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Home / Equine Research Bank / J Hered / Population Networks Associated with Runs of Homozygosity Rev...
The Journal of heredity2018; 109(4); 384-392; doi: 10.1093/jhered/esx114

Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse.

Abstract: Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Haflingers, 78 Austrian Haflingers, 190 Noriker, 23 Bosnian Mountain Horses, 20 Gidran, 33 Shagya Arabians, and 155 Purebred Arabians. Model-based cluster analysis identified substructures within Purebred Arabian, Haflinger, and Noriker that reflected distinct genealogy (Purebred Arabian), geographic origin (Haflinger), and coat color patterns (Noriker). Analysis of ROH revealed that the 2 Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306-397 Mb). The Noriker and the Austrian Haflinger showed the lowest ROH coverage (228, 282 Mb). Our combined visualization approach made it feasible to clearly identify outbred (admixture) and inbred (ROH segments) horses. Genomic inbreeding coefficients (FROH) ranged from 10.1% (Noriker) to 17.7% (Purebred Arabian). Finally it could be demonstrated, that the Austrian Haflinger sample has a lack of longer ROH segments and a deviating ROH spectrum, which is associated with past bottleneck events and the recent mating strategy favoring out-crosses within the breed.
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Publication Date: 2018-01-03 PubMed ID: 29294044DOI: 10.1093/jhered/esx114Google Scholar: Lookup
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  • 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.

The research presents a study that combines population structure and homozygosity measures using high-resolution population networks with runs of homozygosity (ROH) to investigate the breeding history of the Haflinger horse. Using a dataset of more than 500 horses, the researchers were able to identify substructures reflecting breed origin, geographic origin, and coat color patterns.

Research Methodology

  • The researchers collected high-density genotype information from 531 horses from 7 populations involved in the formation of the Haflinger horse. These were divided between Italian Haflingers, Austrian Haflingers, Noriker, Bosnian Mountain Horses, Gidran, Shagya Arabians, and Purebred Arabians.
  • They utilized model-based cluster analysis to identify substructures. These substructures correlated with distinct genealogy (Purebred Arabian), geographic origin (Haflinger), and coat color patterns (Noriker).
  • Analysis was also performed on ROH to determine the genome proportion covered by ROH segments.
  • The combination of population networks with ROH enabled the identification of outbred (admixture) and inbred (ROH segments) horses.

Major Findings

  • The study revealed that the two Arabian populations (Purebred and Shagya Arabians), Gidran and the Bosnian Mountain Horse had the highest genome proportion covered by ROH segments (306-397 Mb).
  • Noriker and the Austrian Haflinger showed the lowest coverage of ROH (228, 282 Mb).
  • Genomic inbreeding coefficients (FROH) varied across breeds, with 10.1% (Noriker) to 17.7% (Purebred Arabian).
  • A key finding was that the Austrian Haflinger sample showed a lack of longer ROH segments and a deviating ROH spectrum. This suggests past bottleneck events and a recent mating strategy that favours out-crosses within the breed.

Implication of the Research

  • The findings contribute to the understanding of the Haflinger horse’s breeding history. It also offers valuable insights into the population structure and homozygosity of the horse breeds involved in the formation of the Haflinger.
  • The combined implementation of population networks with ROH, as demonstrated in this study, could be an efficient approach for future genetic diversity analyses.

Cite This Article

APA
Druml T, Neuditschko M, Grilz-Seger G, Horna M, Ricard A, Mesaric M, Cotman M, Pausch H, Brem G. (2018). Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse. J Hered, 109(4), 384-392. https://doi.org/10.1093/jhered/esx114

Publication

The Journal of heredity
ISSN: 1465-7333
NlmUniqueID: 0375373
Country: United States
Language: English
Volume: 109
Issue: 4
Pages: 384-392

Researcher Affiliations

Druml, Thomas
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.
Neuditschko, Markus
  • Agroscope, Swiss National Stud Farm, Avenches, Switzerland.
Grilz-Seger, Gertrud
  • Pöckau, Arnoldstein, Austria.
Horna, Michaela
  • Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Nitra-Chrenová, Slovak Republic.
Ricard, Anne
  • Institut National de la Recherche Agronomique, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.
  • Institut Français du Cheval et de l'Equitation, Recherche et Innovation, Exmes, France.
Mesaric, Matjaz
  • Clinic for Reproduction and Large Animals, Veterinary Faculty, University of Lubljana, Cesta v Mestni log, Ljubljana, Slovenia.
Cotman, Marco
  • Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Cesta v Mestni log, Ljubljana, Slovenia.
Pausch, Hubert
  • Animal Genomics, ETH Zürich, Zürich, Switzerland.
Brem, Gottfried
  • Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Vienna, Austria.

MeSH Terms

  • Animals
  • Breeding
  • Female
  • Genetic Variation
  • Genetics, Population
  • Genome / genetics
  • Genomics
  • Genotype
  • Homozygote
  • Horses / classification
  • Horses / genetics
  • Inbreeding
  • Male
  • Polymorphism, Single Nucleotide / genetics

Citations

This article has been cited 27 times.
  1. Gmel AI, Guichard M, Dainat B, Williams GR, Eynard S, Vignal A, Servin B, Neuditschko M. Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole-genome sequencing data. Ecol Evol 2023 Jan;13(1):e9723.
    doi: 10.1002/ece3.9723pubmed: 36694553google scholar: lookup
  2. 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
  3. 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
  4. Yordanov G, Mehandjyiski I, Palova N, Atsenova N, Neov B, Radoslavov G, Hristov P. Genetic Diversity and Structure of the Main Danubian Horse Paternal Genealogical Lineages Based on Microsatellite Genotyping. Vet Sci 2022 Jul 1;9(7).
    doi: 10.3390/vetsci9070333pubmed: 35878350google scholar: lookup
  5. Colpitts J, McLoughlin PD, Poissant J. Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds. BMC Genomics 2022 Jul 12;23(1):501.
    doi: 10.1186/s12864-022-08729-9pubmed: 35820826google scholar: lookup
  6. Criscione A, Mastrangelo S, D'Alessandro E, Tumino S, Di Gerlando R, Zumbo A, Marletta D, Bordonaro S. Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern. J Anim Breed Genet 2022 Sep;139(5):540-555.
    doi: 10.1111/jbg.12680pubmed: 35445758google scholar: lookup
  7. Vostry L, Vostra-Vydrova H, Citek J, Gorjanc G, Curik I. Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse. Anim Genet 2021 Aug;52(4):422-430.
    doi: 10.1111/age.13075pubmed: 33970495google scholar: lookup
  8. Zsoldos RR, Khayatzadeh N, Soelkner J, Schroeder U, Hahn C, Licka TF. Comparison of gluteus medius muscle activity in Haflinger and Noriker horses with polysaccharide storage myopathy. J Anim Physiol Anim Nutr (Berl) 2021 May;105(3):549-557.
    doi: 10.1111/jpn.13504pubmed: 33609063google scholar: lookup
  9. Mancin E, Ablondi M, Mantovani R, Pigozzi G, Sabbioni A, Sartori C. Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information. Animals (Basel) 2020 Jul 30;10(8).
    doi: 10.3390/ani10081310pubmed: 32751586google scholar: lookup
  10. Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020 Jun 8;10(6).
    doi: 10.3390/ani10061005pubmed: 32521830google scholar: lookup
  11. Addo S, Klingel S, Hinrichs D, Thaller G. Runs of Homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds. PLoS One 2019;14(12):e0225847.
    doi: 10.1371/journal.pone.0225847pubmed: 31800604google scholar: lookup
  12. Singer-Berk MH, Knickelbein KE, Lounsberry ZT, Crausaz M, Vig S, Joshi N, Britton M, Settles ML, Reilly CM, Bentley E, Nunnery C, Dwyer A, Lassaline ME, Bellone RR. Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses. Int J Genomics 2019;2019:3610965.
    doi: 10.1155/2019/3610965pubmed: 31637255google scholar: lookup
  13. Ablondi M, Viklund Å, Lindgren G, Eriksson S, Mikko S. Signatures of selection in the genome of Swedish warmblood horses selected for sport performance. BMC Genomics 2019 Sep 18;20(1):717.
    doi: 10.1186/s12864-019-6079-1pubmed: 31533613google scholar: lookup
  14. Fawcett JA, Sato F, Sakamoto T, Iwasaki WM, Tozaki T, Innan H. Genome-wide SNP analysis of Japanese Thoroughbred racehorses. PLoS One 2019;14(7):e0218407.
    doi: 10.1371/journal.pone.0218407pubmed: 31339891google scholar: lookup
  15. Kvist L, Niskanen M, Mannermaa K, Wutke S, Aspi J. Genetic variability and history of a native Finnish horse breed. Genet Sel Evol 2019 Jul 1;51(1):35.
    doi: 10.1186/s12711-019-0480-8pubmed: 31262246google scholar: lookup
  16. Schurink A, Shrestha M, Eriksson S, Bosse M, Bovenhuis H, Back W, Johansson AM, Ducro BJ. The Genomic Makeup of Nine Horse Populations Sampled in the Netherlands. Genes (Basel) 2019 Jun 25;10(6).
    doi: 10.3390/genes10060480pubmed: 31242710google scholar: lookup
  17. Grilz-Seger G, Druml T, Neuditschko M, Mesarič M, Cotman M, Brem G. Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size. Anim Genet 2019 Aug;50(4):334-346.
    doi: 10.1111/age.12797pubmed: 31199540google scholar: lookup
  18. Velie BD, Solé M, Fegraeus KJ, Rosengren MK, Røed KH, Ihler CF, Strand E, Lindgren G. Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits. Genet Sel Evol 2019 May 27;51(1):22.
    doi: 10.1186/s12711-019-0465-7pubmed: 31132983google scholar: lookup
  19. Nolte W, Thaller G, Kuehn C. Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse. PLoS One 2019;14(4):e0215913.
    doi: 10.1371/journal.pone.0215913pubmed: 31022261google scholar: lookup
  20. Grilz-Seger G, Druml T, Neuditschko M, Dobretsberger M, Horna M, Brem G. High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse. BMC Genomics 2019 Mar 5;20(1):174.
    doi: 10.1186/s12864-019-5564-xpubmed: 30836959google scholar: lookup
  21. Chessari G, Reich P, Criscione A, Falker-Gieske C, Mastrangelo S, Tumino S, Bordonaro S, Marletta D, Tetens J. Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds. BMC Genomics 2025 Nov 29;26(1):1086.
    doi: 10.1186/s12864-025-12256-8pubmed: 41318401google scholar: lookup
  22. Duderstadt S, Distl O. Insights into Genomic Patterns of Homozygosity in the Endangered Dülmen Wild Horse Population. Genes (Basel) 2025 Sep 8;16(9).
    doi: 10.3390/genes16091054pubmed: 41009997google scholar: lookup
  23. Asti V, Summer A, Ablondi M, Sartori C, Giontella A, Pilastro V, Mecocci S, Cappelli K, Mancin E, Oian A, Mantovani R, Capomaccio S, Sabbioni A. Selection signatures and inbreeding: exploring genetic diversity in five native horse breeds. BMC Vet Res 2025 May 16;21(1):346.
    doi: 10.1186/s12917-025-04794-wpubmed: 40380299google scholar: lookup
  24. Sievers J, Distl O. Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse. Genes (Basel) 2025 Mar 11;16(3).
    doi: 10.3390/genes16030327pubmed: 40149478google scholar: lookup
  25. Azcona F, Molina A, Demyda-Peyrás S. Genomic-Inbreeding Landscape and Selection Signatures in the Polo Argentino Horse Breed. Int J Mol Sci 2024 Dec 24;26(1).
    doi: 10.3390/ijms26010026pubmed: 39795883google scholar: lookup
  26. 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
  27. Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J. Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. PLoS One 2024;19(3):e0299109.
    doi: 10.1371/journal.pone.0299109pubmed: 38442089google scholar: lookup
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