ARS | Publication request: Population structure of putative rice-red rice hybrid derivatives in the Southern U.S.

Submitted to: Weed Science Society of America Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: February 7, 2007
Publication Date: February 7, 2007
Citation: Gealy, D.R., Agrama, H., Estorninos, Jr., L.E., Eizenga, G.C. 2007 Population structure of putative rice-red rice hybrid derivatives in the Southern U.S. Weed Science Society of America Meeting Proceedings. 47:P92.

Technical Abstract: Rice and red rice can readily intercross in southern U.S. rice fields, however, the extent to which progeny of these rice-red rice hybrids may have successfully moved into red rice populations is unknown. Approximately 430 red rice accessions were obtained from farm samples in 1999 and 2000. Forty-five of these, which exhibited traits consistent with known hybrid derivatives, were selected for this study and were divided into four groups of 10 to 13 individuals each. The groups were: 1) plants that were much shorter (~100 to116 cm) than typical red rice plants (~130 to167 cm); 2) plants with brief flowering periods (~3 to 5 days from initiation of flowering to completion) that are common in commercial rice cultivars and of shorter duration than those of typical red rice types (~6 to 12 days); 3) plants with very short awns (~0.5 to 1 cm) that are typical of known hybrid derivatives; and 4) plants with various combinations of the three traits above. Approximately 15 red rice types chosen at random and long grain commercial rice cultivars were included for comparison. Nineteen SSR markers that were distributed among all 12 chromosomes were visualized on an ABI3730 automated DNA sequencer using DNA isolated from leaf tissues and analyzed in Genemapper software. To determine the population structure of these plants, a model-based Bayesian cluster analysis was performed using all red rice accessions and rice cultivars. Five independent runs in the STRUCTURE software using k values (hypothetical number of subpopulations) from 3 to 6 showed the highest number of accessions assigned to a specific cluster with a probability higher than 80% was obtained with K = 6, thus indicating the presence of complex relationships among accessions. Using the clustering diagrams with K = 6, the subpopulations identified by STRUCTURE largely correspond to pools originating from commercial rice, and red rice with normal-length awns, very short awns, or without awns. There was no evidence of a shared genetic background between any of the four groups of putative rice-red rice hybrid derivatives or the standard red rice types and the long grain cultivars tested, however, the red rice groups appeared to share common alleles with indica rice germplasm. This suggests that the unusual red rice types in our collection may have arisen from preexisting allelic diversity within the red rice populations. It is also possible that rice alleles which may have been transferred to red rice plants through intercrossing, were subsequently lost from these populations due to selection pressure. Analyses using additional rice standards and markers are underway to address these hypotheses.