ArticleBMC genomics2015
WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed, 124 citations in OpenAlex.
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- Major differences in the dynamics of haematological and biochemical variables between trypanotolerant and susceptible cattle during Trypanosoma congolense infection.BMC veterinary research · 2025Article
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- Uncovering the architecture of production-driven introgression in Cinisara cattle breed.BMC genomic data · 2025Article
- Genome-wide insights into selection signatures for transcription factor binding sites in cattle ROH regions.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- DCMS analysis revealed differential selection signatures in the transboundary Sahiwal cattle for major economic traits.Scientific reports · 2025Article
- Genomic diversity of Cameroonian Gudali and Gudali-cross cattle.Scientific reports · 2025Article
- Uncovering genomic diversity and signatures of selection in red Angus × Chinese red steppe crossbred cattle population.Scientific reports · 2025Article
- Genomic diversity and population structure analysis of four geographically distinct Holstein cattle populations using genome-wide DNA profiling.Archives animal breeding · 2025Article
- Comparative genomic insights into adaptation, selection signatures, and population dynamics in indigenous Indian sheep and foreign breeds.Frontiers in genetics · 2025Article
- Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations.Heredity · 2025Article
- Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe advent and democratization of next generation sequencing and genotyping technologies lead to a huge amount of data for the characterization of population genetic diversity in model and non model-species. However, efficient storage, management, cross-analyzing and exploration of such dense genotyping datasets remain challenging. This is particularly true for the bovine species where many SNP datasets have been generated in various cattle populations with different genotyping tools. DESCRIPTION: We developed WIDDE, a Web-Interfaced Next Generation Database that stands as a generic tool applicable to a wide range of species and marker types ( http://widde.toulouse.inra.fr). As a first illustration, we hereby describe its first version dedicated to cattle biodiversity, which includes a large and evolving cattle genotyping dataset for over 750,000 SNPs available on 129 (89 public) different cattle populations representative of the world-wide bovine genetic diversity and on 7 outgroup bovid species. This version proposes an optional marker and individual filtering step, an export of genotyping data in different popular formats, and an exploration of genetic diversity through a principal component analysis. Users can also explore their own genotyping data together with data from WIDDE, assign their samples to WIDDE populations based on distance assignment method and supervised clustering, and estimate their ancestry composition relative to the populations represented in the database.
conclusionThe cattle version of WIDDE represents to our knowledge the first database dedicated to cattle biodiversity and SNP genotyping data that will be very useful for researchers interested in this field. As a generic tool applicable to a wide range of marker types, WIDDE is overall intended to the genetic diversity exploration of any species and will be extended to other species shortly. The structure makes it easy to include additional output formats and new tools dedicated to genetic diversity exploration.
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