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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 #345805
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 - Recombinetics, Inc
item Schroeder, Steven - Steve
item AJMONE-MARSAN, PAOLO - Institute Of Zootechnics - Italy
item NEGRINI, RICCARDO - Collaborator
item PASQUARIELLO, ROLANDO - Collaborator
item RAMELLI, PAOLA - Collaborator
item COLETTA, ANGELO - Collaborator
item GARCIA, JOSE - Universidade Estadual Paulista (UNESP)
item ALI, AHMAD - Comsats Institute Of Information Technology
item RAMUNNO, LUIGI - Universita Di Napoli
item COSENZA, GIANFRANCO - Universita Di Napoli
item DE OLIVEIRA, DENISE - Universidade Federal De Minas Gerais
item DRUMMOND, MARCELA - Universidade Federal De Minas Gerais
item BASTIANETTO, EDUARDO - Universidade Federal De Minas Gerais
item DAVASSI, ALESSANDRO - Affymetrix, Inc
item PIRANI, ALI - Affymetrix, Inc
item BREW, FIONA - Affymetrix, Inc
item WILLIAMS, JOHN - Affymetrix, Inc

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: 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 aiding genetic selection by predicting a “direct genomic breeding value” (DGV) using DNA markers. This approach has been successfully applied to dairy and beef cattle selection. The creation of a panel of single nucleotide polymorphism (SNP) DNA markers is described here. The SNP markers will enable these selection approaches for water buffalo. The genomes of buffaloes of different breeds were sequenced and compared to the cattle genome. This comparison enabled the identification of millions of SNP markers in the buffalo genomes. Based on frequencies of SNP within and across buffalo breeds and their distribution across the genome, which was inferred from the bovine genome sequence, a total of 90,000 SNP 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 variable SNP. The SNP chip was then used to investigate the structure of buffalo populations and for a study to identify genomic regions associated with differences in milk production.

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.