Comprehensive Overview of Agricultural Genomic Databases

In agricultural research, a plethora of databases provides vital information on various plant species, facilitating research and development efforts. Below, we present an overview of key plant-related databases, followed by a detailed classification of databases specific to different species.

Part 1: General Plant Research Databases

This section highlights essential databases that cover a broad spectrum of plant species, offering critical genomic resources that help researchers advance their understanding of plant biology, genetics, and agricultural applications.

These databases include comprehensive collections of plant genomic, proteomic, and interaction data. For instance, resources such as EnsemblPlants and JGI Phytozome provide access to plant genome sequences and annotations, while InterPro and PRGdb focus on protein families and resistance genes, respectively. Other databases like PlantPromoterDB specialize in regulatory elements and plant-pathogen interactions, supporting a wide range of research from basic plant biology to applied breeding efforts.

1. AgBioData
AgBioData is an alliance of professionals dedicated to addressing common challenges in agricultural biological databases and creating more accessible and discoverable resources.
Website: https://www.agbiodata.org/

2. EnsemblPlants
EnsemblPlants integrates genomic data across multiple plant species, providing comprehensive access to sequences, genes, and annotations.
Website: http://plants.ensembl.org/

3. GRIN (Germplasm Resources Information Network)
GRIN provides plant taxonomic information alongside genetic resources and genomic data.
Website: https://www.ars-grin.gov/

4. InterPro (Integrated Resource of Protein Families, Domains, and Sites)
InterPro offers a platform for annotating and classifying plant protein sequences through integrated protein classification databases.
Website: https://www.ebi.ac.uk/interpro/

5. JGI Phytozome
Phytozome serves as a comprehensive repository of plant genomic data, promoting accurate comparative genomics through integrated annotations.
Website: https://phytozome-next.jgi.doe.gov/

6. NGS Databases & sRNA Tools
This database offers RNA and genomic data resources from next-generation sequencing (NGS) focused on plant research.
Website: http://tools4mirs.org/ngs-database/

7. PlantPromoterDB 3.0
PPDB provides essential information about plant promoter sequences and transcriptional regulatory elements.
Website: http://ppdb.agrinome.org/

8. PRGdb 4.0
PRGdb is a database dedicated to plant resistance genes, offering insights into plant-pathogen interactions.
Website: https://prgdb.org/

9. Pulse Crop Database (PCD)
PCD is designed to assist genomics-assisted breeding in pulse crops, providing tools for identifying trait-related genes.
Website: http://www.pulsedb.org/

10. Plant Genome Editing Database (PGED)
PGED provides CRISPR/Cas9-related information for plants, allowing users to explore gene mutations and transformation experiments.
Website: http://plantcrispr.org/cgi-bin/crispr/index.cgi

11. TRY
The TRY database focuses on plant traits, providing critical data for understanding biodiversity and ecosystem changes.
Website: https://www.try-db.org/

Part 2: Species-Specific Databases

This section details databases focused on specific plant species, offering tailored resources for research and development. These databases cater to the unique genetic, genomic, and phenotypic traits of various crops, facilitating advancements in breeding programs and agricultural practices.

Key species represented include rice, wheat, cotton, soybean, Brassica (which includes crops like canola and cabbage), Solanaceae (including tomatoes and potatoes), cacao, citrus fruits, Arabidopsis thaliana, and members of the Rosaceae family, such as apples and strawberries. Each database provides specialized resources that enhance our understanding of these important crops, supporting efforts to improve yield, disease resistance, and nutritional quality.

Rice (Oryza sativa)

Rice is a staple food for over half of the global population, playing an indispensable role in global food security. The Rice Genome Database (RAP) offers comprehensive genomic annotations, serving as a pivotal resource for researchers aiming to enhance rice varieties with improved yield, disease resistance, and adaptability to climate change.

• Rice Genome Database (RAP)
  RAP provides a detailed annotation of the rice genome, enhancing data accessibility for researchers.
  Website: https://rapdb.dna.affrc.go.jp/

Wheat (Triticum aestivum)

Wheat stands as one of the most extensively cultivated crops worldwide, essential for delivering vital energy and nutrition. The Wheat Genome Database (IWGSC) is instrumental in propelling wheat genomics forward, accelerating genome sequencing to improve crop resilience and quality.

• Wheat Genome Database (IWGSC)
  The IWGSC offers crucial genomic data, bolstering breeding and research initiatives.
  Website: https://wheatgenome.org/
• Wheat Proteome Database
  This database is dedicated to proteomic studies across diverse wheat tissues, supplying analytical tools and insights into wheat biology.
  Website: http://wheatproteome.org

Cotton (Gossypium spp.)

Cotton is a prominent cash crop, yielding fibers for textiles and oils from its seeds. The Cotton Functional Genomics Database (CottonFGD) amalgamates genomic and transcriptomic data, supporting research into enhanced fiber quality and pest resistance.

• Cotton Functional Genomics Database (CottonFGD)
  CottonFGD aggregates data to facilitate advanced cotton research and breeding efforts.
  Website: https://www.cottongen.org/

Soybean (Glycine max)

Soybean serves as a critical source of protein and oil, broadly employed in food products and animal feed. The Soybean Genome and Genetic Database (SoyBase) provides a comprehensive collection of genomic information, aiding researchers in augmenting nutritional content and yield.

• Soybean Genome and Genetic Database (SoyBase)
  SoyBase offers valuable genomic sequences and annotations vital for soybean research and breeding advances.
  Website: https://soybase.org/

Brassica (Brassica spp.)

Brassica species, including canola and cabbage, are noted for their nutritional value and economic significance. The Brassica Multi-Omics Database (BnIR) synthesizes various omics data to augment research and breeding aimed at improved yield and disease resistance.

• Brassica Multi-Omics Database (BnIR)
  BnIR fosters research and breeding efforts by providing integrated omics data for Brassica species.
  Website: https://yanglab.hzau.edu.cn/BnIR/
• Brassicaceae Database (BRAD)
  BRAD supplies extensive resources, including gene annotations and analytical tools, to support breeding programs for Brassica species.
  Website: http://brassicadb.cn/

Solanaceae (Solanum spp.)

The Solanaceae family encompasses crucial crops like tomatoes and potatoes, essential for global food security. The Sol Genomics Network (SGN) functions as a comprehensive repository for genomic data, enhancing research aimed at improving flavor, nutritional quality, and pest resistance.

• Sol Genomics Network (SGN)
  SGN provides critical tools for genetic research and breeding efforts in Solanaceae species.
  Website: https://solgenomics.net/
• Tomato Gene Prioritization Platform (TomatoNet)
  TomatoNet facilitates the genetic analysis of complex traits in tomatoes, associating genes with functional roles to improve breeding outcomes.
  Website: https://www.inetbio.org/tomatonet/

Cacao (Theobroma cacao)

Cacao is the chief source of cocoa, vital for chocolate production and global economies. The Cacao Genome Database aids breeding endeavors focused on enhancing yield, flavor, and disease resistance, promoting sustainable farming practices.

• Cacao Genome Database
  This database offers access to cocoa genome sequences, facilitating research and breeding for superior cocoa varieties.
  Website: https://cocoa-genome-hub.southgreen.fr/

Citrus (Citrus spp.)

Citrus fruits are globally cherished for their flavor and nutritional benefits. The Citrus Genome Database supports research aimed at improving disease resistance, fruit quality, and yield, which are vital for the citrus industry.

• Citrus Genome Database
  This database underpins fundamental and applied research in citrus genomics, providing essential data for breeding initiatives.
  Website: https://www.citrusgenomedb.org/

Arabidopsis (Arabidopsis thaliana)

Arabidopsis thaliana is a prominently used model organism in plant biology research, renowned for its simple genome and rapid life cycle. AraNet integrates diverse omics data to construct a functional gene network, fostering the discovery of gene functions vital for crop advancement.

• AraNet
  This platform enables the exploration of gene functions and supports ongoing research in Arabidopsis.
  Website: https://www.inetbio.org/aranet/

Rosaceae

The Rosaceae family includes economically important crops such as apples and strawberries. The RosBREED Initiative focuses on advancing these cultivars through modern DNA techniques, enhancing traits like disease resistance and horticultural quality.

• RosBREED
  The RosBREED Initiative employs modern DNA sequencing and breeding techniques to elevate the development of new rosaceous cultivars.
  Website: https://www.rosbreed.org/

Conclusion

This article provides a comprehensive overview of agricultural genomic databases, highlighting their essential role in advancing research and development across various plant species. Part 1 presents general plant research databases, such as AgBioData and EnsemblPlants, which facilitate access to vital genomic information and resources. In Part 2, species-specific databases are detailed, showcasing platforms like the Rice Genome Database and the Wheat Genome Database, each tailored to enhance breeding and genetic studies for key crops. By consolidating these valuable resources, the article emphasizes the significance of genomic data in improving agricultural practices, crop yield, and resilience against environmental challenges, ultimately contributing to global food security.

Reference

1. Yang, Z., Wang, S., et al. 2023. BnIR: A multi-omics database with various tools for Brassica napus research and breeding. Molecular Plant, 16(4), pp.775-789.