Dataset Information

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

ABSTRACT: 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.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.This 90K "SNP-Chip" 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.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.

SUBMITTER: Iamartino D

PROVIDER: S-EPMC5628821 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Iamartino Daniela D Nicolazzi Ezequiel L EL Van Tassell Curtis P CP Reecy James M JM Fritz-Waters Eric R ER Koltes James E JE Biffani Stefano S Sonstegard Tad S TS Schroeder Steven G SG Ajmone-Marsan Paolo P Negrini Riccardo R Pasquariello Rolando R Ramelli Paola P Coletta Angelo A Garcia José F JF Ali Ahmad A Ramunno Luigi L Cosenza Gianfranco G de Oliveira Denise A A DAA Drummond Marcela G MG Bastianetto Eduardo E Davassi Alessandro A Pirani Ali A Brew Fiona F Williams John L JL

PloS one 20171005 10

<h4>Background</h4>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 ...[more]

PMID: 28981529

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Project description:Toxoplasmosis and neosporosis are diseases with worldwide distribution that are associated with reproductive problems in livestock and responsible for economic losses. This review presents an overview of the current knowledge relative to these diseases in water buffalo (Bubalus bubalis). In general, buffalo are considered resistant to clinical toxoplasmosis because there are studies only reporting serological evidence of natural infection in these animals. Studies have described age, poor hygienic status of the farm, and presence of cats as risk factors for the development of Toxoplasma gondii infection in buffalo. It must be highlighted that buffalo meat, which does not receive adequate freezing treatment, could be a potential source for toxoplasmic human infection as well as the importance of raw buffalo milk in the transmission of toxoplasmosis to human beings. Neospora caninum is considered one of the major causes of abortion and responsible for huge economic losses in cattle. Vertical transmission is the main route to infect calves, and is responsible for maintaining the parasite within a herd. In buffalo, vertical transmission is also described; moreover, although there are indications that N. caninum may be associated with abortion in dairy buffalo, the reproductive importance of neosporosis is apparently lower in buffalo relative to cattle. Most studies have identified a higher time of exposition to N. caninum oocysts relative to age. The household system was also described as a risk factor for infection, possibly due to persistent contact between the home-raised buffalo and canids. The fetal immune competence of buffalo is similar to bovine, and buffalo fetus are highly susceptible to infection during the first trimester of pregnancy, indicating that N. caninum may be an abortigenic agent in buffaloes. Alternatively, it is interesting to note there is evidence that the inflammatory response in pregnant buffalo infected with N. caninum is mild enough to avoid abortion in most cases. It is proposed that the possible transmission of toxoplasmosis through unprocessed milk and buffalo meat may occur, which is important in terms of public health. Additionally, there is strong evidence to suggest that N. caninum may be associated with abortion in buffalo.

Dataset Information

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

Publications

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

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