ARS | Publication request: Characterization of the USDA Rice World Genebank usng a core collection strategy

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 15, 2008
Publication Date: March 1, 2008
Citation: Yan, W., Agrama, H., Fjellstrom, R.G., Bryant, R.J., McClung, A.M. 2008. Characterization of the USDA Rice World Genebank using a core collection strategy. In: Proceedings of the 32nd Rice Technical Working Group Meetings, February 18-21, 2008, San Diego, CA. 2008. CDROM.

Technical Abstract: The USDA Rice World Genebank contains more than 18,000 accessions originated from 116 countries displayed at www.ars-grin.gov with descriptive data for each. The resources and expertise required to fully characterize the collection is limited by the sheer number of accessions. Development of a Core Collection, which is defined as a subset of a large genebank that captures most of the genetic variability, is an effective tool to improve characterization efficiency. The USDA rice core subset (RCS) including 1,790 entries from 114 countries was assembled by stratified random sampling in 2002 and comprehensively characterized. Comparative analysis for 14 important descriptors demonstrated that the RCS was highly correlated with the entire genebank (r=0.94, P<0.0001), and information drawn from the RCS could be effectively used to assess the genebank with 88% certainty. A joint effort of federal and state scientists has completely characterized the RCS. The RCS was purified with a single plant selection in 2006 and was genotyped using 48 SSR markers. These include random markers distributed across all 12 chromosomes as well as markers for targeted genes. An additional 32 markers will be genotyped for the RCS, which gives marker coverage every 30 cM. These data will be used for population genetic structure analysis, association mapping for important traits, and identification of gaps and redundancies in the collection. A mini-core collection, about 10% of the RCS, will be subsequently developed for more comprehensive genotypic and phenotypic studies. This will serve as a resource for geneticists to identify genes and alleles for new and more complex traits.