Location: Corn Insects and Crop Genetics Research
2023 Annual Report
Objectives
Objective 1: Provide stewardship of soybean and other major legume genetic, genomic, and phenotypic datasets, to support research and crop improvement. Enable efficient curation of the high volume of data from research communities. Structure and store the data to allow open, standardized data exchange mechanisms to enhance database interoperability and collaboration and facilitate research discoveries through integration and comparison.
Objective 2: Provide analysis and visualization tools to utilize the range of available legume data, integrating genotype and phenotype information to facilitate research and breeding work for legume crops. Provide resources and tools that enable exploration of diversity, variation, and phenotype data, in the context of genomic coordinates, and across evolutionary timespans.
Objective 3: Serve as an organizing center for legume breeding information by collecting and storing phenotypic values for germplasm in USDA and state uniform variety trials.
Objective 4: Support crop improvement by collecting and curating information about genes that underlie important agronomic, nutritional, and stress-response traits. Enable translation of genetic information among different crop species.
Objective 5: Provide community support and research coordination services for the research and breeding communities for soybean and other legumes, and expand outreach activities through workshops, web-based tutorials, and other communications.
Approach
Modern crop improvement methods make extensive use of genetic and genomic information - for example, using genetic markers for marker-assisted or genomic selection, or using predicted genes and diversity data to identify the genetic basis for important agronomic traits. The SoyBase and the Legume Information System project will collect and curate major genetic and genomic data sets for species in the legume family and prepare and store this data in structured formats to support this type of research and improvement in legume crops (Objective 1). The project will also develop and deploy analysis and visualization tools to provide useful access to the assembled genetic data. The data collected under Objective 1 will be stored to enable programmatic access for software systems maintained by the project, providing users of the soybase.org and legumeinfo.org resources to access and investigate the information in intuitive ways (Objective 2). The project will also collect, organize, and provide information about soybean trait (phenotype) information, from USDA and state variety trials (Objective 3). To help researchers and breeders more efficiently select for desired traits, the project will collect and incorporate published information about genes with established associations with traits of interest (Objective 4). Lastly, the project will continue to provide support to research communities for soybean and other legumes, through support of workshops, online tutorials, and other communication methods (Objective 5).
Progress Report
In support of Objective 1, focused on stewardship of soybean and other major legume genetic datasets, we incorporated the genome assemblies and predicted genes for seven additional genome assemblies and predicted genes into legumeinfo.org, including faba bean, hyacinth bean, peanut, and several trees that are used ornamentally and for scientific study of evolutionary patterns in the legume family.
In support of Objective 4, focused on collecting and curating information about gene functions, we curated and incorporated information about more than 100 genes in legume crops that underlie important agronomic, nutritional, and stress-response traits.
In support of Objective 5, focused on research community support and training, we presented a workshop about how to use online tools at SoyBase at the World Soybean Research Conference in Vienna, Austria.
Accomplishments
