ARS | Publication request: GENOTYPING AND PHENOTYPING THE USDA RICE CORE COLLECTION

Submitted to: Annual Conference on Functional Genomics
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2004
Publication Date: December 1, 2004
Citation: Yan, W., Bockelman, H.E., Tai, T., Jia, M.H., Rutger, J.N. 2004. Genotyping and phenotyping the USDA rice core collection [abstract]. Proceedings, 2nd International Rice Functional Genomics Conference, Tucson, Arizona. Paper No. 173.

Technical Abstract: The USDA (United States Department of Agriculture) rice core collection consists of 1,801 entries from 115 countries, representing about 10% of the entirety of 17,395 accessions in the National Small Grains Collection. Following several years of phenotyping, genotyping was started with 183 publicly available rice microsatellite markers (www.gramene.org). These markers were analyzed using an ABI 3700 automated capillary sequencer with fluorescently-labeled primers. Assessment of the core using microsatellite markers will facilitate analysis of genetic relationships and assist in identifying genomic regions that harbor agriculturally important genes. Also, molecular markers related to grain quality descriptors are being analyzed in cooperation with the USDA-Beaumont Research Unit. The following descriptors have been phenotyped: agronomy - days to flowering, plant height, plant type, panicle type and lodging; morphology - awn type, bran color, grain type, hull color, hull cover, kernel length, kernel width, length/width ratio, rough and brown 1000 kernel weights; and physiology - straighthead. Evaluations are under way for grain quality - alkali/spreading value, amylose, aroma, endosperm type, gelatinization temperature, and protein; pest resistance - blast, sheath blight and stink bugs; and physiology - iron and zinc contents. All the data from genotyping and phenotyping will be displayed in GRIN (www.ars-grin.gov). With the information, genetic gaps in the entire collection can be identified for further expansion, genetic drift or change when accessions are regenerated can be monitored, and duplicates from regeneration and new introductions can be determined. Thus breeders will find it easier to locate genes or traits of interest. Background information for those accessions containing the desired traits including genetic distances of these lines from commercial cultivars will help in designing effective strategies for transferring the traits.