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United States Department of Agriculture

Agricultural Research Service

Title: Gene flow from herbicide-resistant and non-resistant rice into red rice populations in U.S. rice fields: A survey of current evidence

Authors
item Gealy, David
item Estorninos, L - UNIV. OF AR RREC
item Agrama, H - UNIV. OF AR RREC
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2005
Publication Date: February 15, 2006
Citation: Gealy, D.R., Estorninos, L.E., Agrama, H.A., Eizenga, G.C. 2006. Gene flow from herbicide-resistant and non-resistant rice into red rice populations in U.S. rice fields: A survey of current evidence. Rice Technical Working Group Meeting Proceedings, February 29-March 1, 2006, Houston, Texas. 2006 CDROM.

Technical Abstract: Diverse red rice types infest U.S. rice fields. These infestations have remained widespread despite recent successes in controlling red rice in newly-introduced herbicide-resistant rice systems. As a result, the distribution and genetic background of red rice, and the degree to which red rice intercrosses with commercial rice, particularly herbicide-resistant rice, have remained topics of great biological and economic interest. Analyses based on PCR-based simple sequence repeat (SSR) markers are being employed at the USDA-ARS, DB NRRC in Stuttgart, AR to address these issues from the basic and practical perspectives. Sixty-two red rice accessions and crosses (or putative crosses) were obtained from the major rice-producing counties in Arkansas and from selected areas of Missouri, Mississippi, Louisiana, and Texas. The genetic background and interrelatedness of these accessions was compared to a wide range of standards which included 84 common U.S. and foreign commercial (white) rice cultivars/lines, 58 red rice cultivars/lines (non weedy types) and 37 additional lines of Oryza species (other than O. sativa) obtained from the USDA-ARS rice germplasm collection. The aforementioned germplasm was genotyped with 32 SSR markers and the data were analyzed with appropriate software to identify genetic distance, population clusters and population structure. With the exception of the rice-red rice crosses, which clustered between the U.S. rice and red rice entries, the U.S. red rice accessions generally clustered closely together and were genetically distant from all U.S. cultivars. Although these accessions were genetically closer to a number of red rice cultivars and other Oryza species, they generally were substantially different from all of the other standards tested. Seven of the 32 SSR markers differentiated between the imidazolinone-resistant cultivars, CL 161 and CL 121, and two markers (RM224 and RM345) differentiated between these cultivars as well as a number of common U.S. cultivars and red rice types. Ten SSR markers, in combination with observations of phenotypic traits, were employed to determine rapidly the presence and apparent identity of unknown red rice types and rice-red rice crosses obtained from grower’s fields. Further analysis of the data has suggested that as few as five of these markers may reliably differentiate between imidazolinone-resistant cultivars and a sizeable number of other commercial cultivars, red rice types and crosses. However, such streamlined approaches to identifying unknown plant types may sacrifice some degree of accuracy for speed and affordability. In a practical example of our efforts, a ‘variable’ population of ‘red rice-looking’ plants obtained from a farm field in Mississippi County, AR in 2005 was shown to contain a number of individuals with green or purple stems; green or pink awns, or no awns; rough or smooth leaves; and red or white seeds. Collectively, these combinations of phenotypic traits are strongly indicative of a segregating population in the F2 generation or later, that was derived from a cross between rice and an awned blackhull red rice type. This tentative diagnosis was strengthened using the ten aforementioned SSR markers to confirm a) the presence of numerous homozygous or heterozygous alleles that were also present in one or both of the commercial rice or awned blackhull red rice standards tested, and b) that the genetic distances between this group of unknowns and both standards were generally similar. This research shows that key phenotypic traits in combination with SSR analyses can be used effectively to genotype unknown red rice types and determine genetic backgrounds of weedy/red rice types derived from herbicide-resistant or non-resistant rice parents.

Last Modified: 7/31/2014