GrainGenes


35616118	GrainGenes: a data-rich repository for small grains genetics and genomics. [PMID: 35616118] Eric Yao, Victoria C Blake, Laurel Cooper, Charlene P Wight, Steve Michel, H Busra Cagirici, Gerard R Lazo, Clay L Birkett, David J Waring, Jean-Luc Jannink, Ian Holmes, Amanda J Waters, David P Eickholt, Taner Z Sen 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. Database (Oxford). 2022:2022() \| 28 Citations (from Europe PMC, 2025-03-22)
31210272	GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. [PMID: 31210272] Victoria C Blake, Margaret R Woodhouse, Gerard R Lazo, Sarah G Odell, Charlene P Wight, Nicholas A Tinker, Yi Wang, Yong Q Gu, Clay L Birkett, Jean-Luc Jannink, Dave E Matthews, David L Hane, Steve L Michel, Eric Yao, Taner Z Sen 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. Database (Oxford). 2019:2019() \| 43 Citations (from Europe PMC, 2025-03-22)

GrainGenes: a data-rich repository for small grains genetics and genomics. [PMID: 35616118]

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

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.

Database (Oxford). 2022:2022() | 28 Citations (from Europe PMC, 2025-03-22)

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. [PMID: 31210272]

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

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.

Database (Oxford). 2019:2019() | 43 Citations (from Europe PMC, 2025-03-22)

URL:	https://wheat.pw.usda.gov
Full name:	GrainGenes
Description:	tGrainGenes is a centralized database for curated, peer-reviewed datasets useful for research on wheat, barley, rye and oat and contain molecular and phenotypic information. This database manages genomic, genetic, germplasm and phenotypic datasets. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes.
Year founded:	2019
Last update:
Version:
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Plant
Database category:	Genotype phenotype and variation
Major species:	Triticum aestivum Hordeum vulgare Avena sativa Secale cereale
Keywords:	small grain triticeae and avena

University/Institution:	Western Regional Research Center
Address:	USDA ARS WRRC, 800 Buchanan Street, Albany, CA 94710-1105
City:
Province/State:
Country/Region:	United States
Contact name (PI/Team):	Taner Sen
Contact email (PI/Helpdesk):	taner.sen@usda.gov

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Database Commons a catalog of worldwide biological databases