4 research outputs found
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