Whole genome genetic diversity of buffalo.

The domestication of water buffalo likely took place between 4000 and 6000 years ago in the regions of Indus and Yangtze valleys. Domestic water buffalo comprises two subspecies that differ in a number of phenotypic traits, including morphology and behaviour, in geographic range and number of chromosomes. River buffalo has 50 chromosomes and is mainly reared in India, Southwest Asia and the Mediterranean region, including Italy, where the mozzarella di bufala campana cheese is produced from river buffalo milk contributing to the excellent reputation of the made in Italy brand worldwide. Swamp buffalo has 48 chromosomes and is mainly reared in Southeast Asia and China. The river buffalo genome has been recently sequenced and de-novo assembled, through the coordinated effort of an international Consortium led by a core group of Italian scientists. An associated HapMap project has sequenced 47 river buffaloes from 4 breeds at low coverage. As a result, more than 22M SNPs were discovered, permitting the development of the Axiom Buffalo Genotyping 90K (Affymetrix) marker panel. In this study, the SNP panel has been used to assess the main genetic parameters and genetic diversity of different water buffalo breeds sampled in Italy and elsewhere. Genotyping accuracy and main population genetic indexes have been compared between the 90K SNPs from the SNPchip and the 22M SNPs discovered by sequencing. Data were filtered for missing data, MAF ??? 0.05 and deviation from HW equilibrium. Sequence data was filtered for quality score and SNP coverage. Preliminary analyses indicate that genotypes from SNP arrays are better suited to diversity studies than low pass sequence by correctly detecting genotypes at SNP loci. Both sequence and SNP data indicate that expected heterozygosity values are quite variable among breeds. Sequence and SNP array data produced similar estimates of the Fst index (5.2% and 5.6% respectively), revealing that a moderate proportion of the total genetic diversity is explained by the between breed component. Principal Component Analysis showed a clear differentiation among breeds corresponding to geographic origin