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Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations

Published online by Cambridge University Press:  26 July 2011

J. M. Prystupa ,
R. Juras ,
E. G. Cothran ,
F. C. Buchanan  and
Y. Plante
J. M. Prystupa*
Affiliation:
Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada Agriculture & Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
R. Juras
Affiliation:
College of Veterinary Medicine & Biomedical Sciences, Texas A & M University, College Station, Texas 77848-4458, USA
E. G. Cothran
Affiliation:
College of Veterinary Medicine & Biomedical Sciences, Texas A & M University, College Station, Texas 77848-4458, USA
F. C. Buchanan
Affiliation:
Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
Y. Plante
Affiliation:
Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada Agriculture & Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
*
†E-mail: [email protected]
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Abstract

As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated that 13.3% of genetic diversity was explained by breed differences, whereas 84.6% and 2.1% of diversity came from within and among individuals, respectively. The average effective number of alleles and allelic richness was the lowest in the Eriskay (2.51 and 3.98) and Lac La Croix (2.83 and 4.01) populations, whereas it was highest in the New Forest (4.31 and 6.01) and Welsh (4.33 and 5.87) breeds, followed closely by the Newfoundland-CDN (4.23 and 5.86) population. Expected heterozygosities varied from 0.61 in the Lac La Croix to 0.74 in the Welsh and in Newfoundland. Observed heterozygosities ranged from 0.57 in the Exmoor and 0.58 in the Sable Island herd to 0.77 in the Kerry Bog and 0.76 in the New Forest breeds. Structure and admixture analyses revealed that the most likely number of clusters was 21, although some substructure was also observed when K = 16, compared with the 24 predefined populations. Information gathered from this study should be combined with other available phenotypic and pedigree data to develop, or amend, a suitable conservation strategy for all populations examined.

Keywords

geneticshorseCanadamicrosatellite markersconservation
Type
Full Paper
Information
animal , Volume 6 , Issue 1 , January 2012 , pp. 19 - 30
Copyright
Copyright © The Animal Consortium 2011

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Supplementary material: File

Prystupa Supplementary Table 1

Supplementary Table 1 A detail summary including the multiplex, location, primer sequence, allele size (ISAG markers have been standardized), dye, volume and reference of each microsatellite locus utilized this study (taken and modified from Glowatzki-Mullis et al. (2006).

Download Prystupa Supplementary Table 1(File)
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Supplementary material: File

Prystupa Supplementary Table 2

Supplementary Table 2 A overall summary of the statistics parameters estimated including: average number of alleles (Na), effective number of alleles (Ne), observed heterzygosity (Ho), expected heterzygosity (He), and F indices (FIS, FST, FIT) for each individual locus tested where P=0.05

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