ARS | Publication request: CREATION OF A GENOTYPIC AND PHENOTYPIC DATABASE FOR THE NSGC RICE COLLECTION

Submitted to: HortScience
Publication Type: Proceedings
Publication Acceptance Date: June 1, 2006
Publication Date: July 1, 2006
Citation: McClung, A.M., Yan, W., Lee, F.N., Marchetti, M.A., Bockelman, H.E., Fjellstrom, R.G. 2006. Creation of a genotypic and phenotypic database for the NSGC rice collection. HortScience. 41(4):936.

Technical Abstract: There are over 18,000 accessions that have been collected from some 100 countries that comprise the rice germplasm collection in the United States. This collection is systematically evaluated for a set of phenotypic descriptors to help researchers identify germplasm possessing traits of scientific interest. These data are curated on the GRIN website and made available to the general public. Development of genomic tools has allowed for the genotypic assessment of the germplasm collection in addition to the standard trait data. A core subset of the rice collection has been developed that is representative of the entire collection but is only 10% of its size. The core collection is being evaluated genotypically using both random DNA markers and markers that are linked with traits of economic importance (e.g., grain cooking quality and disease resistance). The marker and trait data can be used together to: identify sources of allelic diversity for a trait or at a chromosomal region; develop associative mapping studies; identify admixtures and maintain quality control; and, in general, bring greater value to interested users of the collection. Data on the genomic and phenotypic characterization of the rice core collection will be available to the public through websites such as GRIN and Gramene that serve a broad research community that includes breeders and geneticists.