Cacao Genome Database

The release of the cacao genome sequence will provide researchers with access to the latest genomic tools, enabling more efficient research and accelerating the breeding process, thereby expediting the release of superior cacao cultivars. The sequenced genotype, Matina 1-6, is representative of the genetic background most commonly found in the cacao producing countries, enabling results to be applied immediately and broadly to current commercial cultivars.  Matina 1-6 is highly homozygous which greatly reduces the complexity of the sequence assembly process. While the sequence provided is a preliminary release, it already covers 92% of the genome, with approximately 35,000 genes. We will continue to refine the assembly and annotation, working toward a complete finished sequence.

Genomics and Genetics

ARS Microbial Genomic Sequence Database Server

This database server is supported in fulfilment of the research mission of the Mycotoxin Prevention and Applied Microbiology Research Unit at the National Center for Agricultural Utilization Research in Peoria, Illinois. The linked website provides access to gene sequence databases for various groups of microorganisms, such as Streptomyces species or Aspergillus species and their relatives, that are the product of ARS research programs. The sequence databases are organized in the BIGSdb (Bacterial Isolate Genomic Sequence Database) software package developed by Keith Jolley and Martin Maiden at Oxford University.

Genomics and Genetics

TreeGenes

The TreeGenes database provides custom informatics tools to manage the flood of information resulting from high-throughput genomics projects in forest trees from sample collection to downstream analysis. This resource is enhanced with systems that are well connected with federated databases, automated data flows, machine learning analysis, standardized annotations and quality control processes. The database itself contains several curated modules that support the storage of data and provide the foundation for web-based searches and visualization tools.

Ag Data Commons

Plant Expression Database

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

Genomics and Genetics

Cool Season Food Legume Crop Database Resources

Genomic, Genetic and Breeding Resources for Pea, Lentil, Chickpea and Faba Bean Crop Improvement. The database contains genes, genomes, germplasm, maps, markers, QTL/MTL, species information, and transcripts.

Ag Data Commons

Gramene

Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.

Ag Data Commons

AgAR (Agricultural Antibiotic Resistance)

An Environmental Component of a "One Health" approach, the mission of the Agricultural Antibiotic Resistance (AgAR) project is to

  • develop practical tools and protocols to measure antibiotic drugs, resistant bacteria and resistance genes in agriculturally-impacted soil, water, air, and food;
  • design and evaluate agricultural
Agroecosystems & Environment

Data from: Color Analysis of Sweetpotato Leaves from the USDA, ARS Germplasm Collection

For this study, 737 sweetpotato accessions were obtained from the USDA, ARS, PGRCU, Griffin, GA. Each PI was grown in the field in replicated plots at the U. S. Vegetable Laboratory, Charleston, SC. The mature leaves of each PI was collected and measured using a Konica Minolta Chroma Meter (CR 400). Data were recorded using CIE 1976 L*a*b* and CIE L*C*h* color spaces. Data from this study is contained in a manuscript that will be submitted to Genetic Resources and Crop Evolution under the title "Color Analysis of Sweetpotato Leaves from the USDA, ARS Germplasm Collection." Data parameters collected were lightness (L*), red-green coordinate (a*), yellow-blue coordinate (b*), color intensity or chroma (C*), and hue angle (h*).

Plants and Crops

Ricebase

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data.

Genomics and Genetics

Musa Germplasm Information System

The Musa Germplasm Information System (MGIS) contains key information on Musa germplasm diversity, including passport data, botanical classification, morpho-taxonomic descriptors, molecular studies, plant photographs and GIS information on 4616 accessions managed in 21 collections around the world, making it the most extensive source of information on banana genetic resources.

MGIS