Biodiversity Among Buffalo Genomes

Archaeozoological data indicate that the water buffalo was domesticated between 4000 and 6000 years ago in the Indus and Yangtze valleys. Historically domestic water buffalo were divided into swamp and river subspecies that differ in morphology, behaviour, geography and chromosome number. The river buffalo has 2n=50 chromosomes and the swamp buffalo has 2n=48 . The swamp buffalo resembles more closely the ancestral wild Bubalus arnee; than the river buffalo. The two subspecies mate only if reared together from calf-hood. River buffalo are mainly found in India, Southwest Asia and the Mediterranean, while swamp buffalo are predominantly in Southeast Asia and China. The International Buffalo Genome Consortium recently sequenced the buffalo genome to create a reference buffalo genome, and has produced low pass whole genome sequences of 48 river buffaloes from 4 breeds: Mediterranean buffalo  sampled in Italy, Jaffarabardi and Murrah breeds sampled in Brazil and Nili-Ravi sampled in Pakistan. Analysis of these data identified over 13M SNPs with MAF≥0.05. We used these data to estimate basic population genetics parameters and the genetic structure of the breeds. Expected heterozygosity varied significantly among breeds. The Fst index revealed that a remarkable portion of the total variability is explained by the between breed component. Principal component analysis of individual animals based on a subset of 50K randomly selected SNPs clustered animals from the same breed and showed a clear differentiation among breeds.