Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Iamartino, Daniela
Nicolazzi, Ezequiel
Reecy, James
Van Tassell, Curtis
Reecy, James
Fritz-Waters, Eric
Koltes, James
Biffani, Stefano
Sonstegard, Tad
Schroeder, Steven
Ajmone-Marsan, Paolo
Negrini, Riccardo
Pasquariello, Rolando
Ramell, Paola
Coletta, Angelo
Garcia, Jose
Ali, Ahmad
Ramunno, Luigi
Cosenza, Gianfranco
de Oliveira, Denise
Drummond, Marcela
Bastianetto, Eduardo
Davassi, Alessandro
Pirani, Ali
Brew, Fiona
Williams, John
Major Professor
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Animal Science
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Animal Science

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 ªSNP-Chipº 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.


This article is published as Iamartino D, Nicolazzi EL, Van Tassell CP, Reecy JM, Fritz-Waters ER, Koltes JE, et al. (2017) Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLoS ONE 12(10): e0185220. doi: 10.1371/journal.pone.0185220.