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

dc.contributor.author Iamartino, Daniela
dc.contributor.author Nicolazzi, Ezequiel
dc.contributor.author Reecy, James
dc.contributor.author Van Tassell, Curtis
dc.contributor.author Reecy, James
dc.contributor.author Fritz-Waters, Eric
dc.contributor.author Koltes, James
dc.contributor.author Biffani, Stefano
dc.contributor.author Sonstegard, Tad
dc.contributor.author Schroeder, Steven
dc.contributor.author Ajmone-Marsan, Paolo
dc.contributor.author Negrini, Riccardo
dc.contributor.author Pasquariello, Rolando
dc.contributor.author Ramell, Paola
dc.contributor.author Coletta, Angelo
dc.contributor.author Garcia, Jose
dc.contributor.author Ali, Ahmad
dc.contributor.author Ramunno, Luigi
dc.contributor.author Cosenza, Gianfranco
dc.contributor.author de Oliveira, Denise
dc.contributor.author Drummond, Marcela
dc.contributor.author Bastianetto, Eduardo
dc.contributor.author Davassi, Alessandro
dc.contributor.author Pirani, Ali
dc.contributor.author Brew, Fiona
dc.contributor.author Williams, John
dc.contributor.department Animal Science
dc.date 2019-04-22T07:50:19.000
dc.date.accessioned 2020-06-29T23:40:43Z
dc.date.available 2020-06-29T23:40:43Z
dc.date.issued 2017-10-05
dc.description.abstract <p>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.</p> <p>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.</p> <p>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.</p> <p>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.</p>
dc.description.comments <p>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 (<em>Bubalus bubalis</em>). PLoS ONE 12(10): e0185220. doi: <a href="https://doi.org/10.1371/journal.pone.0185220">10.1371/journal.pone.0185220</a>.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/ans_pubs/424/
dc.identifier.articleid 1430
dc.identifier.contextkey 14061620
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath ans_pubs/424
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/9851
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/ans_pubs/424/2017_Reecy_DesignValidation.pdf|||Sat Jan 15 00:13:38 UTC 2022
dc.source.uri 10.1371/journal.pone.0185220
dc.subject.disciplines Agriculture
dc.subject.disciplines Animal Sciences
dc.subject.disciplines Genetics and Genomics
dc.subject.disciplines Molecular Genetics
dc.title Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication fb994cd9-94d5-4370-94ab-f33934c4cd6f
relation.isOrgUnitOfPublication 85ecce08-311a-441b-9c4d-ee2a3569506f
File
Original bundle
Now showing 1 - 1 of 1
Name:
2017_Reecy_DesignValidation.pdf
Size:
3.41 MB
Format:
Adobe Portable Document Format
Description:
Collections