FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Genes (Basel) / Y-Chromosomal Insights into Breeding History and Sire Line G...
Genes2022; 13(2); 229; doi: 10.3390/genes13020229

Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses.

Abstract: The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.
Get Full Text
Publication Date: 2022-01-26 PubMed ID: 35205275PubMed Central: PMC8871751DOI: 10.3390/genes13020229Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article
  • Research Support
  • Non-U.S. Gov't

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 research explored the breeding history and paternal lineage of Arabian horses using the Y-chromosome as a genetic marker. It revealed three specific haplogroups in Arabian horse lineages and highlighted potential historical connections among Arabian, Turkoman, and Akhal Teke horses. The research further analysed Arabian horse breeding in the Western World over the past 200 years, revealing preferences for certain male lineages and discrepancies in the written pedigree records.

Methods and Data

  • The study gathered Y-chromosome sequence data from 157 male horses across different breeds, using next-generation sequencing techniques. This method offered high-resolution genetic data.
  • The researchers inferred Y-chromosomal haplotypes (sets of genetic variations) specific to Arabian horses by genotyping 145 males, representing most of the globally active Arabian sire lines.

Findings

  • The Arabian sire lines formed three distinct Y-chromosomal haplogroups, with the same groups detected in Arabian populations native to the Middle East. This differentiation from other breeds underlines the uniqueness of Arabian horses’ genetic makeup.
  • A particular haplotype found in Arabians, Turkomans, and Akhal Tekes was linked back to a stallion introduced into English Thoroughbred lines in the late 17th century, hinting at possible historical connections between these horse types.

Implications

  • Through Y-chromosome analysis, the study genetically traced Western Arabian sire line breeding over the past 200 years, confirming a strong selection for certain male lineages. This evidence points to patterns of lineage selection in the breeding history.
  • The genetic analysis also revealed discrepancies in the written pedigree records. Such incongruences can help refine the understanding of breed development and challenge established narratives.
  • By unravelling the paternal genealogies of Arabian horses, this study contributes to the broader understanding of horse ancestry and breeding practices over time. Such insights can be valuable for horse breeders and animal geneticists alike.

Conclusion

  • This study illustrates how fine-scaled Y-chromosome analysis can significantly contribute to understanding how horse breeds have developed over time. This opens up discussions about breeding practices, historical connections among breeds, and the accuracy of written pedigree records.

Cite This Article

APA
Remer V, Bozlak E, Felkel S, Radovic L, Rigler D, Grilz-Seger G, Stefaniuk-Szmukier M, Bugno-Poniewierska M, Brooks S, Miller DC, Antczak DF, Sadeghi R, Cothran G, Juras R, Khanshour AM, Rieder S, Penedo MC, Waiditschka G, Kalinkova L, Kalashnikov VV, Zaitsev AM, Almarzook S, Reißmann M, Brockmann GA, Brem G, Wallner B. (2022). Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes (Basel), 13(2), 229. https://doi.org/10.3390/genes13020229

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 13
Issue: 2
PII: 229

Researcher Affiliations

Remer, Viktoria
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Bozlak, Elif
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Felkel, Sabine
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
  • Institute of Computational Biology, Department of Biotechnology, BOKU University of Life Sciences and Natural Resources, 1190 Vienna, Austria.
Radovic, Lara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
  • Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Rigler, Doris
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Grilz-Seger, Gertrud
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Stefaniuk-Szmukier, Monika
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice, Poland.
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, 30-059 Kraków, Poland.
Bugno-Poniewierska, Monika
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, 30-059 Kraków, Poland.
Brooks, Samantha
  • Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
Miller, Donald C
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
Antczak, Douglas F
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
Sadeghi, Raheleh
  • Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
  • Equestrian Federation of The Islamic Republic of Iran, Tehran 193954754, Iran.
Cothran, Gus
  • College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
Juras, Rytis
  • College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
Khanshour, Anas M
  • College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
  • Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA.
Rieder, Stefan
  • Identitas AG, R&D, 3014 Bern, Switzerland.
Penedo, Maria C
  • Veterinary Genetics Laboratory, University of California, Davis, CA 95617, USA.
Waiditschka, Gudrun
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Kalinkova, Liliya
  • All-Russian Research Institute for Horse Breeding, 391105 Ryazan, Russia.
Kalashnikov, Valery V
  • All-Russian Research Institute for Horse Breeding, 391105 Ryazan, Russia.
Zaitsev, Alexander M
  • All-Russian Research Institute for Horse Breeding, 391105 Ryazan, Russia.
Almarzook, Saria
  • Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
Reißmann, Monika
  • Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
Brockmann, Gudrun A
  • Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
Brem, Gottfried
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Wallner, Barbara
  • Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.

MeSH Terms

  • Animals
  • Female
  • Genetic Variation
  • Haplotypes
  • Horses / genetics
  • Male
  • Pedigree
  • Phylogeny
  • Y Chromosome / genetics

Grant Funding

  • W 1225 / Austrian Science Fund FWF

Conflict of Interest Statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of the data; in the writing of the manuscript; or in the decision to publish the results. The statements made herein are solely the responsibility of the authors.

References

This article includes 58 references
  1. Kelekna P. The Horse in Human History. .
  2. 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/s41586-021-04018-9pmc: PMC8550961pubmed: 34671162google scholar: lookup
  3. Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando L. The Evolutionary Origin and Genetic Makeup of Domestic Horses.. Genetics 2016 Oct;204(2):423-434.
    doi: 10.1534/genetics.116.194860pmc: PMC5068837pubmed: 27729493google scholar: lookup
  4. Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MC, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data.. PLoS One 2013;8(1):e54997.
    doi: 10.1371/journal.pone.0054997pmc: PMC3559798pubmed: 23383025google scholar: lookup
  5. Bower M.A., Campana M.G., Nisbet R., Weller R., Whitten M., Edwards C.J., Stock F., Barrett E., O’Connell T., Hill E.W.. Truth in the bones: Resolving the identity of the founding elite thoroughbred racehorses. Archaeometry 2012;54:916–925.
    doi: 10.1111/j.1475-4754.2012.00666.xgoogle scholar: lookup
  6. 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.12857pmc: PMC6825885pubmed: 31568563google scholar: lookup
  7. Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.. Cell 2019 May 30;177(6):1419-1435.e31.
    doi: 10.1016/j.cell.2019.03.049pmc: PMC6547883pubmed: 31056281google scholar: lookup
  8. Hendricks B. International Encyclopedia of Horse Breeds. .
  9. Arnason T., van Vleck L.D.. Genetic Improvement of the Horse. The Genetics of the Horse 2000. p. 527.
  10. Grilz-Seger G., Druml T. Lipizzaner Hengststämme. .
  11. Petersen JL, Mickelson JR, Cleary KD, McCue ME. The American Quarter Horse: population structure and relationship to the thoroughbred.. J Hered 2014 Mar-Apr;105(2):148-62.
    doi: 10.1093/jhered/est079pmc: PMC3920813pubmed: 24293614google scholar: lookup
  12. Weatherby J. An Introduction to a General Stud Book. .
  13. Cunningham EP, Dooley JJ, Splan RK, Bradley DG. Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses.. Anim Genet 2001 Dec;32(6):360-4.
    doi: 10.1046/j.1365-2052.2001.00785.xpubmed: 11736806google scholar: lookup
  14. McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population.. Sci Rep 2020 Jan 16;10(1):466.
    doi: 10.1038/s41598-019-57389-5pmc: PMC6965197pubmed: 31949252google scholar: lookup
  15. Zechner P., Sölkner J., Bodo I., Druml T., Baumung R., Achmann R., Marti E., Habe F., Brem G. Analysis of diversity and population structure in the Lipizzan horse breed based on pedigree information. Livest. Prod. Sci. 2002;77:137–146.
    doi: 10.1016/S0301-6226(02)00079-9google scholar: lookup
  16. Pjontek J., Kadlečík O., Kasarda R., Horný M. Pedigree analysis in four Slovak endangered horse breeds. Czech J. Anim. Sci. 2012;57:54–64.
    doi: 10.17221/5132-CJASgoogle scholar: lookup
  17. Calafell F, Larmuseau MHD. The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research.. Hum Genet 2017 May;136(5):559-573.
    doi: 10.1007/s00439-016-1740-0pubmed: 27817057google scholar: lookup
  18. Jobling MA, Tyler-Smith C. Fathers and sons: the Y chromosome and human evolution.. Trends Genet 1995 Nov;11(11):449-56.
    doi: 10.1016/S0168-9525(00)89144-1pubmed: 8578602google scholar: lookup
  19. Radovic L., Remer V., Reiter S., Bozlak E., Felkel S., Grilz-Seger G., Brem G., Wallner B. Y chromosome genetic variation and deep genealogies provide new insights on Lipizzan sire lines. J. Equine Vet. Sci. 2021;100:103501.
    doi: 10.1016/j.jevs.2021.103501google scholar: lookup
  20. Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions.. Curr Biol 2017 Jul 10;27(13):2029-2035.e5.
    doi: 10.1016/j.cub.2017.05.086pubmed: 28669755google scholar: lookup
  21. Felkel S, Vogl C, Rigler D, Jagannathan V, Leeb T, Fries R, Neuditschko M, Rieder S, Velie B, Lindgren G, Rubin CJ, Schlötterer C, Rattei T, Brem G, Wallner B. Asian horses deepen the MSY phylogeny.. Anim Genet 2018 Feb;49(1):90-93.
    doi: 10.1111/age.12635pubmed: 29333704google scholar: lookup
  22. Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J, Neuditschko M, Rattei T, Raudsepp T, Rieder S, Rubin CJ, Schaefer R, Schlötterer C, Thaller G, Tetens J, Velie B, Brem G, Wallner B. The horse Y chromosome as an informative marker for tracing sire lines.. Sci Rep 2019 Apr 15;9(1):6095.
    doi: 10.1038/s41598-019-42640-wpmc: PMC6465346pubmed: 30988347google scholar: lookup
  23. Han H, Wallner B, Rigler D, MacHugh DE, Manglai D, Hill EW. Chinese Mongolian horses may retain early domestic male genetic lineages yet to be discovered.. Anim Genet 2019 Aug;50(4):399-402.
    doi: 10.1111/age.12780pubmed: 31073991google scholar: lookup
  24. Liu S, Yang Y, Pan Q, Sun Y, Ma H, Liu Y, Wang M, Zhao C, Wu C. Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers.. Front Genet 2020;11:467.
    doi: 10.3389/fgene.2020.00467pmc: PMC7253630pubmed: 32508879google scholar: lookup
  25. Castaneda C, Juras R, Khanshour A, Randlaht I, Wallner B, Rigler D, Lindgren G, Raudsepp T, Cothran EG. Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines.. Genes (Basel) 2019 Aug 20;10(8).
    doi: 10.3390/genes10080629pmc: PMC6722507pubmed: 31434327google scholar: lookup
  26. Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G. Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds.. PLoS One 2013;8(4):e60015.
    doi: 10.1371/journal.pone.0060015pmc: PMC3616054pubmed: 23573227google scholar: lookup
  27. Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M, Prabhu A, Bucca S, Bugno-Poniewierska M, Wallner B, Malek J, Miller DC, Clark AG, Antczak DF, Brooks SA. Genome Diversity and the Origin of the Arabian Horse.. Sci Rep 2020 Jun 16;10(1):9702.
    doi: 10.1038/s41598-020-66232-1pmc: PMC7298027pubmed: 32546689google scholar: lookup
  28. Glazewska I. Speculations on the origin of the Arabian horse breed. Livest. Sci. 2010;129:49–55.
    doi: 10.1016/j.livsci.2009.12.009google scholar: lookup
  29. About the World Arabian Horse Organization (WAHO) [(accessed on 27 October 2021)]. Available online: http://www.waho.org.
  30. Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging.. BMC Res Notes 2016 Feb 12;9:88.
    doi: 10.1186/s13104-016-1900-2pmc: PMC4751634pubmed: 26868221google scholar: lookup
  31. Gómez-Sánchez D, Schlötterer C. ReadTools: A universal toolkit for handling sequence data from different sequencing platforms.. Mol Ecol Resour 2018 May;18(3):676-680.
    doi: 10.1111/1755-0998.12741pubmed: 29171165google scholar: lookup
  32. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009 Jul 15;25(14):1754-60.
    doi: 10.1093/bioinformatics/btp324pmc: PMC2705234pubmed: 19451168google scholar: lookup
  33. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools.. Bioinformatics 2009 Aug 15;25(16):2078-9.
    doi: 10.1093/bioinformatics/btp352pmc: PMC2723002pubmed: 19505943google scholar: lookup
  34. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.. Genome Res 2010 Sep;20(9):1297-303.
    doi: 10.1101/gr.107524.110pmc: PMC2928508pubmed: 20644199google scholar: lookup
  35. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features.. Bioinformatics 2010 Mar 15;26(6):841-2.
    doi: 10.1093/bioinformatics/btq033pmc: PMC2832824pubmed: 20110278google scholar: lookup
  36. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.. Brief Bioinform 2013 Mar;14(2):178-92.
    doi: 10.1093/bib/bbs017pmc: PMC3603213pubmed: 22517427google scholar: lookup
  37. Garrison E., Marth G. Haplotype-based variant detection from short-read sequencing. arXiv 20121207.3907.
  38. Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.. Investig Genet 2014;5:13.
    doi: 10.1186/2041-2223-5-13pmc: PMC4174254pubmed: 25254093google scholar: lookup
  39. Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies.. Mol Biol Evol 1999 Jan;16(1):37-48.
    doi: 10.1093/oxfordjournals.molbev.a026036pubmed: 10331250google scholar: lookup
  40. . A nomenclature system for the tree of human Y-chromosomal binary haplogroups.. Genome Res 2002 Feb;12(2):339-48.
    doi: 10.1101/gr.217602pmc: PMC155271pubmed: 11827954google scholar: lookup
  41. Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MC, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt HJ, Torroni A. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2449-54.
    doi: 10.1073/pnas.1111637109pmc: PMC3289334pubmed: 22308342google scholar: lookup
  42. Raswan C.R., Seydel H. Der Araber und Sein Pferd. Dritte Nac.. .
  43. Forbis J. Das klassische arabische Pferd. .
  44. Arab Families by Grace Dashiell (Western Horseman June, 1950) [(accessed on 23 November 2021)]. Available online: https://wiwfarm.com/GDArabianFamilies.html.
  45. Wells M.L. The Illustrated Guide to The Morab Horse. 1st ed.. .
  46. The two Siglavys with world influence by Furrer, B in Arabische Pferde in the Focus (1/2019) [(accessed on 21 January 2022)]. Available online: https://in-the-focus.com/2019/04/ap-1-2019-ist-online/
  47. Pruski W. Dwa Wieki Polskiej Hodowli Koni Arabskich (1778–1978) i Jej Sukcesy na Świecie. 1983. pp. 278–322.
  48. Jobling MA, Tyler-Smith C. Human Y-chromosome variation in the genome-sequencing era.. Nat Rev Genet 2017 Aug;18(8):485-497.
    doi: 10.1038/nrg.2017.36pubmed: 28555659google scholar: lookup
  49. Almarzook S, Reissmann M, Arends D, Brockmann GA. Genetic diversity of Syrian Arabian horses.. Anim Genet 2017 Aug;48(4):486-489.
    doi: 10.1111/age.12568pubmed: 28568646google scholar: lookup
  50. Khanshour AM, Cothran EG. Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing.. BMC Genet 2013 Sep 13;14:83.
    doi: 10.1186/1471-2156-14-83pmc: PMC3847362pubmed: 24034565google scholar: lookup
  51. Khanshour A, Conant E, Juras R, Cothran EG. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.. J Hered 2013 May-Jun;104(3):386-98.
    doi: 10.1093/jhered/est003pubmed: 23450090google scholar: lookup
  52. Machmoum M, Boujenane I, Azelhak R, Badaoui B, Petit D, Piro M. Genetic Diversity and Population Structure of Arabian Horse Populations Using Microsatellite Markers.. J Equine Vet Sci 2020 Oct;93:103200.
    doi: 10.1016/j.jevs.2020.103200pubmed: 32972687google scholar: lookup
  53. Flade J.E. Das Araberpferd. 3rd ed.. 1977. p. 144.
  54. Wrangel G.C.G. Die Rassen des Pferdes. Ihre Entstehung, Geschichtliche Entwicklung und Charakteristische Kennzeichen. Erster Band.. .
  55. Nissen J. Enzyklopädie der Pferderassen, Europa Band 2. .
  56. Orlando L. Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics.. Bioessays 2020 Jan;42(1):e1900164.
    doi: 10.1002/bies.201900164pubmed: 31808562google scholar: lookup
  57. Bowling AT, Del Valle A, Bowling M. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses.. Anim Genet 2000 Feb;31(1):1-7.
    doi: 10.1046/j.1365-2052.2000.00558.xpubmed: 10690354google scholar: lookup
  58. Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A. Reconstructing the origin and spread of horse domestication in the Eurasian steppe.. Proc Natl Acad Sci U S A 2012 May 22;109(21):8202-6.
    doi: 10.1073/pnas.1111122109pmc: PMC3361400pubmed: 22566639google scholar: lookup

Citations

This article has been cited 15 times.
  1. Sharif MB, Mohaseb AF, Orlando L, Saliari K, Kunst GK, Czeika S, Mashkour M, Cucchi T, Peters J, Trixl S, Mohandesan E. Late Iron Age and Roman equine breeding north of the Alps: Genetic insights and cultural implications. iScience 2025 Sep 19;28(9):113224.
    doi: 10.1016/j.isci.2025.113224pubmed: 40837235google scholar: lookup
  2. Radovic L, Remer V, Rigler D, Bozlak E, Allen L, Brem G, Reissman M, Brockmann GA, Ropka-Molik K, Stefaniuk-Szmukier M, Kalinkova L, Kalashnikov VV, Zaitev AM, Raudsepp T, Castaneda C, von Butler-Wemken I, Patterson Rosa L, Brooks SA, Novoa-Bravo M, Kostaras N, Abdurasulov A, Antczak DF, Miller DC, Lopes MS, da Câmara Machado A, Lindgren G, Juras R, Cothran G, Wallner B. The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome. Proc Natl Acad Sci U S A 2024 Dec 3;121(49):e2414408121.
    doi: 10.1073/pnas.2414408121pubmed: 39556761google scholar: lookup
  3. Gmel AI, Mikko S, Ricard A, Velie BD, Gerber V, Hamilton NA, Neuditschko M. Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed. Genet Sel Evol 2024 Jul 10;56(1):53.
    doi: 10.1186/s12711-024-00922-6pubmed: 38987703google scholar: lookup
  4. Musiał AD, Radović L, Stefaniuk-Szmukier M, Bieniek A, Wallner B, Ropka-Molik K. Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population. PeerJ 2024;12:e17549.
    doi: 10.7717/peerj.17549pubmed: 38912049google scholar: lookup
  5. Bozlak E, Pokharel K, Weldenegodguad M, Paasivaara A, Stammler F, Røed KH, Kantanen J, Wallner B. Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies. Ecol Evol 2024 Jun;14(6):e11573.
    doi: 10.1002/ece3.11573pubmed: 38863721google scholar: lookup
  6. Atroshchenko M, Dementieva N, Shcherbakov Y, Nikolaeva O, Azovtseva A, Ryabova A, Nikitkina E, Makhmutova O, Datsyshin A, Zakharov V, Zaitsev A. The Genetic Diversity of Horse Native Breeds in Russia. Genes (Basel) 2023 Nov 28;14(12).
    doi: 10.3390/genes14122148pubmed: 38136970google scholar: lookup
  7. Giontella A, Cardinali I, Sarti FM, Silvestrelli M, Lancioni H. Y-Chromosome Haplotype Report among Eight Italian Horse Breeds. Genes (Basel) 2023 Aug 9;14(8).
    doi: 10.3390/genes14081602pubmed: 37628653google scholar: lookup
  8. Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia. Saudi J Biol Sci 2023 Sep;30(9):103741.
    doi: 10.1016/j.sjbs.2023.103741pubmed: 37575470google scholar: lookup
  9. Machmoum M, Badaoui B, Petit D, Germot A, El Alaoui MA, Boujenane I, Piro M. Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses. Animals (Basel) 2023 Jun 17;13(12).
    doi: 10.3390/ani13122021pubmed: 37370531google scholar: lookup
  10. Mousavi SF, Razmkabir M, Rostamzadeh J, Seyedabadi HR, Naboulsi R, Petersen JL, Lindgren G. Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Heredity (Edinb) 2023 Aug;131(2):96-108.
    doi: 10.1038/s41437-023-00624-7pubmed: 37308718google scholar: lookup
  11. Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. Refining the evolutionary tree of the horse Y chromosome. Sci Rep 2023 Jun 2;13(1):8954.
    doi: 10.1038/s41598-023-35539-0pubmed: 37268661google scholar: lookup
  12. Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022 Dec 2;13(12).
    doi: 10.3390/genes13122272pubmed: 36553539google scholar: lookup
  13. 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
  14. Szmatoła T, Gurgul A, Jasielczuk I, Oclon E, Ropka-Molik K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types. Animals (Basel) 2022 Nov 25;12(23).
    doi: 10.3390/ani12233293pubmed: 36496815google scholar: lookup
  15. Radovic L, Remer V, Krcal C, Rigler D, Brem G, Rayane A, Driss K, Benamar M, Machmoum M, Piro M, Krischke D, Butler-Wemken IV, Wallner B. Y Chromosome Haplotypes Enlighten Origin, Influence, and Breeding History of North African Barb Horses. Animals (Basel) 2022 Sep 27;12(19).
    doi: 10.3390/ani12192579pubmed: 36230320google scholar: lookup
Subscribe to our newsletter
Join 99,357 horse owners like you who receive our email updates on horse health and nutrition.