Analysis of Genetic Diversity in River Buffalo Populations using a Multivariate Approach

Genetic diversity of different river Buffalo breeds is investigated using a two step approach based on multivariate discriminant analysis. A sample of 185 Riverine buffaloes belonging to 15 breeds were genotyped using the 90K Affymetrix Axiom® Buffalo Genotyping Array. This array is the result of the draft sequence of the Buffalo genome even though SNP positions are tied to the Bos Taurus genome sequence. Editing was performed on SNP call rate (> 0.95), individual call rate > 0.98, MAF (> 0.01). A total of 53,399 SNP were retained for further analysis. A Stepwise discriminant analysis was carried out separately on each chromosome in order to select markers that mostly contribute to differentiate between breeds. Then a canonical discriminant analysis was performed chromosome-wide on SNP preselected in the first step. Canonical variables scores were then considered as new animal genetic coordinates and then plotted in the canonical space to quantify the distance between breeds. SNPs for which the correlation with the canonical variable was in the 99th percentile for a specific chromosome were considered to be significantly associated with that variable. Scores for each canonical variable were calculated and then plotted in the canonical space to assess the distance between breeds. SNPs for which the correlation with the canonical variable was in the 99th percentile for a specific chromosome were considered to significantly contribute to breed differences.