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Whole genome re-sequencing reveals adaptation prior to the divergence of buffalo subspecies

journal contribution
posted on 21.12.2020, 03:22 by Mostafa Rafiepour, Esmaeil Ebrahimie, Mohammad Farhad Vahidi, Ghasem Hosseini Salekdeh, Ali Niazi, Mohammad Dadpasand, Dong Liang, Jingfang Si, Xiangdong Ding, Jianlin Han, Yi Zhang, Saber Qanbari
Abstract The application of high throughput genotyping or sequencing data helps us to understand the genomic response to natural and artificial selection. In this study, we scanned the genomes of five indigenous buffalo populations belong to three recognized breeds, adapted to different geographical and agro-ecological zones in Iran, to unravel the extent of genomic diversity and to localize genomic regions and genes underwent past selection. A total of 46 river buffalo whole genomes, from West and East Azerbaijan, Gilan, Mazandaran and Khuzestan provinces, were re-sequenced. Our sequencing data reached to a coverage above 99% of the river buffalo reference genome and an average read depth around 9.2X per sample. We identified 20.55 million SNPs, including 63,097 missense, 707 stop-gain and 159 stop-loss mutations that might have functional consequences. Genomic diversity analyses showed modest structuring among Iranian buffalo populations following frequent gene flow or admixture in the recent past. Evidence of positive selection was investigated using both differentiation (Fst) and fixation (Pi) metrics. Analysis of fixation revealed three genomic regions in all three breeds with aberrant polymorphism contents on BBU2, 20 and 21. Fixation signal on BBU2 overlapped with the OCA2-HERC2 genes, suggestive of adaptation to UV exposure through pigmentation mechanism. Further validation using re-sequencing data from other five bovine species as well as the Axiom® Buffalo Genotyping Array 90 K data of river and swamp buffaloes indicated that these fixation signals persisted across river and swamp buffaloes and extended to taurine cattle, implying an ancient evolutionary event occurred before the speciation of buffalo and taurine cattle. These results contributed to our understanding of major genetic switches that took place during the evolution of modern buffaloes.

History

Publication Date

12/11/2020

Journal

Genome Biology and Evolution

Article Number

evaa231

Pagination

40p.

Publisher

Oxford University Press

ISSN

1759-6653

Rights Statement

The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.

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