FREE SHIPPING over $40
OVER 10000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Ecology and evolution2021; 11(21); 14555-14572; doi: 10.1002/ece3.8118

16 Years of breed management brings substantial improvement in population genetics of the endangered Cleveland Bay Horse.

Abstract: The consequences of poor breed management and inbreeding can range from gradual declines in individual productivity to more serious fertility and mortality concerns. However, many small and closed groups, as well as larger unmanaged populations, are plagued by genetic regression, often due to a dearth in breeding support tools which are accessible and easy to use in supporting decision-making. To address this, we have developed a population management tool (BCAS, Breed Conservation and Management System) based on individual relatedness assessed using pedigree-based kinship, which offers breeding recommendations for such populations. Moreover, we demonstrate the success of this tool in 16 years of employment in a closed equine population native to the UK, most notably, the rate of inbreeding reducing from more than 3% per generation, to less than 0.5%, or that attributed to genetic drift, as assessed over the last 16 years of implementation. Furthermore, with adherence to this program, the long-term impact of poor management has been reversed and the genetic resource within the breed has grown from an effective population size of 20 in 1994 to more than 140 in 2020. The development and availability of our BCAS for breed management and selection establish a new paradigm for the successful maintenance of genetic resources in animal populations.
© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
Get Full Text
Publication Date: 2021-10-03 PubMed ID: 34765125PubMed Central: PMC8571631DOI: 10.1002/ece3.8118Google 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

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 demonstrates a successful application of a population management tool (BCAS) to reduce inbreeding and improve genetic health in a closed equine population over a span of 16 years. Implemented among the endangered Cleveland Bay Horse, the tool has resulted in a significant reduction in the rate of inbreeding, an increase in genetic diversity, and a reversal of previously poor management impacts.

Overview of the Research

  • This study introduces a population management tool named BCAS (Breed Conservation and Management System) designed to slow down genetic regression, particularly in closed or small animal populations. This tool aids in breeding decision-making, taking into consideration the kinship or relatedness of individual animals based on their pedigree.
  • The effectiveness of the tool was demonstrated in a closed breed of horse native to the United Kingdom—the endangered Cleveland Bay Horse—effectively reducing the rate of inbreeding over a span of 16 years. The rate of inbreeding decreased from over 3% per generation to less than 0.5%, a value similar to that caused by genetic drift.

Results and Impact of BCAS Tool

  • Implementing the BCAS tool helped counteract the detrimental effects of previous poor breed management, leading to a substantial improvement in the genetic resource within the breed.
  • The effective population size of Cleveland Bay Horses grew significantly, from 20 in 1994 to over 140 in 2020, implying an increase in genetic diversity.
  • This successful implementation suggests the transformative potential of the BCAS tool in ensuring the maintenance of genetic resources in animal populations, providing breeding recommendations based on pedigree-based kinship, and ultimately reducing inbreeding and improving the genetic health of a population.

Significance of the Study

  • This research helps address the common problem of genetic regression in small, closed, or unmanaged animal populations, where conventional breeding support tools may be inadequate or lacking completely.
  • While the BCAS tool was specifically employed for the endangered Cleveland Bay Horse, its clear success indicates that similar applications could benefit other animal breeds or populations facing challenges related to inbreeding and poor genetic diversity.
  • The research underscores the importance of well-thought breed management in preserving and enhancing animal populations’ genetic health, demonstrating the potential to recover even severely affected breeds using appropriate tools and methods.

Cite This Article

APA
Dell A, Curry M, Hunter E, Dalton R, Yarnell K, Starbuck G, Wilson PB. (2021). 16 Years of breed management brings substantial improvement in population genetics of the endangered Cleveland Bay Horse. Ecol Evol, 11(21), 14555-14572. https://doi.org/10.1002/ece3.8118

Publication

Ecology and evolution
ISSN: 2045-7758
NlmUniqueID: 101566408
Country: England
Language: English
Volume: 11
Issue: 21
Pages: 14555-14572

Researcher Affiliations

Dell, Andrew
  • Department of Biological Sciences University of Lincoln Lincoln UK.
  • School of Animal, Rural and Environmental Sciences Nottingham Trent University, Brackenhurst Campus Southwell UK.
Curry, Mark
  • Department of Biological Sciences University of Lincoln Lincoln UK.
Hunter, Elena
  • School of Animal, Rural and Environmental Sciences Nottingham Trent University, Brackenhurst Campus Southwell UK.
Dalton, Ruth
  • Whinpot Farm Kendal UK.
Yarnell, Kelly
  • School of Animal, Rural and Environmental Sciences Nottingham Trent University, Brackenhurst Campus Southwell UK.
Starbuck, Gareth
  • School of Animal, Rural and Environmental Sciences Nottingham Trent University, Brackenhurst Campus Southwell UK.
Wilson, Philippe B
  • School of Animal, Rural and Environmental Sciences Nottingham Trent University, Brackenhurst Campus Southwell UK.

Conflict of Interest Statement

None declared.

References

This article includes 67 references
  1. Alderson GLH. A system to maximize the maintenance of genetic variability in small populations. pp. 18–29.
  2. Ballou JD, Gilpin M, Foose TJ. Population management for survival & recovery: Analytical methods and strategies in small population conservation. .
  3. Ballou JD, Lacy RC. Identifying genetically important individuals for management of genetic variation in pedigreed populations. In Ballou JD, Gilpin M & Foose TJ (Eds.), Population management for survival and recovery: Analytical methods and strategies in small population conservation (pp. 76, 375).
  4. Banks RG, Brown DJ. Genetic improvement in the Australasian Merino – Management of a diverse gene pool for changing markets. Animal Genetic Resources Information 45(1), 29–36.
    doi: 10.1017/S1014233909990290google scholar: lookup
  5. Berg P, Sorensen MK, Nielsen J. EVA interface program. .
  6. Caballero A, Santiago E, Toro MA. Systems of mating to reduce inbreeding in selected population. Animal Science 62, 431.
  7. Caballero A, Toro MA. Analysis of genetic diversity for the management of conserved subdivided populations. Conservation Genetics 3, 289.
  8. Colleau JJ, Moureaux S. Optimizing management of kinship and inbreeding coefficients in dairy cattle selection. Gestion optimisee de la parente et de la consanguinite dans les programmes de selection des bovins laitiers. Productions Animales (Paris) 19(1), 3.
  9. Daleszczyk K, Bunevich AN. Population viability analysis of European bison populations in Polish and Belarusian parts of Białowieża Forest with and without gene exchange. Biological Conservation 142(12), 3068–3075.
    doi: 10.1016/j.biocon.2009.08.006google scholar: lookup
  10. Dell AC, Curry MC, Yarnell KM, Starbuck GR, Wilson PB. Mitochondrial D‐loop sequence variation and maternal lineage in the endangered Cleveland Bay horse. PLoS One 15(12), e0243247.
    pmc: PMC7714183pubmed: 33270708
  11. Dell A, Curry M, Yarnell K, Starbuck G, Wilson PB. Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data. PLoS One 15(10), e0240410.
    doi: 10.1371/journal.pone.0240410pmc: PMC7595272pubmed: 33119607google scholar: lookup
  12. Dent A. Cleveland Bay horses. pp. 87.
  13. Earnheardt JM. SPARKS software. .
  14. Eding H, Crooijmans RP, Groenen MA, Meuwissen TH. Assessing the contribution of breeds to genetic diversity in conservation schemes. Genetics Selection Evolution 34(5), 613–633.
    doi: 10.1186/1297-9686-34-5-613pmc: PMC2705437pubmed: 12427389google scholar: lookup
  15. Eding H, Meuwissen THE. Marker‐based estimates of between and within population kinships for the conservation of genetic diversity. Journal of Animal Breeding and Genetics 118(3), 141–159.
    doi: 10.1046/j.1439-0388.2001.00290.xgoogle scholar: lookup
  16. Eding H, Meuwissen THE. Linear methods to estimate kinships from genetic marker data for the construction of core sets in genetic conservation schemes. Journal of Animal Breeding and Genetics 120(5), 289–302.
    doi: 10.1046/j.1439-0388.2003.00399.xgoogle scholar: lookup
  17. Emik LO, Terrill CE. Systematic procedures for calculating inbreeding coefficients. Journal of Heredity 40(2), 51–55.
    doi: 10.1093/oxfordjournals.jhered.a105986pubmed: 18116093google scholar: lookup
  18. Emmerson S. Cleveland Bay Horse Society Centenary Studbook. pp. 296.
  19. Falconer DS, MacKay TFC. Introduction to quantitative genetics. .
    pmc: PMC1471025pubmed: 15342495
  20. FAO I. Guidelines for development of national farm animal genetics resources management plans. Measurement of domestic animal diversity (MoDAD): Recommended microsatellite markers. New microsatellite marker sets. Recommendations of Joint ISAG/FAO Standing Committee. .
  21. Flury C, Täubert H, Simianer H. Extension of the concept of kinship, relationship, and inbreeding to account for linked epistatic complexes. Livestock Science 103(1–2), 131–140.
    doi: 10.1016/j.livsci.2006.02.005google scholar: lookup
  22. Frankham R, Ballou JD, Briscoe DA. Introduction to conservation genetics. .
  23. Goncalves da Silva A, Lalonde DR, Quse V, Shoemaker A, Russello MA. Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation. Journal of Heredity 101(5), 581–590.
    doi: 10.1093/jhered/esq055pubmed: 20484384google scholar: lookup
  24. Groeneveld E, Westhuizen B, Maiwashe A, Voordewind F, Ferraz JB. POPREP: A generic report for population management. Genetics and Molecular Research 8(3), 1158–1178.
    doi: 10.4238/vol8-3gmr648pubmed: 19866435google scholar: lookup
  25. Grundy B, Villanueva B, Wooliams JA. Dynamic selection procedures for constrained inbreeding and their consequences for pedigree development. Genetics Research 72(02), 159–168.
  26. Gutierrez JP, Cervantes I, Goyache F. Improving the estimation of realized effective population sizes in farm animals. Journal of Animal Breeding and Genetics 126(4), 327–332.
    pubmed: 19630884
  27. Gutierrez JP, Goyache F. A note on ENDOG: A computer program for analysing pedigree information. Journal of Animal Breeding and Genetics 122(3), 172–176.
    doi: 10.1111/j.1439-0388.2005.00512.xpubmed: 16130468google scholar: lookup
  28. Hall SJG. Livestock biodiversity: Genetic resources for the farming of the future. .
  29. Hedrick PW, Fredrickson RJ. Captive breeding and the reintroduction of Mexican and red wolves. Molecular Ecology 17(1), 344–350.
    doi: 10.1111/j.1365-294X.2007.03400.xpubmed: 18173506google scholar: lookup
  30. Henderson CR. Best linear unbiased prediction using relationship matrices derived from selected base populations. Journal of Dairy Science 68(2), 443–448.
    doi: 10.3168/jds.S0022-0302(85)80843-2google scholar: lookup
  31. Henryon M, Sorensen AC, Berg P. Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection. Animal 3(10), 1339–1346.
    doi: 10.1017/S1751731109004807pubmed: 22444927google scholar: lookup
  32. Khanshour AM, Hempsey EK, Juras R, Cothran EG. Genetic characterization of Cleveland Bay horse breed. Diversity 11(10), 174.
    doi: 10.3390/d11100174google scholar: lookup
  33. Lacy RC. Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biology 8, 111.
    doi: 10.1002/zoo.1430080203google scholar: lookup
  34. Lacy RC. GENES version 1.1.8. .
  35. Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C. Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. Genetics Selection Evolution 45(1), 1.
    doi: 10.1186/1297-9686-45-1pmc: PMC3599586pubmed: 23281913google scholar: lookup
  36. Malècot G. Les mathématiques de l'hérédité. .
  37. Margan SH, Nurthen RK, Montgomery ME, Woodworth LM, Lowe EH, Briscoe DA, Frankham R. Single large or several small? Population fragmentation in the captive management of endangered species. Zoo Biology 17(6), 467–480.
    doi: 10.1002/(SICI)1098-2361(1998)17:6<467:AID-ZOO1>3.0.CO;2-3google scholar: lookup
  38. 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. Scientific Reports 10(1), 1–12.
    pmc: PMC6965197pubmed: 31949252
  39. Meuwissen TH. Maximizing the response of selection with a predefined rate of inbreeding. Journal of Animal Science 75(4), 934–940.
    doi: 10.2527/1997.754934xpubmed: 9110204google scholar: lookup
  40. Meuwissen T. Genetic management of small populations: A review. Acta Agriculturae Scandinavica, Section A – Animal Science 59(2), 71.
    doi: 10.1080/09064700903118148pmc: PMC4936439pubmed: 27453634google scholar: lookup
  41. Montgomery ME, Ballou JD, Nurthen RK, England PR, Briscoe DA, Frankham R. Minimizing kinship in captive breeding programs. Zoo Biology 16(5), 377–389.
    doi: 10.1002/(SICI)1098-2361(1997)16:5<377:AID-ZOO1>3.0.CO;2-7google scholar: lookup
  42. Mrode R, Kearney JF, Biffani S, Coffey M, Canavesi F. Short communication: Genetic relationships between the Holstein cow populations of three European dairy countries. Journal of Dairy Science 92(11), 5760–5764.
    doi: 10.3168/jds.2008-1931pubmed: 19841236google scholar: lookup
  43. Nielsen HM, Kargo M. An endangered horse breed can be conserved by using optimum contribution selection and preselection of stallions. Acta Agriculturae Scandinavica, Section A – Animal Science 69(1–2), 127–130.
    doi: 10.1080/09064702.2020.1728370google scholar: lookup
  44. Oldenbroek K. Utilisation and conservation of farm animal genetic resources. vol. 232.
  45. Oldenrboek K, Van der Waaij L. Textbook of animal breeding: Animal breeding and genetics for BSc students. .
  46. Oliehoek PA, Bijma P, van der Meijden A. History and structure of the closed pedigreed population of Icelandic Sheepdogs. Genetics Selection Evolution 41(1), 3.
    doi: 10.1186/1297-9686-41-39pmc: PMC2736928pubmed: 19660133google scholar: lookup
  47. Pease AE. Cleveland bay studbook. .
  48. Pérez-Enciso M. Use of the uncertain relationship matrix to compute effective population size. Journal of Animal Breeding and Genetics 112(1‐6), 327–332.
  49. Pong-Wong R, Woolliams JA. Optimisation of contribution of candidate parents to maximise genetic gain and restricting inbreeding using semidefinite programming (open access publication). Genetics Selection Evolution 39, 3.
    doi: 10.1186/1297-9686-39-1-3pmc: PMC2739432pubmed: 17212945google scholar: lookup
  50. Scarth-Dixon W. The influence of racing and the thoroughbred horse on light horse breeding. pp. 247.
  51. Sonesson A. Managing inbreeding in selection and genetic conservation schemes of livestock. .
  52. Sonesson AK, Meuwissen TH. Mating schemes for optimum contribution selection with constrained rates of inbreeding. Genetics Selection Evolution 32(3), 231–248.
    doi: 10.1186/1297-9686-32-3-231pmc: PMC2706885pubmed: 14736390google scholar: lookup
  53. Sonesson AK, Meuwissen TH. Minimization of rate of inbreeding for small populations with overlapping generations. Genetical Research 77(3), 285–292.
    doi: 10.1017/S0016672301005079pubmed: 11486511google scholar: lookup
  54. Sonesson AK, Meuwissen TH. Non‐random mating for selection with restricted rates of inbreeding and overlapping generations. Genetics Selection Evolution 34(1), 23–39.
    doi: 10.1186/1297-9686-34-1-23pmc: PMC2705421pubmed: 11929623google scholar: lookup
  55. Todd ET, Ho SYW, Thomson PC, Ang RA, Velie BD, Hamilton NA. Founder‐specific inbreeding depression affects racing performance in thoroughbred horses. Scientific Reports 8, 6167.
    doi: 10.1038/s41598-018-24663-xpmc: PMC5906619pubmed: 29670190google scholar: lookup
  56. Toro MA, Nieto B, Salgado C. A note on minimization of inbreeding in small‐scale selection programmes. Livestock Production Science 20(4), 317.
  57. VanDyke F. Conservation biology: Foundations, concepts, applications. .
  58. Vila C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H. Widespread origins of domestic horse lineages. Science 291(5503), 474–477.
    doi: 10.1126/science.291.5503.474pubmed: 11161199google scholar: lookup
  59. Villanueva B, Pong-Wong R, Woolliams JA, Avendaño S. Managing genetic resources in selected and conserved populations. BSAP Occasional Publication vol. 30, pp. 113–132.
    doi: 10.1017/S0263967X00041987google scholar: lookup
  60. Villanueva B, Woolliams JA, Simm G. Strategies for controlling rates of inbreeding in MOET nucleus schemes for beef cattle. Genetics Selection Evolution 26(6), 517.
    doi: 10.1186/1297-9686-26-6-517google scholar: lookup
  61. Walling G. Cleveland Bay Horse Society Studbook. Vol. XXXIII, pp. 160.
  62. Weitzman ML. On diversity. The Quarterly Journal of Economics 107(2), 363–405.
    doi: 10.2307/2118476google scholar: lookup
  63. Wellmann R. Optimum contribution selection for animal breeding and conservation: The R package optiSel. BMC Bioinformatics 20(1), 25.
    doi: 10.1186/s12859-018-2450-5pmc: PMC6332575pubmed: 30642239google scholar: lookup
  64. Woolliams JA, Toro M. What is genetic diversity. In Oldenbroek K. (Ed.), Utilisation and conservation of farm animal genetic resources (pp. 55–74).
  65. Wright S. Coefficients of inbreeding and relationship. American Naturalist 56(645), 330–338.
    doi: 10.1086/279872google scholar: lookup
  66. Wright S. Mendelian analysis of the pure breeds of livestock: I. The measurement of inbreeding and relationship. Journal of Heredity 14(8), 339–348.
    doi: 10.1086/279872google scholar: lookup
  67. Wright S. Evolution in Mendelian populations. Genetics 16(2), 97–159.
    doi: 10.1093/genetics/16.2.97pmc: PMC1201091pubmed: 17246615google scholar: lookup

Citations

This article has been cited 3 times.
  1. Marašinskienė Š, Šveistienė R, Razmaitė V, Račkauskaitė A, Juškienė V. Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations. Animals (Basel) 2023 Nov 13;13(22).
    doi: 10.3390/ani13223506pubmed: 38003124google scholar: lookup
  2. Ludwig EK, Hallowell K, Womble M, O'Neil E. Bilateral patellar aplasia in a foal. Vet Med Sci 2023 May;9(3):1143-1148.
    doi: 10.1002/vms3.1083pubmed: 36734120google scholar: lookup
  3. 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
Subscribe to our newsletter
Join 99,780 horse owners like you who receive our email updates on horse health and nutrition.