OUP accepted manuscript

Victoria Blake ,Nicholas A Tinker ,David Matthews ,Sarah G Odell ,Jean‐Luc Jannink ,David L Hane ,Eric Yao,Margaret R Woodhouse ,Yong Gu ,Steve L Michel ,Gerard R Lazo ,Yi Wang,Clayton L Birkett ,Charlene P Wight ,Taner Z Sen

doi:10.1093/database/baz065

Abstract

GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.

Highlights

Since 1992, GrainGenes has served as an international centralized hub for peer-reviewed biological data for small grains researchers working on wheat, barley, rye and oat
Since wheat alone constitutes 20% of the calories and 20% of proteins consumed by humans [3], access to the wealth of data in crop databases like GrainGenes contributes to worldwide food security
Reflecting the global importance of small grains and crop diversity, the userbase of GrainGenes is distributed across six continents

Summary

Introduction

Since 1992, GrainGenes has served as an international centralized hub for peer-reviewed biological data for small grains researchers working on wheat, barley, rye and oat. These pages link to tools at GrainGenes and to other biological databases where users can learn more about their biological entities of interest (e.g. genes, markers, genomic regions). We describe the most recent additions to the curated data content and tools at GrainGenes that are available to our users.

Results

Conclusion