,This is a public resource highlighting efforts at ARS in developing genome information for the Citrus Carrizo Genome. Updates and progress are reported here.,,

,MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays. Genomic, genetic, sequence, germplasm, gene product, metabolic pathways, functional characterization, literature reference, diversity, and expression are among the datatypes stored at MaizeGDB. At the project's website are custom interfaces enabling researchers to browse data and to seek out specific information matching explicit search criteria. First released in 1991 with the name MaizeDB, the Maize Genetics and Genomics Database, now MaizeGDB (since 2003), is funded, developed, and hosted by the USDA-ARS located at Ames, Iowa.,,

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

,Our mission is to support application of low-input sustainable agriculture by: Providing, to the best of our ability, technical information about rhizobia, their preservation, and cultural and symbiotic characteristics; Acquiring and preserving the nitrogen-fixing bacterial symbionts of leguminous plants with the goal of maintaining widest possible genetic diversity; Maintaining quality control of new and existing germplasm by evaluation of microbiological purity and by examination of nodulation of the original trap host plant; Distributing cultures to the public and private sectors without charge for these services; Developing or adapting techniques in molecular biology for the determination of genetic diversity of rhizobia, to investigate interactions with their host plants and to identify novel characteristics; Acquiring, maintaining, evaluating quality, and distributing type strains for all the different taxa of nitrogen-fixing legume symbionts; Participating in the UNESCO program.,

,This is an Aegilops tauschii genome database containing genetic and physical maps, genetic markers and genomic sequences and up-to-date releases on Ae. tauschii genome mapping.,,

,GrainGenes is an international, centralized crop database for peer-reviewed small grains data and information portal that serves the small grains research and breeding communities (wheat, barley, oat, and rye). The GrainGenes project ensures long-term data curation, accessibility, and sustainability so that small grains researchers can develop new, more nutritious, disease and pest resistant, high yielding cultivars. As a digital platform, GrainGenes houses peer-reviewed and curated genetic, genomic, and protein data. It has been hard-funded by the U.S. Department of Agriculture-Agricultural Research Service to ensure long-term data sustainability through a functional and integrated web interface for wheat, barley, oat, and rye.,,

,SoyBase is a repository for genetics, genomics and related data resources for soybean. It contains current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits.,SoyBase database was established in the 1990s as the USDA Soybean Genetics Database. Originally, it contained only genetic information about soybeans such as genetic maps and information about the Mendelian genetics of soybean. In time SoyBase was expanded to include molecular data regarding soybean genes and sequences as they became available. In 2010, the soybean genome sequence was published and it and supporting gene sequences have been integrated into the SoyBase sequence browser. SoyBase genetic maps were used in the assembly of both the Williams 82 2010 assembly (Wm82.a1.v1) and the newest genome assembly (Wm82.a2.v1).,SoyBase also incorporates information about mutant and other soybean genetic stocks and serves as a contact point for ordering strains from those populations. As association analyses continue due to various re-sequencing efforts SoyBase will also incorporate those data into the soybean genome browser as they become available. Gene expression patterns are also available at SoyBase through the SoyBase expression pages and the Soybean Gene Atlas. Other expression/transcriptome/methylomic data sets also have been and continue to be incorporated into the SoyBase genome browser.,Project No:3625-21000-062-00D Accession No: 0425040,

,Sweetpotato (Ipomoea batatas) plays a critical role in food security and is the most important root crop worldwide following potatoes and cassava. In the United States (US), it is valued at over $700 million USD. There are two sweetpotato germplasm collections (Plant Genetic Resources Conservation Unit and US Vegetable Laboratory) maintained by the USDA, ARS for sweetpotato crop improvement. To date, no genome-wide assessment of genetic diversity within these collections has been reported in the published literature. In our study, population structure and genetic diversity of 417 USDA sweetpotato accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species. Population structure using Bayesian clustering analyses (STRUCTURE) with 32,784 segregating SNPs grouped the accessions into four genetic groups and indicated a high degree of mixed ancestry. A neighbor-joining cladogram and principal components analysis based on a pairwise genetic distance matrix of the accessions supported the population structure analysis. Pairwise FST values between broad geographical regions based on the origin of accessions ranged from 0.017 (Far East – Pacific Islands) to 0.110 (Australia – South America) and supported the clustering of accessions based on genetic distance. The markers developed for use with this collection of accessions provide an important genomic resource for the sweetpotato community, and contribute to our understanding of the genetic diversity present within the US sweetpotato collection and the species.,,

,United States agricultural researchers have many options for making their data available online. This dataset aggregates the primary sources of ag-related data and determines where researchers are likely to deposit their agricultural data. These data serve as both a current landscape analysis and also as a baseline for future studies of ag research data.,As sources of agricultural data become more numerous and disparate, and collaboration and open data become more expected if not required, this research provides a landscape inventory of online sources of open agricultural data.,An inventory of current agricultural data sharing options will help assess how the Ag Data Commons, a platform for USDA-funded data cataloging and publication, can best support data-intensive and multi-disciplinary research. It will also help agricultural librarians assist their researchers in data management and publication. The goals of this study were to,The National Agricultural Library team focused on Agricultural Research Service (ARS), Natural Resources Conservation Service (NRCS), and United States Forest Service (USFS) style research data, rather than ag economics, statistics, and social sciences data. To find domain-specific, general, institutional, and federal agency repositories and databases that are open to US research submissions and have some amount of ag data, resources including re3data, libguides, and ARS lists were analysed. Primarily environmental or public health databases were not included, but places where ag grantees would publish data were considered.,We first compiled a list of known domain specific USDA / ARS datasets / databases that are represented in the Ag Data Commons, including ARS Image Gallery, ARS Nutrition Databases (sub-components), SoyBase, PeanutBase, National Fungus Collection, i5K Workspace @ NAL, and GRIN. We then searched using search engines such as Bing and Google for non-USDA / federal ag databases, using Boolean variations of “agricultural data” /“ag data” / “scientific data” + NOT + USDA (to filter out the federal / USDA results). Most of these results were domain specific, though some contained a mix of data subjects.,We then used search engines such as Bing and Google to find top agricultural university repositories using variations of “agriculture”, “ag data” and “university” to find schools with agriculture programs. Using that list of universities, we searched each university web site to see if their institution had a repository for their unique, independent research data if not apparent in the initial web browser search. We found both ag specific university repositories and general university repositories that housed a portion of agricultural data. Ag specific university repositories are included in the list of domain-specific repositories. Results included Columbia University – International Research Institute for Climate and Society, UC Davis – Cover Crops Database, etc. If a general university repository existed, we determined whether that repository could filter to include only data results after our chosen ag search terms were applied. General university databases that contain ag data included Colorado State University Digital Collections, University of Michigan ICPSR (Inter-university Consortium for Political and Social Research), and University of Minnesota DRUM (Digital Repository of the University of Minnesota). We then split out NCBI (National Center for Biotechnology Information) repositories.,Next we searched the internet for open general data repositories using a variety of search engines, and repositories containing a mix of data, journals, books, and other types of records were tested to determine whether that repository could filter for data results after search terms were applied. General subject data repositories include Figshare, Open Science Framework, PANGEA, Protein Data Bank, and Zenodo.,Finally, we compared scholarly journal suggestions for data repositories against our