Genetic diversity in Canadian horse breeds based on microsatellite analysis applications for livestock conservation

An analysis of sixteen horse breeds comprising rare and common breeds was undertaken to investigate the applicability of microsatellite data to livestock conservation. Breeds studied included three rare Canadian breeds, two French breeds and eleven common North American breeds of Race and/or Riding, Draft and Pony types. The focus of this project was the Canadian Horse (le Cheval Canadien), a unique breed which has been isolated for over 300 years, with the intention of providing a realistic framework applicable towards conservation efforts directed at other endangered livestock breeds.; A new panel of 15 multiplexed microsatellite markers was developed which, when combined with a previously developed multiplex, yields a panel of 25 loci, providing a cost-efficient system for genotyping large numbers of animals. A total of 1027 animals were genotyped at 11 loci, of which 318 animals were typed at the full panel of 25 loci, in order to investigate the effect of sample size, number of loci and different distance measures on the ability to reconstruct genetic relationships through phylogenetic analysis.; Phylogenetic analysis revealed a separation of Race/Riding type breeds from Draft and Pony breeds. These results were consistent for varied genetic distance measures, small sample sizes, and fewer loci than are currently recommended for livestock conservation genotyping programs. Genotyping fewer animals at more loci was more effective in resolving closer breed relationships than typing more animals at fewer loci. These empirical results confirm published predictions based on simulation results. Assignment of individual animals to their breeds was possible based on their genotype for breeds that were distantly related.; The Cheval Canadien was found to be most closely related to the Morgan horse, corroborating theories of its influence on some of the ancestors of the Morgan, and to the two French breeds, which are believed to be descendants of some of the Cheval Canadien's founding breeds.; Heterozygosity estimates ranged from 0.609 to 0.732 in the 16 breeds studied. Average inbreeding coefficients were estimated at 10.6%. Inbreeding levels were not found to be elevated within three rare Canadian breeds in comparison with more common breeds, although the level of heterozygosity was very low in one breed (the Lac LaCroix Pony). Levels of expected heterozygosity and inbreeding levels estimated from these microsatellite data were consistent with published data based on blood type loci and inbreeding coefficients computed from pedigree data.