Plante, Yves2011-06-202013-01-042012-06-242013-01-042011-062011-06-01June 2011http://hdl.handle.net/10388/etd-06202011-205904The legally binding international declaration of the Convention on Biological Diversity (signed by over 180 countries) recently acknowledged the importance of conserving genetic diversity within livestock species. This study aimed to help Canada assess molecular diversity in its horse and pony (Equus ferus caballus) genetic resources. Here, 24 populations were examined, with special focus on the native Canadian, Mountain and Moorland, and Nordic pony populations, using two well accepted molecular tools. Additional horse breeds and feral populations were also included in this project as some may have influenced the development of the three equine groups of interest. Altogether, 821 individuals were genotyped at 38 microsatellite loci, and 280 individuals were sequenced using a 421 base pair portion of the mitochondrial displacement Hypervariable Region I. Results from the microsatellite analyses indicated that 13.33% of genetic diversity arose from breed differences, whereas 84.60% and 2.07% of diversity arose from within and among individuals respectively. The New Forest and Welsh breeds were found to be the most diverse while having the highest average effective number of alleles and allelic richness (4.31 and 6.01; 4.33 and 5.87 respectively). The Eriskay and Lac La Croix breeds were found to have the lowest average effective number of alleles and allelic richness (2.51 and 3.98; 2.83 and 4.01 respectively). Expected heterozygosities were lowest in the Lac La Croix (0.61) and highest in the Welsh and New Forest (0.74) breeds, whereas observed heterozygosities were highest in the Kerry Bog (0.77) and lowest in the Exmoor (0.57) breeds. The genetic structure and admixture analyses suggested that the most probable number of unique genetic clusters was 21 as opposed to the 24 predefined populations. Results from the mitochondrial sequence data revealed that there were 36 informative sites producing 62 haplotypes, 20 of which were previously unreported. The Connemara was found to have the highest haplotype diversity of the pony breeds (0.89); however, the Highland pony was found to have the highest nucleotide diversity and pairwise difference (0.16 and 6.73 respectively). In contrast, the Fell pony had the lowest haplotype diversity (0.22), and the feral Sable Island population had the lowest nucleotide diversity and pairwise difference (0.01 and 0.29 respectively). Multiple phylogenetic trees were reconstructed and produced similar topologies. In general, the Mountain and Moorland and Nordic breeds were spread among the clades, whereas native Canadian populations were most frequent in the D and E clades. Interestingly, a large portion of ponies were found within the rare E clade as opposed to horses. Information gathered from this project can be incorporated with other available data into pre-existing conservation/breeding programs currently managed by the various breed societies to ensure that the most optimal and sustainable strategies are in place.en-USconservationmtDNAmicrosatellitecharacterizationEquus ferus caballustext