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Common protein-coding variants influence the racing phenotype in galloping racehorse breeds

Han, Haige and McGivney, Beatrice A. and Allen, Lucy and Bai, Dongyi and Corduff, Leanne R. and Davaakhuu, Gantulga and Davaasambuu, Jargalsaikhan and Dorjgotov, Dulguun and Hall, Thomas J. and Hemmings, Andrew J. and Holtby, Amy R. and Jambal, Tuyatsetseg and Jargalsaikhan, Badarch and Jargalsaikhan, Uyasakh and Kadri, Naveen K. and MacHugh, David E. and Pausch, Hubert and Readhead, Carol and Warburton, David and Dugarjaviin, Manglai and Hill, Emmeline W. (2022) Common protein-coding variants influence the racing phenotype in galloping racehorse breeds. Communications Biology, 5 . Art. No. 1320. ISSN 2399-3642. PMCID PMC9748125. doi:10.1038/s42003-022-04206-x.

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Selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, G6PC2, HDAC9, KTN1, MYLK2, NTM, SLC16A1 and SYNDIG1, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.

Item Type:Article
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URLURL TypeDescription CentralArticle Data for Figure 2
Han, Haige0000-0002-0812-3000
McGivney, Beatrice A.0000-0002-8841-4544
Davaakhuu, Gantulga0000-0003-3792-7101
Dorjgotov, Dulguun0000-0001-7751-5473
Hall, Thomas J.0000-0002-4116-3506
Holtby, Amy R.0000-0002-7307-6159
Jambal, Tuyatsetseg0000-0001-7037-6693
Kadri, Naveen K.0000-0002-2799-3896
MacHugh, David E.0000-0002-8112-4704
Pausch, Hubert0000-0002-0501-6760
Warburton, David0000-0002-4605-1298
Dugarjaviin, Manglai0000-0002-3152-8137
Hill, Emmeline W.0000-0002-1805-2250
Additional Information:We thank the Khentii herdsmen and Henry Seebach for assistance with collection of the Mongolian Racing horse samples; horse owners for agreement for the use of samples in research; Jonathan O’Grady (O’Grady Advisors) for assistance compiling the Thoroughbred race record phenotypes; and Gillian McHugo for assistance with data visualisation. This work was supported by National Key R&D Program of China (Grant Code 2017YFE0108700); National Natural Science Foundation of China (Grant Code 3191101008,31960657); Science Foundation Ireland (Grant Code 19FFP6879); National Institutes of Health (Grant Code NIEHS-1D43ES02286201); Royal Agricultural University Cirencester Fund; Plusvital Ltd. Contributions. H.H. compiled the SNP data, performed the population genomics analyses, coordinated the sample acquisition of Asian horses, coordinated the WGS study, interpreted the results, and assisted with writing the original manuscript. B.A.M. designed and performed the SNP association analyses, assisted with the population genomics analyses, assisted with the WGS study, interpreted the results, and assisted with writing the original manuscript. L.A. and A.J.H. were involved in planning and performing the sample acquisition and DNA extraction of Mongolian Racing horses. D.B., D.D. and T.J. were involved in the sample acquisition of Asian horses. B.J., J.D. and U.J. facilitated and were involved in the sample acquisition of Mongolian Racing horses. A.R.H. and L.R.C. prepared the phenotypes and samples for the SNP association analyses. N.K.K. and H.P. performed the downstream WGS analyses. T.J.H. and D.E.M. designed and performed the integrative genomics analyses and assisted with writing the original manuscript. C.R. and D.W. conceived the study and facilitated and performed the sample acquisition of Mongolian Racing horses. M.D. facilitated the sample acquisition of Asian horses and supervised the WGS study. E.W.H. conceived, designed and coordinated the study, performed the sample acquisition of Mongolian Racing horses, supervised the analyses, interpreted the results and wrote the original manuscript. Data availability. SNP array derived genotypes generated in this study have been deposited in the European Variation Archive with the accession IDs PRJEB55561 (Project), ERZ12817059 (Mongolian horse analysis), and ERZ12817060 (Arabian horse analysis). The whole genome sequence data have been deposited in the Sequence Read Archive with the BioProject ID: PRJNA867509. The source data for Fig. 2 is available at Source data is available at The SNP genotype data generated for the validation study are subject to the following licenses/restrictions: The phenotype and genotype data are the property of Plusvital Ltd. and subject to a confidentiality agreement with the animal owners.
Funding AgencyGrant Number
National Key Research and Development Program of China2017YFE0108700
National Natural Science Foundation of China3191101008
National Natural Science Foundation of China31960657
Science Foundation, Ireland19FFP6879
Royal Agricultural UniversityUNSPECIFIED
PubMed Central ID:PMC9748125
Record Number:CaltechAUTHORS:20230123-451841300.35
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:118900
Deposited By: Research Services Depository
Deposited On:16 Feb 2023 16:51
Last Modified:16 Feb 2023 16:51

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