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. 2022 May 25:2022:baac034.
doi: 10.1093/database/baac034.

GrainGenes: a data-rich repository for small grains genetics and genomics

Eric Yao  1   2 , Victoria C Blake  1   3 , Laurel Cooper  4 , Charlene P Wight  5 , Steve Michel  1 , H Busra Cagirici  1 , Gerard R Lazo  1 , Clay L Birkett  6 , David J Waring  7 , Jean-Luc Jannink  6   7 , Ian Holmes  2 , Amanda J Waters  8 , David P Eickholt  8 , Taner Z Sen  1
Affiliations

GrainGenes: a data-rich repository for small grains genetics and genomics

Eric Yao et al. Database (Oxford). .

Abstract

As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository. Database URL:https://wheat.pw.usda.gov.

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Figures

Figure 1.
Figure 1.
The GrainGenes’ homepage (https://wheat.pw.usda.gov) shows a wide range of services and jump points available through an intuitive, graphic interface. The top menu buttons open up new links.
Figure 2.
Figure 2.
Genome Browsers page at GrainGenes. Note that the 10+ Wheat Genome Project and Barley PanGenome Project buttons open up multiple single-assembly browsers.
Figure 3.
Figure 3.
eQTL search result table in gene feature details.
Figure 4.
Figure 4.
The BLAST page allows users to enter a DNA sequence and select from our database collection.
See this image and copyright information in PMC

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