Characterization of linkage disequilibrium and consistency of gametic phase in Canadian goats
Luiz F. Brito1, Mohsen Jafarikia2, Daniela Grossi1, Laurence Maignel2, Mehdi Sargolzaei1,3, Flavio Schenkel1
1Centre For Genetic Improvement of Livestock, Department of Animal & Poultry Science, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1Abstract: The objective of this study was to estimate genome-wide levels of linkage disequilibrium (LD) in six Canadian goat breeds and to evaluate the persistence of gametic phase using the Illumina goat SNP50 BeadChip. A total of 976 animals were included in the analyses. The average values of LD between adjacent SNPs were 0.14, 0.15, 0.24, 0.19, 0.27 and 0.28 for Alpine, Saanen, Toggenburg, LaMancha, Nubian and Boer breeds, respectively. This indicates that, with a large enough training population, genomic selection could potentially be implemented within breed with the current 50k panel, but the Alpine and Saanen breeds might benefit from a denser panel. The gametic phase consistency (correlation between the signed square root of r2) between adjacent markers was not high enough (~0.50) to support the pooling of breeds in a training population for genomic selection. For multi-breed genomic evaluation, a denser SNP panels seems to be required.
More Information:Presented at the 10th World Congress on Genetics Applied to Livestock Production, August 17-24, Vancouver, BC, Canada