To date the International Buffalo Consortium has sequenced almost 80 river and swamp animals from different countries (Brazil, Pakistan, Italy, Iran, China and the Philippines). Past demographic events were deduced from whole genome sequences. The pairwise sequentially Markovian coalescent (PSMC) developed by Li and Durbin (2011) was applied to newly assembled buffalo sequence. The model relies on the distribution of heterozygous sites within an individual sequence to infer historical Ne. A generation interval of 6 years and a rate of 2-8 mutations per site per generation were applied as parameters. The inferred demography shows a sharp reduction in Ne around 200,000 years ago. A second strong reduction is observed around 5000 years ago, probably as a consequence of domestication. The Consortium is now genotyping with the 90K Affymetrix Axiom® Buffalo Genotyping Array river buffoloes from Egypt, Iran, Romania, Italy , Brazil, Pakistan and Turkey, and swamp buffaloes from China, Philippines, Thailand, Indonesia and Brazil. The wild related species Anoa and Cape Buffalo are also being characterised at the same SNPs to identify the SNP ancestral allelic status. Geographic patterns of diversity in river and swamp buffaloes, as well as breed relationships inferred from SNP data will be described and discussed.

An overview of Bus bubalis genetic diversity

RAMUNNO, LUIGI;COSENZA, GIANFRANCO;
2014

Abstract

To date the International Buffalo Consortium has sequenced almost 80 river and swamp animals from different countries (Brazil, Pakistan, Italy, Iran, China and the Philippines). Past demographic events were deduced from whole genome sequences. The pairwise sequentially Markovian coalescent (PSMC) developed by Li and Durbin (2011) was applied to newly assembled buffalo sequence. The model relies on the distribution of heterozygous sites within an individual sequence to infer historical Ne. A generation interval of 6 years and a rate of 2-8 mutations per site per generation were applied as parameters. The inferred demography shows a sharp reduction in Ne around 200,000 years ago. A second strong reduction is observed around 5000 years ago, probably as a consequence of domestication. The Consortium is now genotyping with the 90K Affymetrix Axiom® Buffalo Genotyping Array river buffoloes from Egypt, Iran, Romania, Italy , Brazil, Pakistan and Turkey, and swamp buffaloes from China, Philippines, Thailand, Indonesia and Brazil. The wild related species Anoa and Cape Buffalo are also being characterised at the same SNPs to identify the SNP ancestral allelic status. Geographic patterns of diversity in river and swamp buffaloes, as well as breed relationships inferred from SNP data will be described and discussed.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11588/567202
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