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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #334293
Title: Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Author
item IAMARTINO, DANIELA - Collaborator
item NICOLAZZI, EZEQUIEL - Collaborator
item Van Tassell, Curtis - Curt
item REECY, JAMES - Iowa State University
item FRITZ-WATERS, ERIC - Iowa State University
item KOLTES, JAMES - Iowa State University
item BIFFANI, STEFANO - Collaborator
item SONSTEGARD, TAD - Former ARS Employee
item Schroeder, Steven - Steve
item AJMONE-MARSAN, PAOLO - Institute Of Zootechnics - Italy
item NEGRINI, RICCARDO - Institute Of Zootechnics - Italy
item PASQUARIELLO, ROLANDO - Collaborator
item RAMELLI, PAOLA - Collaborator
item COLETTA, ANGELO - Collaborator
item GARCIA, JOSE - Collaborator
item ALI, AHMAD - Collaborator
item RAMUNNO, LUIGI - Collaborator
item COSENZA, GIANFRANCO - Collaborator
item DE OLIVEIRA, DENISE - Collaborator
item DRUMMOND, MARCELA - Collaborator
item BASTIANETTO, EDUARDO - Collaborator
item DAVASSI, ALESSANDRO - Collaborator
item PIRANI, ALI - Collaborator
item BREW, FIONA - Collaborator
item WILLIAMS, JOHN - Collaborator

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2017
Publication Date: 10/5/2017
Citation: Iamartino, D., Nicolazzi, E.L., Van Tassell, C.P., Reecy, J.M., Fritz-Waters, E.R., Koltes, J.E., Biffani, S., Sonstegard, T., Schroeder, S.G., Ajmone-Marsan, P., Negrini, R., Pasquariello, R., Ramelli, P., Coletta, A., Garcia, J.F., Ali, A., Ramunno, L., Cosenza, G., De Oliveira, D.A., Drummond, M.G., Bastianetto, E., Davassi, A., Pirani, A., Brew, F., Williams, J.L. 2017. Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLoS One. 12(10): e0185220. https://doi.org/10.1371/journal.pone.0185220.
DOI: https://doi.org/10.1371/journal.pone.0185220

Interpretive Summary: The water buffalo is a major source of food, draught power and fuel for the marginal farmers in many poor countries worldwide, and an important source of milk for specialized markets. The buffalo represents a key agricultural animal, able to adapt to diverse environments, bringing new products and markets for smallholder producers in low-income economies. Systems of buffalo production vary widely through the different regions of the world and are determined by several interacting factors including climate, cropping systems, the primary purpose of buffalo production and management. Genetic selection using traditional approaches has been successful in more advances production systems, but it is difficult in low-income economies where target traits are not recorded. This paper describes a molecular tool to facilitate genome-assisted selection for buffalo improvement and to support the conservation of genetic diversity of the buffalo worldwide.

Technical Abstract: The completion of the human genome sequence in 2001 was a major step forward in knowledge necessary to understand the variations between individuals. For farmed species, genomic information will facilitate the selection of animals optimised to live, and be productive in particular environments. The availability of the cattle genome sequence has improved various genomic analyses, from defining genetic diversity to aiding genetic selection. One of the most interesting aspects of this genomic revolution for the breeding industry is the possibility to predict a “direct genomic breeding value” (DGV) using genome-wide DNA markers. This approach is already applied to dairy and beef cattle selection. The creation of a panel of single nucleotide DNA markers as described here, will create the opportunity to use molecular selection approaches for water buffalo. The genomes of buffaloes of different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of millions of sequence variants in 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. This “SNP-Chip” was tested in buffalo population from Italy and found to have ~70% high quality and polymorphic SNPs. The 90K SNP chip was then used to investigate the structure of buffalo populations, and for a Genome Wide Association Study to identify genomic regions putatively involved in milk production.