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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

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Design and validation of a 90K SNP genotyping assay for the Water Buffalo (Bubalus bubalis)

Author
item Iamartino, Daniela
item Nicolazzi, Ezequiel
item Van Tassell, Curtis - Curt
item Reecy, James
item Fritz-waters, Eric
item Koltes, James
item Biffani, Stefano
item Sonstegard, Tad
item Schroeder, Steven - Steve
item Ajmone-marsan, Paolo
item Negrini, Riccardo
item Pasquariello, Rolando
item Ramelli, Paola
item Coletta, Angelo
item Garcia, Jose
item Ali, Ahmad
item Ramunno, Luigi
item Cosenza, Gianfranco
item De Oliveira, Denise
item Drummond, Marcela
item Bastianetto, Eduardo
item Davassi, Alessandro
item Pirani, Ali
item Brew, Fiona
item Williams, John

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.S., 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., 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.

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.