Journal
ANIMAL GENETICS
Volume 41, Issue -, Pages 8-15Publisher
WILEY
DOI: 10.1111/j.1365-2052.2010.02092.x
Keywords
effective population size; horse; linkage disequilibrium; population history; single nucleotide polymorphism; Thoroughbred
Funding
- British Equestrian Federation
- Biosciences Knowledge Transfer Network
- Biotechnology and Biological Sciences Research Council (BBSRC)
- Horserace Betting Levy Board
- Thoroughbred Breeders' Association
- Bioscience CASE Studentship
- Quality Meat Scotland, EBLEX
- Aviagen
- Cobb
- Biotechnology and Biological Sciences Research Council [BBS/E/D/05191133] Funding Source: researchfish
- BBSRC [BBS/E/D/05191133] Funding Source: UKRI
Ask authors/readers for more resources
P>Many genomic methodologies rely on the presence and extent of linkage disequilibrium (LD) between markers and genetic variants underlying traits of interest, but the extent of LD in the horse has yet to be comprehensively characterized. In this study, we evaluate the extent and decay of LD in a sample of 817 Thoroughbreds. Horses were genotyped for over 50 000 single nucleotide polymorphism (SNP) markers across the genome, with 34 848 autosomal SNPs used in the final analysis. Linkage disequilibrium, as measured by the squared correlation coefficient (r2), was found to be relatively high between closely linked markers (> 0.6 at 5 kb) and to extend over long distances, with average r2 maintained above non-syntenic levels for single nucleotide polymorphisms (SNPs) up to 20 Mb apart. Using formulae which relate expected LD to effective population size (N-e), and assuming a constant actual population size, N-e was estimated to be 100 in our population. Values of historical N-e, calculated assuming linear population growth, suggested a decrease in N-e since the distant past, reaching a minimum twenty generations ago, followed by a subsequent increase until the present time. The qualitative trends observed in N-e can be rationalized by current knowledge of the history of the Thoroughbred breed, and inbreeding statistics obtained from published pedigree analyses are in agreement with observed values of N-e. Given the high LD observed and the small estimated N-e, genomic methodologies such as genomic selection could feasibly be applied to this population using the existing SNP marker set.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available