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Type: Journal article
Title: Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)
Author: Iamartino, D.
Nicolazzi, E.
Van Tassell, C.
Reecy, J.
Fritz-Waters, E.
Koltes, J.
Biffani, S.
Sonstegard, T.
Schroeder, S.
Ajmone-Marsan, P.
Negrini, R.
Pasquariello, R.
Ramelli, P.
Coletta, A.
Garcia, J.
Ali, A.
Ramunno, L.
Cosenza, G.
De Oliveira, D.
Drummond, M.
et al.
Citation: PLoS ONE, 2017; 12(10):e0185220-1-e0185220-18
Publisher: Public Library of Science (PLoS)
Issue Date: 2017
ISSN: 1932-6203
Statement of
Daniela Iamartino, Ezequiel L. Nicolazzi, Curtis P. Van Tassell, James M. Reecy, Eric R. Fritz-Waters, James E. Koltes, Stefano Biffani, Tad S. Sonstegard, Steven G. Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramelli, Angelo Coletta, José F. Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A.A. de Oliveira, Marcela G. Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L. Williams
Abstract: Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K "SNP-Chip" was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.
Keywords: Buffalo; Genome-Wide Association Study
Rights: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
RMID: 0030076501
DOI: 10.1371/journal.pone.0185220
Appears in Collections:Animal and Veterinary Sciences publications

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