Hostname: page-component-8448b6f56d-gtxcr Total loading time: 0 Render date: 2024-04-23T20:27:43.213Z Has data issue: false hasContentIssue false
  • English
  • Français

Optimization of the sampling strategy for establishing a gene bank: storing PrP alleles following a scrapie eradication plan as a case study

Published online by Cambridge University Press:  13 March 2007

J. Fernández ,
T. Roughsedge ,
J. A. Woolliams  and
B. Villanueva
J. Fernández*
Affiliation:
INIA, Carretera La Coruña Km 7, 28040 Madrid, Spain
T. Roughsedge
Affiliation:
Scottish Agricultural College, West Mains Road, Edinburgh, EH9 3JG, UK
J. A. Woolliams
Affiliation:
Roslin Institute (Edinburgh), Roslin, Midlothian, EH25 9PS, UK
B. Villanueva
Affiliation:
Scottish Agricultural College, West Mains Road, Edinburgh, EH9 3JG, UK
*
†Email: jmj@inia.es
Get access

Abstract

Gene banks are usually used for storing general genetic variability of endangered living populations but can be also used for storing alleles of a particular locus that are being eradicated through artificial selection programmes. In such scenarios gene banks would allow future re-introduction of one or more of the alleles being eradicated (and the associated diversity) into living populations. Frequencies within the bank for the locus of interest should have pre-determined target values. In this study, an algorithm is derived to obtain the optimal contributions of all candidate donors to achieve the target frequencies of the removed alleles in the bank while maintaining at the same time genetic variability in other loci unlinked to those targeted in the eradication programme. The efficiency of the algorithm is tested using the case of gene banks storing prion protein alleles currently disfavoured in scrapie eradication programmes (i.e., the AHQ, ARH, ARQ and VRQ alleles). Results showed that the algorithm was able to find the combinations of candidate contributions fulfilling different objectives regarding target frequencies and restrictions on coancestry. The most important factors influencing the optimal contributions were the allelic frequencies and the levels of diversity (coancestry) of the living population. Heterozygotes were favoured over homozygous individuals as, for a given number of animals contributing to the bank, the use of heterozygotes leads to lower levels of coancestry. Notwithstanding, almost all donors were sampled when restrictions on the global genetic diversity to be stored were severe.

Keywords

disease controlfrequency dependent selectiongene banksgenetic diversityscrapie
Type
Research Article
Information
Animal Science , Volume 82 , Issue 6 , December 2006 , pp. 813 - 821
Copyright
Copyright © British Society of Animal Science 2006

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Caballero, A. and Toro, M. A. 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetical Research 75: 331–343.Google Scholar
Dawson, M., Hoinville, L. J., Hosie, B. D. and Hunter, N. 1998. Guidance on the use of PrP genotyping as an aid to the control of clinical scrapie. Veterinary Record 142: 623–625.Google Scholar
Eglin, R. D., Warner, R., Gubbins, S., Sivam, S. K. and Dawson, M. 2005. Frequencies of PrP genotypes in 38 breeds of sheep sampled in the National Scrapie Plan for Great Britain. Veterinary Record 156: 433–437.CrossRefGoogle ScholarPubMed
Grundy, B., Villanueva, B. and Woolliams, J. A. 1998. Dynamic selection procedures for constrained inbreeding and their consequences for pedigree development. Genetical Research 72: 159–168.CrossRefGoogle Scholar
Kirkpatrick, S., Gelatt, C. D. and Vecchi, M. P. 1983. Optimization by simulated annealing. Science 220: 671–680.Google Scholar
Moum, T., Olsaker, I., Hopp, P., Moldal, T., Valheim, M., Moum, T. and Benestad, S. L. 2005. Polymorphisms at codons 141 and 154 in the ovine prion protein gene are associated with scrapie Nor98 cases. Journal of General Virology 86: 231–235.CrossRefGoogle ScholarPubMed
Roughsedge, T., Villanueva, B. and Woolliams, J. A. 2006. Determining the relationship between restorative potential and size of a gene bank to alleviate the risks inherent in a scrapie eradication breeding programme. Livestock Science 100: 231–241.CrossRefGoogle Scholar
Sonesson, A. K. G., Janss, L. L. and Meuwissen, T. H. E. 2003. Selection against genetic defects in conservation schemes while controlling inbreeding. Genetics Selection Evolution 35: 353–368.CrossRefGoogle ScholarPubMed
Villanueva, B., Pong-Wong, R., Woolliams, J. A.Avendaño, S. 2004. Managing genetic resources in commercial breeding populations. In Farm animal genetic resources Simm, G., Villanueva, B., Sinclair, K. D., Townsend, S. pp. 113–131. BSAS occasional publication no. 30. Nottingham University Press, Nottingham.Google Scholar
Windig, J. J., Eding, L., Moll, H. and Kaal, L. 2004. Effects on inbreeding of different strategies aimed at eliminating scrapie sensitivity alleles in rare sheep breeds in The Netherlands. Animal Science 79: 11–20.Google Scholar