, MSTN gene, promoter region, heterozygosity, Animals, Selection, Genetic, gene, 030304 developmental biology, Evolutionary Biology, nonhuman, population structure, Genomic Evolution, Myostatin, lcsh:Genetics, Haplotypes, Quarter horse, Genetic Polymorphism, homozygosity, Gene Function, Animal Genetics, Genome-Wide Association Study
Abstract

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an FST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse., Author Summary A breed of the horse typically consists of individuals sharing very similar aesthetic and performance traits. However, a great deal of variation in traits exists between breeds. The range of variation observed among breeds can be illustrated by the size difference between the Miniature horse (0.74 m and 100 kg) and draft horse (1.8 m and 900 kg), or by comparing the optimum racing distance of the Quarter Horse (1/4 mile) to that of the Arabian (100 miles or more). In this study, we exploited the breed structure of the horse to identify regions of the genome that are significantly different between breeds and therefore may harbor genes and genetic variants targeted by selective breeding. This work resulted in the identification of variants in the Paint and Quarter Horse significantly associated with altered muscle fiber type proportions favorable for increased sprinting ability. A strong signature of selection was also identified in breeds that perform alternative gaits, and several genomic regions identified are hypothesized to be involved in the determination of size. This study has demonstrated the utility of this approach for studying the equine genome and is the first to show a functional consequence of selective breeding in the horse.

Published
2013
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