Submitted to: Weed Science
Publication Type: Peer reviewed journal
Publication Acceptance Date: 7/27/2009
Publication Date: 12/31/2009
Publication URL: handle.net/10113/37243
Citation: Gealy, D.R., Agrama, H.A., Eizenga, G.C. 2009. Exploring genetic and spatial structure of U.S. weedy red rice (Oryza sativa) in relation to rice relatives worldwide. Weed Science. 57:627-643. DOI: 10.1614/WS-09-018.1. Interpretive Summary: Weedy red rice (Oryza sativa) damages rice production and quality in the U.S., and increasingly, throughout the world. Effective control of red rice is difficult because populations in the U.S. can be biologically diverse in different geographic regions, red rice is genetically and physiologically very similar to the rice (Oryza sativa) crop it infests, and it can intercross with crop rice. We aimed to use DNA markers (fingerprinting) to determine genetic differences between U.S. red rice red rice populations, U.S. rice varieties, and close relatives found throughout the world, and to determine whether the different genetic groupings could be structured to reveal the presence of potential ancestral and/or geographical relationships. Twenty-five of the 31 markers used to analyze these samples proved very effective in determining important genetic differences among and between red rice and rice. The DNA fingerprinting analysis revealed two main red rice groups, awnless strawhull (SA-) and awned blackhull (BA+). These and 14 additional distinct ancestral backgrounds were observed among the 180 entries used in this study. DNA fingerprints were the most uniform in BA+ rice, whereas SA- red rice exhibited a more pronounced correlation in differences in DNA fingerprints over geographic distance. Some awned red rice entries appeared to have formed through natural outcrossing between diverse red rice plant types. U.S. red rice plants appear not to have come to U.S. farm fields directly from any of their foreign relatives analyzed in this study, but the genetic makeup of SA- red rice was typically most similar to tropical (indica) rice types while the genetic makeup of BA+ red rice was generally associated more closely with a close wild ancestor of rice (Oryza nivara).
Technical Abstract: Red rice (Oryza sativa) is a highly troublesome weed of cultivated rice in the U.S. and throughout the world. Effective management of this weed has remained challenging to farmers in part due to the biological diversity among red rice populations, lack of effective control measures, and genetic similarities with cultivated rice (Oryza sativa) that allow intercrossing. The aim of this research was to genetically differentiate U.S. weedy red rice populations and to determine their genetic relatedness to cultivated U.S. rice, to international cultivars, and to wild related species; and to determine the degree of genetic and spatial (geographic) structure present for each group. Thirty-one SSR markers were used to analyze 180 Oryza entries revealing allele numbers ranging from 3 to 20, and polymorphism information content of 0.379 to 0.900. Twenty-five SSR markers that were highly informative for the genetic distinction between weedy red rice and rice cultivars present in the U.S. were identified. U.S. red rice accessions clustered clearly into two main SSR-based populations, awnless strawhull (SA-) and awned blackhull (BA+), based on genetic distance analysis and principle coordinate analysis. An analysis of genetic structure clearly identified SA- and BA+ red rice, rice-red rice hybrids, commercial japonica rice cultivars, indica rice, and a number of foreign Oryza spp. standards (e.g. O. sativa cultivars with red pericarp, and O. nivara, O. rufipogon, and O. glaberimma) as different ancestral groups (genetic backgrounds). Although the SA- red rice exhibited greater spatial structure than BA+ accessions. the overall genetic variability within SA- red rice accessions was less than for BA+ accessions, suggesting that the SA- types may be genetically less compatible than BA+ types with other Oryza plants (i.e. rice or other red rice types) present in rice fields. Several of the awned red rice entries exhibited evidence of natural intercrossing between different red rice populations. Our results suggest that the SA- and BA+ red rice populations have dramatically different genetic backgrounds. Although they appear not to have descended directly from introductions of any of the global Oryza standards analyzed, SA- accessions generally associated most closely with indica-like red- or white-pericarp O. sativa cultivar standards while BA+ accessions generally associated more closely with O. nivara or O. nivara-like O. sativa entries.