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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #411131
Research Project: Conservation and Utilization of Temperate-Adapted Fruit, Nut, and Other Specialty Crop Genetic Resources

Location: National Clonal Germplasm Repository

Title: Developing a new crop ontology for blueberry

Author
item Bassil, Nahla
item HISLOP, LILY - Savanna Institute
item Hulse-Kemp, Amanda
item ZHANG, DONGYAN - Cornell University
item SHEEHAN, MOIRA - Cornell University
item HUMANN, JODI - Washington State University
item MAIN, DORRIE - Washington State University
item IORIZZO, MASSIMO - North Carolina State University
item Babiker, Ebrahiem

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2023
Publication Date: 1/12/2024
Citation: Bassil, N.V., Hislop, L., Hulse-Kemp, A.M., Zhang, D., Sheehan, M., Humann, J., Main, D., Iorizzo, M., Babiker, E.M. 2024. Developing a new crop ontology for blueberry. Plant and Animal Genome Conference.

Interpretive Summary:

Technical Abstract: A common and structured vocabulary used by breeders, collection managers, and allied scientists to describe their data is needed in blueberry to allow integration and use in various genetic analyses. Crop ontology (CO) creates this vocabulary and its development in blueberry was a collaborative effort led by the Breeding Insight (BI) Initiative and supported by the Genome Database for Vaccinium (GDV). We will provide an overview of its development, lessons learned, suggestions for improvement and questions arising from users at this time. Up to 14 breeders / allied researchers from public and private institutions participated in describing trait, method and scale for the phenotypes they measure in the United States. The ontology is publicly available through the Crop Ontology (CO) website, BreedBase (Breeding Insight, for ARS scientists), and the Breeding Information Management System (accessed through GDV). At this time, it contains 183 traits with their corresponding methods and scales. Surveying its current use provided insight on its usefulness, challenges, and current and future needs. Breeders appreciate the potential for wide data sharing and curators from GDV are using it in curating quantitative trait loci data. Suggestions for improvements include: ability and a clear procedure to easily add traits; a central location; expansion to include additional morphological, physiological, and anatomical traits of use in more disciplines (like taxonomy); and agreeing on a standardized method and scale for traits. While the blueberry ontology has already begun to be useful to breeders that are using it, its continued use and utility will require further work.