Water buffalo genome characterization by the Illumina BovineHD BeadChip

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dc.contributor.authorBorquis, R. R. A. [UNESP]
dc.contributor.authorBaldi, F. [UNESP]
dc.contributor.authorCamargo, G. M. F. de [UNESP]
dc.contributor.authorCardoso, D. F. [UNESP]
dc.contributor.authorSantos, D. J. A. [UNESP]
dc.contributor.authorLugo, N. H. [UNESP]
dc.contributor.authorSargolzaei, M.
dc.contributor.authorSchenkel, F. S.
dc.contributor.authorAlbuquerque, L. G. [UNESP]
dc.contributor.authorTonhati, H. [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionUniv Guelph
dc.contributor.institutionUniversidade Federal de Viçosa (UFV)
dc.date.accessioned2015-03-18T15:56:26Z
dc.date.available2015-03-18T15:56:26Z
dc.date.issued2014-01-01
dc.description.abstractTo define the best strategies for genomic association studies and genomic selection, it is necessary to determine the extent of linkage disequilibrium (LD) and the genetic structure of the study population. The current study evaluated the transference of genomic information contained in the Illumina BovineHD BeadChip from cattle to buffaloes, and assessed the extent of the LD in buffaloes. Of the 688,593 bovine single nucleotide polymorphism (SNP) that were successfully genotyped from the 384 buffalo samples, only 16,580 markers were polymorphic, and had minor allele frequencies greater than 0.05. A total of 16,580 polymorphic SNPs were identified, which were uniformly distributed throughout the autosomes, because the density and mean distance between markers were similar for all autosomes. The average minor allele frequency for the 16,580 SNPs was 0.23. The overall mean LD for pairs of adjacent markers was 0.29 and 0.71, when measured as for r(2) and vertical bar D'vertical bar, respectively. The 16,580 polymorphic SNPs were matched to Bos taurus chromosome in the current bovine genome assembly (Btau 4.2), and could be utilized in association studies. In conclusion, the Illumina BovineHD BeadChip contains approximately 16,580 polymorphic markers for the water buffalo, which are broadly distributed across the genome. These data could be used in genomic association and genomic selection studies; however, it might be necessary to develop a panel with specific SNP markers for water buffaloes.en
dc.description.affiliationUniv Estadual Paulista, Fac Ciencias Agr & Vet, Jaboticabal, SP, Brazil
dc.description.affiliationUniv Guelph, Anim & Poultry Sci Dept, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1, Canada
dc.description.affiliationUniv Fed Vicosa, Inst Nacl Ciencia & Tecnol Ciencia Anim, Vicosa, MG, Brazil
dc.description.affiliationUnespUniv Estadual Paulista, Fac Ciencias Agr & Vet, Jaboticabal, SP, Brazil
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.format.extent4202-4215
dc.identifierhttp://dx.doi.org/10.4238/2014.June.9.6
dc.identifier.citationGenetics And Molecular Research. Ribeirao Preto: Funpec-editora, v. 13, n. 2, p. 4202-4215, 2014.
dc.identifier.doi10.4238/2014.June.9.6
dc.identifier.fileWOS000339876200006.pdf
dc.identifier.issn1676-5680
dc.identifier.lattes7445254960858159
dc.identifier.urihttp://hdl.handle.net/11449/117564
dc.identifier.wosWOS:000339876200006
dc.language.isoeng
dc.publisherFunpec-editora
dc.relation.ispartofGenetics And Molecular Research
dc.relation.ispartofsjr0,439
dc.rights.accessRightsAcesso aberto
dc.sourceWeb of Science
dc.subjectBuffaloen
dc.subjectGenetic markeren
dc.subjectLinkage disequilibriumen
dc.subjectIllumina BovineHD BeadChipen
dc.titleWater buffalo genome characterization by the Illumina BovineHD BeadChipen
dc.typeArtigo
dcterms.rightsHolderFunpec-editora
unesp.author.lattes7445254960858159
unesp.author.orcid0000-0002-2030-7590[9]
unesp.campusUniversidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabalpt

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