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Animal genetics2018; 50(1); 74-77; doi: 10.1111/age.12753

Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses.

Abstract: Whole-genome sequencing studies are vital to gain a thorough understanding of genomic variation. Here, we summarize the results of a whole-genome sequencing study comprising 88 horses and ponies from diverse breeds at 19.1× average coverage. The paired-end reads were mapped to the current EquCab3.0 horse reference genome assembly, and we identified approximately 23.5 million single nucleotide variants and 2.3 million short indel variants. Our dataset included at least 7 million variants that were not previously reported. On average, each individual horse genome carried ∼5.7 million single nucleotides and 0.8 million small indel variants with respect to the reference genome assembly. The variants were functionally annotated. We provide two examples for potentially deleterious recessive alleles that were identified in a heterozygous state in individual genome sequences. Appropriate management of such deleterious recessive alleles in horse breeding programs should help to improve fertility and reduce the prevalence of heritable diseases. This comprehensive dataset has been made publicly available, will represent a valuable resource for future horse genetic studies and supports the goal of accelerating the rates of genetic gain in domestic horse.
© 2018 Stichting International Foundation for Animal Genetics.
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Publication Date: 2018-12-07 PubMed ID: 30525216DOI: 10.1111/age.12753Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This study presents the results of a comprehensive sequencing of 88 horse genomes to identify and categorize the underlying genetic variations. New, previously unreported variants were discovered and characterized, providing insights which could potentially be helpful for managing recessive alleles in horse breeding programs.

Methodology and Results

  • The researchers used whole-genome sequencing to analyze the DNA of 88 horses and ponies from a variety of breeds. Whole-genome sequencing is a comprehensive method that allows researchers to look at nearly all of the genetic information contained within an organism.
  • The sequencing data, comprising 19.1x average coverage, was mapped to the current horse reference genome, known as EquCab3.0. This high coverage means each part of the genome was read, on average, 19.1 times, which ensures a higher reliability and accuracy in variant calling.
  • Approximately 23.5 million single nucleotide variants (SNVs) and 2.3 million short indel (insertions or deletions of bases in the genome) variants were identified across all the horses. These represent changes in the DNA sequence at specific points.
  • Of these identified variants, 7 million had not been reported previously, making these novel discoveries in horse genetic variations.
  • On average, each individual horse genome carried around 5.7 million single nucleotides and 0.8 million small indels variants as compared to the reference genome assembly.

Functional Annotation and Utilization of Data

  • The identified genetic variants were functionally annotated, meaning they were categorized based upon the likely impact they could have on the function of genes. This is a critical step for understanding their relevance to horse health, traits, and diseases.
  • The study presents two examples of potentially deleterious recessive alleles that were identified in a heterozygous state in the individual genome sequences. These problematic genes are the ones that could cause problems if an individual were to inherit two copies.
  • Identifying such harmful recessive alleles has implications for horse breeding programs as their management can help improve fertility and reduce the prevalence of heritable diseases.
  • Finally, the data gathered from this study is publicly available, making it a valuable resource for future horse genetic studies.
  • By facilitating greater understanding of horse genetic variation, this study supports the goal of ‘accelerating the rates of genetic gain’ in domestic horse breeding – an aim centered around strategically improving horse traits through targeted selection of breeding individuals.

Cite This Article

APA
Jagannathan V, Gerber V, Rieder S, Tetens J, Thaller G, Drögemüller C, Leeb T. (2018). Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses. Anim Genet, 50(1), 74-77. https://doi.org/10.1111/age.12753

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 50
Issue: 1
Pages: 74-77

Researcher Affiliations

Jagannathan, V
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
Gerber, V
  • Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern, and Agroscope, Länggassstrasse 124, 3012, Bern, Switzerland.
Rieder, S
  • Swiss National Stud Farm, Agroscope, 1580, Avenches, Switzerland.
Tetens, J
  • Department of Animal Sciences, Functional Breeding Group, Georg-August University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany.
Thaller, G
  • Institute of Animal Breeding and Husbandry, Christian-Albrechts University Kiel, Hermann-Rodewald-Strasse 6, 24098, Kiel, Germany.
Drögemüller, C
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
Leeb, T
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.

MeSH Terms

  • Animals
  • Breeding
  • Chromosome Mapping
  • Genetic Variation
  • Genome
  • Horses / genetics
  • INDEL Mutation

Citations

This article has been cited 27 times.
  1. Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023 Aug 15;24(1):187.
    doi: 10.1186/s13059-023-03023-7pubmed: 37582787google scholar: lookup
  2. Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Takahashi Y, Nagata SI. Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses. Genes (Basel) 2023 Mar 3;14(3).
    doi: 10.3390/genes14030638pubmed: 36980910google scholar: lookup
  3. Sharif MB, Fitak RR, Wallner B, Orozco-terWengel P, Frewin S, Fremaux M, Mohandesan E. Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses. Animals (Basel) 2022 Dec 12;12(24).
    doi: 10.3390/ani12243508pubmed: 36552427google scholar: lookup
  4. Suminda GGD, Ghosh M, Son YO. The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. Life (Basel) 2022 Nov 15;12(11).
    doi: 10.3390/life12111893pubmed: 36431028google scholar: lookup
  5. Reich P, Falker-Gieske C, Pook T, Tetens J. Development and validation of a horse reference panel for genotype imputation. Genet Sel Evol 2022 Jul 4;54(1):49.
    doi: 10.1186/s12711-022-00740-8pubmed: 35787788google scholar: lookup
  6. Valberg SJ, Henry ML, Herrick KL, Velez-Irizarry D, Finno CJ, Petersen JL. Absence of myofibrillar myopathy in Quarter Horses with a histopathological diagnosis of type 2 polysaccharide storage myopathy and lack of association with commercial genetic tests. Equine Vet J 2023 Mar;55(2):230-238.
    doi: 10.1111/evj.13574pubmed: 35288976google scholar: lookup
  7. Durward-Akhurst SA, Schaefer RJ, Grantham B, Carey WK, Mickelson JR, McCue ME. Genetic Variation and the Distribution of Variant Types in the Horse. Front Genet 2021;12:758366.
    doi: 10.3389/fgene.2021.758366pubmed: 34925451google scholar: lookup
  8. Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes. Nature 2021 Oct;598(7882):634-640.
    doi: 10.1038/s41586-021-04018-9pubmed: 34671162google scholar: lookup
  9. Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Nagata SI. Rare and common variant discovery by whole-genome sequencing of 101 Thoroughbred racehorses. Sci Rep 2021 Aug 6;11(1):16057.
    doi: 10.1038/s41598-021-95669-1pubmed: 34362995google scholar: lookup
  10. Buckley RM, Davis BW, Brashear WA, Farias FHG, Kuroki K, Graves T, Hillier LW, Kremitzki M, Li G, Middleton RP, Minx P, Tomlinson C, Lyons LA, Murphy WJ, Warren WC. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 2020 Oct;16(10):e1008926.
    doi: 10.1371/journal.pgen.1008926pubmed: 33090996google scholar: lookup
  11. Valberg SJ, Finno CJ, Henry ML, Schott M, Velez-Irizarry D, Peng S, McKenzie EC, Petersen JL. Commercial genetic testing for type 2 polysaccharide storage myopathy and myofibrillar myopathy does not correspond to a histopathological diagnosis. Equine Vet J 2021 Jul;53(4):690-700.
    doi: 10.1111/evj.13345pubmed: 32896939google scholar: lookup
  12. Todd ET, Thomson PC, Hamilton NA, Ang RA, Lindgren G, Viklund Å, Eriksson S, Mikko S, Strand E, Velie BD. A genome-wide scan for candidate lethal variants in Thoroughbred horses. Sci Rep 2020 Aug 4;10(1):13153.
    doi: 10.1038/s41598-020-68946-8pubmed: 32753654google scholar: lookup
  13. Williams ZJ, Velez-Irizarry D, Petersen JL, Ochala J, Finno CJ, Valberg SJ. Candidate gene expression and coding sequence variants in Warmblood horses with myofibrillar myopathy. Equine Vet J 2021 Mar;53(2):306-315.
    doi: 10.1111/evj.13286pubmed: 32453872google scholar: lookup
  14. Ghosh S, Davis BW, Rosengren M, Jevit MJ, Castaneda C, Arnold C, Jaxheimer J, Love CC, Varner DD, Lindgren G, Wade CM, Raudsepp T. Characterization of A Homozygous Deletion of Steroid Hormone Biosynthesis Genes in Horse Chromosome 29 as A Risk Factor for Disorders of Sex Development and Reproduction. Genes (Basel) 2020 Feb 27;11(3).
    doi: 10.3390/genes11030251pubmed: 32120906google scholar: lookup
  15. Qanbari S. On the Extent of Linkage Disequilibrium in the Genome of Farm Animals. Front Genet 2019;10:1304.
    doi: 10.3389/fgene.2019.01304pubmed: 32010183google scholar: lookup
  16. Tanaka J, Leeb T, Rushton J, Famula TR, Mack M, Jagannathan V, Flury C, Bachmann I, Eberth J, McDonnell SM, Penedo MCT, Bellone RR. Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies. Genes (Basel) 2019 Oct 19;10(10).
    doi: 10.3390/genes10100826pubmed: 31635058google scholar: lookup
  17. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019 Dec;50(6):569-597.
    doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
  18. Gmel AI, Druml T, von Niederhäusern R, Leeb T, Neuditschko M. Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses. Genes (Basel) 2019 May 14;10(5).
    doi: 10.3390/genes10050370pubmed: 31091839google scholar: lookup
  19. Seong HS, Kim NY, Kim DC, Hwang NH, Son DH, Shin JS, Lee JH, Chung WH, Choi JW. Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse. Genes Genomics 2019 Jun;41(6):621-628.
    doi: 10.1007/s13258-019-00795-wpubmed: 30941726google scholar: lookup
  20. Drögemüller M, Fouché N, Wyler M, Gurtner C, Meister SL, Neuditschko M, Jagannathan V, Gerber V, Leeb T. LMF1 frameshift deletion in Franches-Montagnes horses with hypertriglyceridemia-induced pancreatitis. Sci Rep 2025 Aug 6;15(1):28667.
    doi: 10.1038/s41598-025-13954-9pubmed: 40764662google scholar: lookup
  21. Ramos-Almodóvar F, Gao Z, Voight BF, Mathieson I. Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes. bioRxiv 2025 May 30;.
    doi: 10.1101/2025.05.28.656604pubmed: 40502127google scholar: lookup
  22. Assanbayev T, Akilzhanov R, Sharapatov T, Bektayev R, Samatkyzy D, Karabayev D, Gabdulkayum A, Daniyarov A, Rakhimova S, Kozhamkulov U, Sarbassov D, Akilzhanova A, Kairov U. Whole genome sequencing and de novo genome assembly of the Kazakh native horse Zhabe. Front Genet 2024;15:1466382.
    doi: 10.3389/fgene.2024.1466382pubmed: 39529846google scholar: lookup
  23. Bailey E, Finno CJ, Cullen JN, Kalbfleisch T, Petersen JL. Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations. Sci Rep 2024 Oct 2;14(1):22930.
    doi: 10.1038/s41598-024-73645-9pubmed: 39358442google scholar: lookup
  24. Lovász L, Sommer-Trembo C, Barth JMI, Scasta JD, Grancharova-Hill R, Lemoine RT, Kerekes V, Merckling L, Bouskila A, Svenning JC, Fages A. Rewilded horses in European nature conservation - a genetics, ethics, and welfare perspective. Biol Rev Camb Philos Soc 2025 Feb;100(1):407-427.
    doi: 10.1111/brv.13146pubmed: 39279124google scholar: lookup
  25. Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024 Apr 10;14(1):8396.
    doi: 10.1038/s41598-024-57872-8pubmed: 38600096google scholar: lookup
  26. Palomino Lago E, Baird A, Blott SC, McPhail RE, Ross AC, Durward-Akhurst SA, Guest DJ. A Functional Single-Nucleotide Polymorphism Upstream of the Collagen Type III Gene Is Associated with Catastrophic Fracture Risk in Thoroughbred Horses. Animals (Basel) 2023 Dec 28;14(1).
    doi: 10.3390/ani14010116pubmed: 38200847google scholar: lookup
  27. Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Nagata SI. Construction of an individual identification panel for horses using insertion and deletion markers. J Equine Sci 2023 Sep;34(3):83-92.
    doi: 10.1294/jes.34.83pubmed: 37781568google scholar: lookup
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