Patterns of diversity in swamp and river buffalo as revealed by SNP molecular markers

After sequencing the Buffalo genome, the International Buffalo Consortium has used the derived 90K Affymetrix Axiom® Buffalo Genotyping Array to characterize a set of river buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil. SNP genotype data have been analyzed with Bayesian clustering algorithms (ADMIXTURE software), multivariate statistics (Multi- Dimensional Scaling plots) and graph tools highlighting population splits and migration events (TREEMIX software) to estimate the levels of molecular diversity, population structure and the historical relationships among populations. When placed in the geographical context, the patterns of diversity confirmed archeozoological evidence for the domestication of river and swamp buffalo in the Indian subcontinent and in Southeast Asia, respectively, and provided hints on buffalo migrations and history. Admixture analysis revealed the presence of three main gene pools in pure river buffalo populations: one characterizes the breeds from the Indian subcontinent (Pakistan) and those recently exported from there to Bulgaria, Brazil and Colombia; the second includes breeds that, from the domestication center, spread westwards to Iran, Egypt and Turkey; the third includes the Italian Mediterranean buffalo, sampled both in Italy and in Mozambique where it has recently been exported. Among the breeds analysed, Mediterranean buffalo represents the most differentiated river buffalo gene pool, which is most likely due to genetic bottlenecks, isolation, selection and possible genetic contributions from breeds not included in our sampling. Four gene pools have been identified in pure swamp buffalo populations: the first from China; the second in Indonesian islands, other than Sumatra; the third in the Philippines and the fourth in Thailand and Sumatra. Some level of admixture is seen between river and swamp buffalo in the Philippines and in Brazil. TREEMIX software analyses confirmed the gene flows identified by Bayesian population structure analysis including those from the river buffalo gene pool to the admixed swamp populations and, within river buffaloes, from the Mediterranean to the breeds from Colombia and Brazil. Furthermore, these analyses revealed some unexpected migration patterns, which suggest that the westward spread of domestic buffaloes may have followed alternative migration routes.