ARS | Publication request: Development and evaluation of a core subset of the USDA rice (Oryza sativa L.) germplasm collection

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 23, 2006
Publication Date: February 28, 2007
Citation: Yan, W., Rutger, J.N., Bockelman, H.E., Fjellstrom, R.G., Chen, M.H., Tai, T., McClung, A.M. 2007. Development and evaluation of a core subset of the USDA rice (Oryza sativa L.) germplasm collection. Crop Science. 47(2):869-878.

Interpretive Summary: Comprehensive evaluation of the collection for numerous descriptors, particularly those involving disease resistance and grain quality, has been hindered by the sheer number of accessions. It also is much harder to analyze such large collections using molecular means. Core strategy has been proved effective in this regard. The United States Department of Agriculture (USDA) rice (Oryza sativa L.) core subset (RCS) was assembled by stratified random sampling. The RCS consists of 1,790 entries from 114 countries, about 10% of the 18,412 accessions in the rice whole collection (RWC). Analysis for 14 descriptors proved that the RCS was highly representative of the RWC. Thus, information drawn from the RCS could be effectively used to assess the RWC with 88% certainty. This paper justifies effectiveness of assessing the RWC with comprehensively phenotyping and genotyping the RCS. The RCS has been evaluated for all descriptors including disease resistance and grain quality set by Rice Crop Germplasm Committee, plus micro-nutrient elements, cold tolerance, etc. Analyzing target genes with molecular markers in the RCS and DNA fingerprinting the RCS are under the way with a joint effort of scientists in the federal and state agencies.

Technical Abstract: A valuable core collection that is a subset of a whole germplasm collection should capture most of the variation present in the whole collection, while allowing for more efficient evaluation and management due to smaller size. The United States Department of Agriculture (USDA) rice (Oryza sativa L.) core subset (RCS), assembled by stratified random sampling, consists of 1,790 entries from 114 countries and represents approximately 10% of the 18,412 accessions in the rice whole collection (RWC). Data for this study were obtained from the USDA germplasm system at www.ars-grin.gov for the RWC and from an evaluation conducted in 2002 for the RCS. Comparative analysis for frequency distributions of 14 descriptors demonstrated that the RCS was highly correlated with the RWC (r=0.94, P<0.0001). Thus, information drawn from the RCS could be effectively used to assess the RWC with 88% certainty. Correlation coefficients between the RCS and the RWC for eight descriptors were less than or equal to 0.9, indicating that the RCS was highly representative of the RWC. Correlation coefficients for the other six descriptors were lower (0.65 - 0.88), but still significant.