Optimum contribution selection (OCS) analyses prompted successful conservation actions for Faroese Horse population

Main Article Content

Anne Kettunen
https://orcid.org/0000-0002-1217-7079
Signa Kallsoy Joensen
https://orcid.org/0000-0003-4607-0832
Peer Berg
https://orcid.org/0000-0002-7306-5898

Abstract

The Faroese horse, an endangered indigenous horse breed, is a part of the cultural and societal heritage of the Faroe Islands. Population history describes a severe bottleneck, prompting for quantification of the genetic diversity (level of inbreeding, probability of gene origin, effective population size) and assessment of sustainable conservation potential (Optimum Contribution Selection, OCS) of the Faroese horse population. The pedigree completeness (PCI) of the Faroese horse is adequate for a realistic estimation of the level of inbreeding (PCI5 = 0.96). In concordance with the known population history, the average inbreeding is exceptionally high; in the last cohort, it was equal to 26.8%. An estimate of the effective population size, based on individual increase in inbreeding and coancestry, accounting for the whole population history, was eight. OCS offers a tool to understand and control the increase in the average relationships in the population. Within a fixed number of matings, the repetitive use of stallions resulted in the lowest level of average relationships. Successful follow-up of mating schemes planned together with a holistic assessment of the suitability of an individual as a breeding candidate, will minimize the increase in inbreeding in future generations and maximize the possibility to increase the census size of the Faroese horse population.

Article Details

How to Cite
Kettunen, A., Kallsoy Joensen, S. and Berg, P. (2022) “Optimum contribution selection (OCS) analyses prompted successful conservation actions for Faroese Horse population”, Genetic Resources, 3(5), pp. 59-67. doi: 10.46265/genresj.KKXV5870.
Section
Original Articles
References

Berg, P, J Nielsen, and M K Sørensen (2006). “EVA: realized and predicted optimal genetic contributions”. In: 8th World Congress on Genetics Applied to Livestock Production.

Bjørk, E A (1984). Færøsk bygderet 1ste del: Husbruget m.v. (Torshavn: Matrikulstovan).

Boichard, D, L Maignel, and É Verrier (1997). “The value of using probabilities of gene origin to measure genetic variability in a population”. Genetics Selection Evolution 29(1). DOI: https://doi.org/10.1186/1297-9686-29-1-5.

Caballero, A and M A Toro (2000). “Interrelations between effective population size and other pedigree tools for the management of conserved populations”. Genet Res 75(3), pp. 331–374. DOI: https://doi.org/10.1017/s0016672399004449.

Cervantes, I et al. (2011). “Estimation of effective population size from the rate of coancestry in pedigreed populations”. J Anim Breed Genet 128(1), pp. 56–63. DOI: https://doi.org/10.1111/j.1439-0388.2010.00881.x.

Duru, S (2017). “Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability”. Animal 11(9), pp. 1449–1456. DOI: https://doi.org/10.1017/s175173111700009x.

Gandini, G C et al. (1992). “Inbreeding in the Italian Haflinger horse”. Journal of Animal Breeding and Genetics 109(1-6), pp. 433–443. DOI: https://doi.org/10.1111/j.1439-0388.1992.tb00424.x.

Giontella, A et al. (2019). “Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure, genetic variability and inbreeding”. Animal 13(1), pp. 15–24. DOI: https://doi.org/10.1017/s1751731118001180.

Gutiérrez, J P, J Altarriba, et al. (2003). “Pedigree analysis of eight Spanish beef cattle breeds”. Genet Sel Evol 35(1), pp. 43–63. DOI: https://doi.org/10.1186/1297-9686-35-1-43.

Gutiérrez, J P and F Goyache (2005). “A note on ENDOG: a computer program for analysing pedigree information”. J Anim Breed Genet 122(3), pp. 172–178. DOI: https://doi.org/10.1111/j.1439-0388.2005.00512.x.

Gutiérrez, J P, I Cervantes, and F Goyache (2009). “Improving the estimation of realized effective population sizes in farm animals”. J Anim Breed Genet 126(4), pp. 327–359. DOI: https://doi.org/10.1111/j.1439-0388.2009.00810.x.

Gutiérrez, J P, I Cervantes, A Molina, et al. (2008). “Individual increase in inbreeding allows estimating effective sizes from pedigrees”. Genet Sel Evol 40(4), pp. 359–78. DOI: https://doi.org/10.1186/1297-9686-40-4-359.

Hasler, H et al. (2011). “Genetic diversity in an indigenous horse breed: implications for mating strategies and the control of future inbreeding”. J Anim Breed Genet 128(5), pp. 394–406. DOI: https://doi.org/10.1111/j.1439-0388.2011.00932.x.

Henryon, M et al. (2015). “Most of the long-term genetic gain from optimum-contribution selection can be realised with restrictions imposed during optimisation”. Genetics Selection Evolution 47(1), pp. 21–21. DOI: https://doi.org/10.1186/s12711-015-0107-7.

I Perdomo-González, D et al. (2020). “Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation”. Animals (Basel)(8), pp. 10–10. DOI: https://doi.org/10.3390/ani10081360.

Joensen, S K (2019). Activation of persistent Streptococcus equi subspecies Zooepidemicus in Faroese mares. Faculty of Science and Technology, University of Faroe Islands.

Kettunen, A et al. (2017). “Cross-Breeding Is Inevitable to Conserve the Highly Inbred Population of Puffin Hunter: The Norwegian Lundehund”. PLOS ONE 12(1), pp. 170039–170039. DOI: https://doi.org/10.1371/journal.pone.0170039.

Kvist, L et al. (2019). “Genetic variability and history of a native Finnish horse breed”. Genet Sel Evol 51, p. 35. DOI: https://doi.org/10.1186/s12711-019-0480-8.

Lacy, R C (1989). “Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents”. Zoo Biology 8(2), pp. 111–123. DOI: https://doi.org/10.1002/zoo.1430080203.

Lacy, R C (1995). “Clarification of genetic terms and their use in the management of captive populations”. Zoo Biology 14(6), pp. 565–577. DOI: https://doi.org/10.1002/zoo.1430140609.

Luís, C et al. (2007). “Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management”. J Hered 98(3), pp. 232–239. DOI: https://doi.org/10.1093/jhered/esm009.

MacCluer, J W et al. (1983). “Inbreeding and pedigree structure in Standardbred horses”. Journal of Heredity 74(6), pp. 394–399. DOI: https://doi.org/10.1093/oxfordjournals.jhered.a109824.

Mancin, E et al. (2020). “Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information”. Animals 10(8), pp. 1310–1310. DOI: https://www.mdpi.com/2076-2615/10/8/1310.

Meuwissen, T H (1997). “Maximizing the response of selection with a predefined rate of inbreeding”. J Anim Sci 75(4), pp. 934–974. DOI: https://doi.org/10.2527/1997.754934x.

Mikko, S T, C. G Leivsson, and T (2004). Genetic diversity of the Faroe pony and relationships to other breeds. Poster in International Society for Animal Genetics (ISAG), Tokyo, Japan 11-16.9.2004.

Nielsen, H M and M Kargo (2020). “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), pp. 127–130. DOI: https://doi.org/10.1080/09064702.2020.1728370.

Olsen, H F, T Meuwissen, and G Klemetsdal (2013). “Optimal contribution selection applied to the Norwegian and the North-Swedish cold-blooded trotter - a feasibility study”. J Anim Breed Genet 130(3), pp. 170–177. DOI: https://doi.org/10.1111/j.1439-0388.2012.01005.x.

Onogi, A et al. (2017). “Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation”. Animal Science Journal 88(12), pp. 1902–1910. DOI: https://onlinelibrary.wiley.com/doi/abs/10.1111/asj.12867.

Pérez-Enciso, M (1995). “Use of the uncertain relationship matrix to compute effective population size”. Journal of Animal Breeding and Genetics 112(1-6), pp. 327–332. DOI: https://doi.org/10.1111/j.1439-0388.1995.tb00574.x.

Poyato-Bonilla, J et al. (2020). “Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse”. Genetics Selection Evolution 52(1), pp. 62–62. DOI: https://doi.org/10.1186/s12711-020-00582-2.

Sairanen, J et al. (2009). “Effects of inbreeding and other genetic components on equine fertility”. Animal 3(12), pp. 1662–72. DOI: https://doi.org/10.1017/s1751731109990553.

Solé, M et al. (2013). “Implementation of Optimum Contributions selection in endangered local breeds: the case of the Menorca Horse population”. J Anim Breed Genet 130(3), pp. 218–244. DOI: https://doi.org/10.1111/jbg.12023.

Somogyvári, E, J Posta, and S Mihók (2018). “Genetic analysis of the Hungarian population of endangered Hucul horses”. Czech Journal of Animal Science 63, pp. 237–246.

Vostrá-Vydrová, H et al. (2016). “Pedigree analysis of the endangered Old Kladruber horse population”. Livestock Science 185, pp. 17–23. DOI: https://doi.org/10.1016/j.livsci.2016.01.001.