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ARS Home » Pacific West Area » Corvallis, Oregon » National Clonal Germplasm Repository » Research » Publications at this Location » Publication #413481
Research Project: Conservation and Utilization of Temperate-Adapted Fruit, Nut, and Other Specialty Crop Genetic Resources

Location: National Clonal Germplasm Repository

Title: Updates on curation and standardization of phenotypic and genotypic data for horticultural databases

Author
item Bushakra, Jill
item JUNG, SOOK - Washington State University
item Bassil, Nahla
item CHENG, CHUN-HUAI - Washington State University
item LEE, TAEIN - Washington State University
item YU, JING - Washington State University
item HUMANN, JODI - Washington State University
item BUBLE, KATHERYN - Washington State University
item ZHENG, PING - Washington State University
item MAIN, DORRIE - Washington State University

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/3/2024
Publication Date: 9/23/2024
Citation: Bushakra, J., Jung, S., Bassil, N.V., Cheng, C., Lee, T., Yu, J., Humann, J.L., Buble, K., Zheng, P., Main, D. 2024. Updates on curation and standardization of phenotypic and genotypic data for horticultural databases. American Society of Horticulture Science Meeting.

Interpretive Summary:

Technical Abstract: The Genome Database for Rosaceae (GDR, https://www.rosaceae.org/), CottonGen (https://cottongen.org/), Pulse Crop Database (PCD, https://www.pulsedb.org/), Genome Database for Vaccinium (GDV, https://www.vaccinium.org/), and Citrus Genome Database (CGD, https://www.citrusgenomedb.org/) are the databases of the NRSP10 project. Germplasm and diversity data in NRSP10 databases include publicly available phenotype and genotype data from researchers, publications, and public repositories such as GRIN. Genotype data include SSR genotype, SNP genotype, and haplotype data. These data from various sources are integrated with other types of data such as whole genome data, QTLs and GWAS using standardized trait terms, marker names, accession names and genome positions. Our new efforts include standardizing trait descriptors from various sources and developing Crop Ontology terms. This presentation will describe our progress on the standardization effort as well as the new data in our databases and how to access each of the data types, genotype, phenotype, and haplotype data.