Added Value Chain

• Arabidopsis Information Resource The Arabidopsis Information Resource (TAIR): genome database for Arabidopsis thaliana. Central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation.
• BarleyBase It is a USDA-funded public data repository for plant microarray data. BarleyBase is expanding to PLEXdb, the comprehensive Plant Expression Database.
• Cereal small RNAs Database (CSRDB) It is a bioinformatic resource for cereal crops consisting of large-scale datasets of maize and rice small RNA sequences generated by 454 Life Science sequencing.
• COPE - Context-Oriented Predictor for variant Effect It is a framework of Context-Oriented Predictor for variant Effect that can be applied to both protein-coding gene and transcription factor binding site.
• The IPK Crop EST Database It is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK.
• European Nucleotide Archive It is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data.
• Host-Pathogen Interaction Database It is a resource that helps annotate, predict and display host-pathogen interactions (HPI). These types of interactions underpin infectious diseases and are critical for developing novel intervention strategies
• International Rice Informatics Consortium It aims to provide access to well-organized information about rice and to facilitate communication and collaboration for the rice community, with germplasm diversity as a focal entry point.
• Genome size in Asteracea database It is is an exhaustive catalogue of genome size data for the family Asteraceae.
• GrainGenes It is a database for Triticeae and Avena mainly, with molecular and phenotypic information for wheat, barley, rye, and other related species, including oat.
• Gramene It is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. It hosts annotations for over 90 plant genomes, including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops and other plants of special or emerging interest.
• MetaCrop It is a manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. It contains information about seven major crop plants.
• New PLACE - A Database of Plant Cis-acting Regulatory DNA Elements A Database of Plant Cis-acting Regulatory DNA Elements.
• Plant DNA C-values Database The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains C-value data for more than 12,273 species.
• PlnTFDB The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have been completely sequenced and annotated.
• PathoPlant - Plant-patogen interactions It is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon certain stimuli like pathogen infection, elicitor treatment, or abiotic stress.
• PNRD - Plant Non-coding RNA Database It is a comprehensive, integrated web resource for ncRNA, allowing searching, browsing, predicting, visualizing and downloading.
• Plant Organelles Database 3 It provides images of various plant organelles that were visualized with fluorescent and nonfluorescent probes in various tissues of several plant species at different developmental stages. The functional analysis database is a collection of protocols for plant organelle research.
• Plant Resistance Genes database - PRGdb This is an open and updated space about Pathogen Receptor Genes (PRGs), in which all information available about these genes is stored, curated and discussed.
• Phytozome - Plant Genomics Portal It is the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere.
• POGs/PlantRBP - Putative Orthologous Groups (POGs) It is a relational database designed to facilitate cross-species inferences about gene functions and gene models in plants. The database integrates data from rice (Orza sativa), maize (Zea mays), Arabidopsis thaliana, and Poplar (Populus trichocarpa) by placing the complete predicted proteomes into "putative orthologous groups" (POGs).
• Tomato 150 Genome project It provides information about the genetic variation in the tomato clade that was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group.
• TropGeneDb - Tropical crops - genomic, genetic and phenotyping TropGeneDB is a database that manages genomic, genetic and phenotypic information about tropical crops. It is organised on a crop basis.
• UCSC Genome browser It is a large database of publicly available sequence and annotation data along with an integrated toolset for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data.
• JBrowse 2 JBrowse is a general-purpose genome annotation browser that runs on the web or as a standalone application. It allows users to share sessions, open multiple genomes, and navigate between views.
• Gene Expression Omnibus It is a database repository of high-throughput gene expression data and hybridization arrays, chips, and microarrays. Tools are provided to help users query and download experiments and curated gene expression profiles.
• Germinate It is an open source plant database infrastructure and application programming platform on which complex data from genetic resources collections can be stored, queried, and visualized using common, reusable, programming components.
• GRIN Germplasm Resources Information Network documents animal, microbial, and plant collections through informational pages, searchable databases, and links to USDA-ARS projects that curate the collections. Search form for plant collections.
• PLEXdb It is the succesor of BarleyBase and it provides a unified web interface to support the functional interpretation of highly parallel microarray experiments integrated with traditional structural genomics and phenotypic data.
• transPLANT It is is a European-Union funded e-infrastructure to support computational analysis of genomic data from crop and model plants.
• REPET It is a package of bioinformatics programs used to tackle biological issues at the genomic scale. It is distributed under the CeCILL license.
• Ephesis It is a web portal dedicated to phenotype and environment experimental trials. It allows the building of phenotyping datasets based on multiple trials, on several years and places.
• PGSB PlantsDB It is a database framework for the comparative analysis and visualization of plant genome data. It provides specialized tools and interfaces to address user demands for intuitive access to complex plant genome data.
• Rice SNP-Seek Database It provides Genotype, Phenotype, and Variety Information for rice (Oryza sativa L.).
• NARO Genebank Plant Search Japan It is the plant search form of the Genebank at the National Agricultural Research Organization (NARO) of Japan.
• PlantRegMap The Plant Transcriptional Regulatory Map provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them, advancing the understanding of plant transcriptional regulatory system.
• BGI Genomics Founded in 1999, BGI is one of the world's leading life science and genomics organizations.
• Database of Plant Diseases in Japan It is a database established based on Common names of plant diseases in Japan compiled by Phytopathological Society of Japan.
• Digital Sequence Information on Genetic Resources under the CBD This page summarizes what has been done on digital sequence information on genetic resources under the CBD process, including the work of the Ad Hoc Open-ended Working Group on Benefit-sharing from the Use of Digital Sequence Information on Genetic Resources
• Ensembl Plants It is an integrative resource presenting genome-scale information for 39 sequenced plant species.
• NCBI - Genome The National Center for Biotechnology Information of the United States of America advances science and health by providing access to biomedical and genomic information, including information about major crops and other plants.
• Plant GARDEN The Genome and Resource Database Entry is a portal site that curates genome and marker information of various plant species. The portal is supported by the Kazusa DNA Research Institute.
• Plant rDNA database 4 It provides information on numbers and positions of ribosomal DNA signals and their structures for 2770 plant species (4948 entries). The data have been obtained from 785 publications on plant molecular cytogenetics.
• The Biodiversity Digital Twin (BioDT) project BioDT brings together major DNA analysis research infrastructures and LUMI Supercomputer technology, to provide FAIR (Findable, Accessible, Interoperable, and Reusable) evidence-based simulations and use cases, on the interactions between species and their environment, including Crop Wild Relatives (CWR), to breed more climate resistant varieties to enhance food security. The Naturalis initiative connects BioDT with other European projects and policies, such as the EU Green Deal, Biodiversity Strategy 2030, and UN Sustainable Development Goals.
• RefSeq The Reference Sequence (RefSeq) collection offers a comprehensive and well-annotated set of genomic DNA, transcripts, and proteins that serves as a stable reference for various biological studies, including genome annotation and mutation analysis. Managed by NCBI, RefSeq encompasses a diverse range of organisms and is continually updated with new data, generated through a combination of computational methods and manual curation.
• Greenphyl GreenPhylDB is a web resource for comparative and functional plant genomics, now featuring version 5.1 with a catalog of gene families from 19 pangenomes and 27 reference genomes across 46 species. Each cluster is functionally annotated and analyzed phylogenetically, with users able to suggest names for gene families.
• Barley Bioresource Database (BarleyDB) The Barley Bioresource Database (BarleyDB), established in 1983 by the National BioResource Project (NBRP) under Dr. Ryuhei Takahashi at Okayama University, contains information on approximately 4,000 cultivars, including variety name, origin, history, and various traits. The database is continually updated with additional genetic traits and stocks, aiming to serve researchers and barley breeders globally.
• SorghumBase SorghumBase is a community portal that integrates genetic, genomic, and breeding resources to enhance sorghum germplasm improvement. Designed for plant breeders, agronomists, and researchers, it centralizes essential data in a user-friendly platform. The initial release includes five reference genome assemblies, genetic variant information, a search interface, links to other repositories, and a content management system for community news and training materials, facilitating collaboration and advancing genomics-assisted breeding.
• Sorghum Genome Science Database (SorGSD) SorGSD, now renamed Sorghum Genome Science Database (SorGSD), is a comprehensive resource for sorghum genomic variations (SNPs and INDELs) across 289 accessions, along with phenotypes and practical tools. The updated database includes new data aligned to the latest sorghum genome assembly (BTx623 v3.1), features such as ID Conversion and Homologue Search, and enhanced user interface and infrastructure for improved accessibility to sorghum research resources and literature.
• PotatoBase PotatoBase is a comprehensive database designed to support potato research by providing access to a wide range of genomic, genetic, and phenotypic data related to potato varieties. It integrates information from various studies, including genetic markers, trait associations, and functional annotations, facilitating data sharing and collaboration among researchers. The platform aims to enhance potato breeding and improvement efforts by making valuable data readily accessible to the scientific community.
• Potato Genomics Resource (Spud DB) Spud DB features potato genome browsers for the updated DM v6.1 pseudomolecules and other completed potato genomes, including RNA-Seq data from the SRA and SolCAP SNP information. The updated search tools offer a BLAST server for assembly and annotation searches, as well as functional annotations through InterPro, GO, and PFAM. Spud DB is maintained by the Buell Lab at the University of Georgia.
• The Unified Potato Genome Annotation Database (UniTato) UniTato is a web-based service that provides access to accurate potato gene models, integrating the latest potato double monoploid (DM) v4 and v6 models from Spud DB. It offers a user-friendly interface for browsing, searching, and downloading curated gene models, as well as editing and contributing annotations, supported by the JBrowse platform.
• Banana Genome Hub (BGH) The Banana Genome Hub (BGH) is a community-driven website that consolidates banana genomic data, developed by Cirad and the Alliance of Bioversity International and CIAT, with support from the South Green Bioinformatics platform. Built on Drupal and Tripal, it integrates various systems (Jbrowse, Galaxy, Gigwa) for plant genome analysis and is part of the South Green genome hubs under the Elixir France Service Delivery plan. BGH is registered in bio.tools and FAIRsharing to enhance interoperability.
• Rice Annotation Project (RAP) The Rice Annotation Project (RAP) was initiated in 2004 following the completion of the genome sequencing of Oryza sativa ssp. japonica cv. Nipponbare by the International Rice Genome Sequencing Project. Its primary goal is to provide the scientific community with precise and timely annotations of the rice genome sequence. A key objective of this project is to enable a thorough analysis of the genome's structure and function based on these annotations.
• Rice Genome Hub (RGH) The Rice Genome Hub (RGH) is a community website that integrates rice genomic data, developed by Cirad and IRD with support from the South Green Bioinformatics platform. Built on Drupal and Tripal, RGH facilitates the integration of various systems (Jbrowse, Galaxy, Gigwa) for plant genome analysis. It is part of the South Green genome hubs within the Elixir France Service Delivery plan and is registered in Elixir bio.tools to enhance interoperability.
• Rice Pan-genome Browser (RPAN) The Rice Pan-genome Browser analyzes 3,010 rice accessions, combining IRGSP reference sequences with de novo assembled contigs to create a comprehensive dataset. This analysis shows that rice species contain nearly double the genomic content of individual genomes, with 15,362 predicted genes. Variations in gene presence/absence were detected in 453 accessions, leading to a phylogenetic study that highlighted significant inter-group variations. Notably, genes absent from the reference genome play critical roles, including responses to freezing and cold acclimation.
• RiceXPro The Rice Expression Profile Database (RiceXPro) collects gene expression profiles from microarray analyses of rice tissues and organs throughout the plant's growth, including responses to phytohormones and specific cell types isolated by laser microdissection. This resource aims to characterize the expression profiles of all predicted rice genes and supports functional genomics, utilizing a unified microarray platform based on curated gene models from RAP-DB and full-length cDNA sequences from KOME.
• RiceVarMap RiceVarMap v2.0 is an extensive database that catalogs genomic variations in rice along with their functional annotations. It includes curated data on 17,397,026 variations (comprising 14,541,446 SNPs and 2,855,580 small INDELs) derived from sequencing 4,726 rice accessions. These variations were detected using GATK software based on the Os-Nipponbare-Reference-IRGSP-1.0 assembly. (Note: RiceVarMap v1.0 is still available for querying variations based on the older Nipponbare MSU v6.1 assembly.)
• YamBase YamBase is a comprehensive database designed for yam research, providing a platform for the storage and analysis of genomic and phenotypic data related to various yam species. It integrates data from sequencing projects, genomic annotations, and trait information to facilitate research and breeding programs. Users can search for specific traits, access genomic sequences, and explore genetic diversity among yam varieties, promoting advancements in yam cultivation and improvement.
• ForageGrassBase ForageGrassBase is a comprehensive database that provides access to genetic and phenotypic information about forage grass species. It supports researchers and breeders in the study and improvement of grass varieties for better agricultural productivity and sustainability.
• CerealsDB This website, created by the Functional Genomics Group at the University of Bristol, provides information on Single Nucleotide Polymorphism (SNP) in bread wheat (Triticum aestivum) and its relatives. The data, including flanking sequences, is available as a searchable online database, encouraging collaboration among wheat geneticists.
• CicerSeq CicerSeq is a public repository that offers a comprehensive map of genomic variation based on the sequencing of 3,366 Cicer genomes. This includes 3,171 accessions of cultivated species and 195 accessions from seven wild species. Users can access information on genotype, passport data, and various variants (compared to the CDC Frontier genome), including SNPs and different structural variations (SVs), as detailed in the article “A global reference for chickpea genetic variation based on sequencing of 3,366 genomes.” This database supports genomics-informed decision-making in chickpea improvement.
• BarleyExpDB: The Barley Expression Database BarleyExpDB is an integrated RNA-seq database that provides easy access to gene expression data from barley RNA-seq libraries, featuring intuitive visual displays and functional annotations from sources like GO, KEGG, PFAM, and SMART. It includes data from 56 transcriptome studies with 3,492 samples across various developmental stages, stresses, and mutant populations, along with tools for search, BLAST, and downloads, aiming to enhance accessibility for the barley research community.

• Integrated breeding platform It is a not-for-profit entity whose mission is to help accelerate the delivery of new climate-resilient crop varieties, especially in developing countries.
• Genetic resources and breeding in Europe Through this site the European Commission offers information about policy, funding opportunities, jobs, projects, publications and databases.
• Breeding Costing Tool It is now available for download. It is a stand-alone software developed by the sorghum team at the Queensland Alliance for Agriculture and Food Innovation at the University of Queensland. It allows researchers to estimate the cost of running a crop breeding activity, or an entire breeding pipeline, using the prices, costs and salaries from a single year. The software is provided with training materials and related videos.
• Breeding Management System It is a data management software specifically designed to meet the needs of modern plant breeders.
• Breedbase It is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high density genotypic information, and provide Genomic Selection related analyses and predictions.
• LettuceKnow It is structured as one integrated research program with synergistic exchange and collaboration between university groups and company researchers.
• Brassicaceae Database It is a community portal that provides services for 41 genomes or genome versions from 26 species.
• MusaBase MusaBase is a comprehensive breeding database designed to manage data and support next-generation breeding protocols for banana species, which are vital food sources in Africa. It integrates high-density marker data, enabling researchers and breeders to optimize breeding strategies, track genetic diversity, and enhance the development of improved banana varieties. MusaBase serves as a valuable resource for the banana research community, facilitating data sharing and collaboration to address challenges in banana cultivation and food security.

• Easy-SMTA It is the Information Technology System developed in support of the users of the Multilateral System of Access and Benefit-sharing of the International Treaty on Plant Genetic Resources for Food and Agriculture. Transfer material using a Standard Material Transfer Agreement.
• Toolbox for Sustainable use of PGRFA The Toolbox is for people seeking information or guidance on policies, strategies and activities that can promote and enhance the sustainable use of PGRFA, particularly at national and local levels.
• CAPFITOGEN tools Tools developed as part of the CAPFITOGEN program are focused on the development of appropriate technologies for countries which are extremely agrobiodiverse but have limited economic resources. Its function is to develop and transfer technology and provide the appropriate training for technical personnel from those Latin American countries signatories to the International Treaty.
• Global Information and Early Warning System on Food and Agriculture (GIEWS) It monitors the condition of major foodcrops across the globe to assess production prospects. To support the analysis and supplement ground-based information, GIEWS utilizes remote sensing data that can provide a valuable insight on water availability and vegetation health during the cropping seasons. In addition to rainfall estimates and the Normalized Difference Vegetation Index (NDVI), GIEWS and FAO's OCB Division have developed the Agricultural Stress Index (ASI), a quick-look indicator for the early identification of agricultural areas probably affected by dry spells, or drought in extreme cases.
• UNCCD Drought Toolbox It is a knowledge hub providing drought stakeholders with easy access to resources to support action on drought preparedness with the aim to boost the resilience of people and ecosystems. it provides information and tools for the monitoring and early warning, vulnerability and risk assessment and risk mitigation measures.
• Pluto Plant Variety Database The PLUTO database of Svalbard plant varieties offers information about the protected plant varieties. Hence, it also provides information on those that were protected and that at a certain point become available.
• European Information System on Forest Genetic Resources EUFGIS provides geo-referenced information on the conservation of forest genetic resources in Europe and access to detailed data on dynamic gene conservation units of forest trees in different countries. The data is provided and frequently updated by national focal points based on pan-European minimum requirements and data standards for the units. EUFGIS serves as a documentation platform linking national inventories on forest genetic resources in Europe. This supports the countries in their efforts to conserve forest genetic resources as part of sustainable forest management, as agreed in the context of Forest Europe, the pan-European forest policy process.
• DivSeek International Network It is a global community driven Not-for-Profit organization that aims to facilitate the generation, integration, and sharing of data and information related to plant genetic resources.
• InforMEA InforMEA is the United Nations Information Portal on Multilateral Environmental Agreements. It is a one-stop portal for information on Multilateral Environmental Agreements – or MEAs - searchable by key terms across treaty texts, COP decisions, national plans and reports, laws, court decisions and more.
• DART Project It provides private and secure national working spaces for Parties to effectively use synergies in the field of knowledge and information management for national reporting to biodiversity-related conventions.
• Biodiversity Indicators Partnership It is a global initiative to promote and coordinate the development and delivery of biodiversity indicators for use by the Convention on Biological Diversity (CBD) and other biodiversity-related conventions.
• GODAN The Global Open Data for Agriculture and Nutrition is an initiative that seeks to "support global efforts to make agricultural and nutritionally relevant data available, accessible, and usable for unrestricted use worldwide".
• CGIAR BIG Data Platform Its goal is to harness the capabilities of big data to accelerate and enhance the impact of international agricultural research.
• Diversity Assessment Tool for Agrobiodiversity and Resilience (DATAR) The Diversity Assessment Tool for Agrobiodiversity and Resilience (DATAR) is a new open-source pilot software platform with a web interface, the DATAR Web Portal, and an Android App that will allow the integration of diverse crop varieties, livestock breeds, and aquatic farmed-types into decision-making plans. The tool has been designed to enable country teams to collaborate and jointly assess biodiversity information from multiple angles.
• OECD Variety List Query It is the official list of varieties that have been accepted as being eligible for certification by the National Designated Authorities of countries participating in the OECD Seed Schemes.
• International Center for Biosaline Agriculture (ICBA) ICBA is a not-for-profit international agricultural research center focused on ensuring sustainable livelihoods and food security in marginal environments. We leverage research and innovation to address challenges and develop resource-efficient, climate-smart crops and technologies suitable for areas affected by salinity, water scarcity, and drought. Our work improves food security, nutrition, and job creation for impoverished rural communities. We also assist policymakers in enhancing natural resource management and adapting to climate change.