title: Water buffalo genome characterization by the Illumina BovineHD BeadChip.
abstract: To 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 r2 and |D'|, 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.
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: R R A
authors.initials: RR
authors.lastname: Borquis
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: F
authors.initials: F
authors.lastname: Baldi
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: G M F
authors.initials: GM
authors.lastname: de Camargo
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: D F
authors.initials: DF
authors.lastname: Cardoso
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: D J A
authors.initials: DJ
authors.lastname: Santos
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: N H
authors.initials: NH
authors.lastname: Lugo
authors.affiliation: Centre for Genetic Improvement of Livestock, Animal and Poultry Science Department, University of Guelph, Guelph, Ontario, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Sargolzaei
authors.affiliation: Centre for Genetic Improvement of Livestock, Animal and Poultry Science Department, University of Guelph, Guelph, Ontario, Canada.
authors.forename: F S
authors.initials: FS
authors.lastname: Schenkel
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil.
authors.forename: L G
authors.initials: LG
authors.lastname: Albuquerque
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil tonhati@fcav.unesp.br.
authors.forename: H
authors.initials: H
authors.lastname: Tonhati
mesh_terms: D000818:Animals; D002020:Buffaloes / Q000235:genetics*; D002417:Cattle; D033481:Chromosomes, Mammalian; D005787:Gene Frequency; D056726:Genetic Association Studies; D016678:Genome; D023281:Genomics / Q000379:methods*; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide