Skip to main content
×
×
Home

Exploring Genetic and Spatial Structure of U.S. Weedy Red Rice (Oryza sativa) in Relation to Rice Relatives Worldwide

  • David R. Gealy (a1), Hesham A. Agrama (a2) and Georgia C. Eizenga (a1)
Abstract

Weedy red rice is a highly troublesome weed of rice in the United States and throughout the world. Effective management of this weed has remained challenging to U.S. farmers, partly because of the biological diversity among red rice populations, resistance to or avoidance of control measures, and genetic similarities with crop rice that allow crossing between the two plant types. The aim of this research was to identify simple sequence repeat (SSR) marker loci that will unambiguously differentiate between U.S. weedy red rice, commercial rice cultivars, and their hybrids, to characterize the genetic diversity and structure of U.S. weedy red rice accessions in relation to Oryza collections from international sources, and to relate genetic and geographic variability within U.S. weedy red rice. Thirty-one SSR markers were used to analyze 180 worldwide Oryza entries and 80 U.S. weedy red rice and U.S. rice cultivars. Twenty-six of the 31 SSR marker loci were highly informative with respect to genetic distinctions between U.S. weedy red rice and U.S. rice cultivars. U.S. red rice are accessions clustered into two main SSR-based collections, awnless strawhull (SA−) and awned blackhull (BA+), according to genetic distance analysis and principal coordinate analysis. Genetic structure analysis clearly identified SA− and BA+ red rice, rice–red rice hybrids, commercial japonica rice cultivars, indica rice, and a number of international and wild Oryza spp. standards (e.g., Oryza nivara, Oryza rufipogon, and Oryza glaberrima) as genetically distinct groups. U.S. SA− red rice exhibited greater spatial structure than did BA+ in that the genetic makeup of SA− accessions changed nearly twice as much with geographic distance as compared to BA+. However, 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 such as rice or other red rice types present in U.S. rice fields. Several of the awned red rice entries exhibited evidence of natural hybridization with different red rice types. Our results suggest that the SA− and BA+ red rice collections have different genetic backgrounds. SA− accessions generally associated most closely with indica-like red- or white-bran Oryza sativa cultivar standards, while BA+ accessions generally associated more closely with O. nivara or O. nivara–like O. sativa entries. Although the U.S. red rice accessions appear not to have descended directly from introductions of the worldwide Oryza standards analyzed, an Oryza red-pericarp entry from Niger (UA 1012; PI 490783) was genetically very similar to some U.S. BA+ accessions.

Copyright
Corresponding author
Corresponding author's E-mail: David.gealy@ars.usda.gov
References
Hide All
Agrama, H. A. and Eizenga, G. C. 2008. Molecular diversity and genome-wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives. Euphytica. 160:339355.
Agrama, H. A., Yan, W., Lee, F. N., Fjellstrom, R., Chen, M. H., Jia, M., and McClung, A. 2009. Genetic assessment of a mini-core subset developed from the USDA rice genebank. Crop Sci. 49:13361346.
Brooks, S. A., Yan, W., Jackson, A. K., and Deren, C. W. 2008. A natural mutation in rc reverts white-rice–pericarp to red and results in a new, dominant, wild-type allele: Rc-g . Theor. Appl. Genet. 117:575580.
Burgos, N. R., Norsworthy, J. K., Scott, R. C., and Smith, K. L. 2008. Red rice (Oryza sativa) status after 5 years of imidazolinone-resistant rice technology in Arkansas. Weed Technol. 22:200208.
Cao, Q., Lu, B. R., Xia, H., Rong, J., Sala, F., Spada, A., and Grassi, F. 2006. Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations round in north-eastern China revealed by simple sequence repeat (SSR) markers. Ann. Bot. 98:12411252.
Delouche, J. C., Burgos, N. R., Gealy, D. R., de San Martin, D. Z., Labrada, R., Larinde, M., and Rosell, C. 2007. Weedy Rices—Origin, Biology, Ecology, and Control. FAO Plant Production and Protection Paper 188. Rome, Italy FAO. 144.
Eizenga, G. C., Agrama, H. A., Lee, F. N., and Jia, Y. 2009. Exploring genetic diversity and potential novel disease resistance genes in a collection of rice (Oryza spp.) wild relatives. Genet. Resour. Crop Evol. 56:6576.
Estorninos, L. E. Jr., Gealy, D. R., and Talbert, R. E. 2002. Growth response of rice (Oryza sativa) and red rice (O. sativa) in a replacement series study. Weed Technol. 16:401406.
Estorninos, L. E. Jr., Gealy, D. R., Talbert, R. E., McClelland, M. R., and Gbur, E. E. 2005. Rice and red rice interference: II. Rice response to population densities of three red rice (Oryza sativa) ecotypes. Weed Sci. 53:683689.
Evanno, G., Regnaut, S., and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:26112620.
Excoffier, L., Laval, G., and Schneider, S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online. 1:4750.
Garris, A. J., Tai, T. H., Colburn, J., Kresovich, S., and McCouch, S. R. 2005. Genetic structure and diversity in Oryza sativa L. Genetics. 169:16311638.
Gealy, D. R. 2005a. Gene movement between rice (Oryza sativa) and weedy rice (Oryza sativa): a U.S. temperate rice perspective. Pages 323354. In Gressel, J. Crop Ferality and Volunteerism. Boca Raton, FL CRC Press. 422.
Gealy, D. R. 2005b. Growth, development, and physiological characteristics of selected red rice (Oryza sativa) accessions from Arkansas. Pages 184200. In Norman, R. J., Meullenet, J. F., and Moldenhauer, K. A. K. Research Series 529, B.R. Wells Rice Research Studies 2004. Fayetteville, AR University of Arkansas. http://arkansasagnews.uark.edu/408.htm.
Gealy, D. R., Agrama, H. A., Estorninos, L. E., and Wilson, C. E. 2007. Characterization of weedy rice populations in the southern U.S. and their gene flow interactions with rice. Pages 158159. In Bocchi, S., Ferrero, A., and Porro, A. Proceedings of the Fourth Temperate Rice Conference, June 25–27, Novara, Italy.
Gealy, D. R. and Black, H. L. 1999. Germination, growth, and photosynthesis response of red rice (Oryza sativa L.) biotypes to chilling temperature. Pages 6672. In Norman, R. J. and Johnson, T. H. Arkansas Agricultural Experiment Station, B. R. Wells Rice Research Studies 1998, Series 468. http://www.uark.edu/depts/agripub/Publications.
Gealy, D. R. and Bryant, R. J. 2008. Seed physicochemical characteristics of field-grown U.S. weedy red rice (Oryza sativa) biotypes: contrasts with commercial cultivars. J. Cereal Sci. 49:239245.
Gealy, D. R., Dilday, R. H., Baldwin, F. L., and Black, H. L. 1999. Imazethapyr (‘Pursuit’) effect on red rice (Oryza sativa L.) biotypes. Pages 7989. In Norman, R. J. and Johnson, T. H. Arkansas Agricultural Experiment Station, B. R. Wells Rice Research Studies 1998, Series 468. http://www.uark.edu/depts/agripub/Publications.
Gealy, D., Saldain, N., and Talbert, R. 2000. Emergence of red rice (Oryza sativa) ecotypes under dry-seeded rice (Oryza sativa) culture. Weed Technol. 14:406412.
Gealy, D. R., Tai, T. H., and Sneller, C. H. 2002. Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Sci. 50:333339.
Gealy, D. R., Wilson, C. E., Estorninos, L. E. Jr., Black, H. L., and Agrama, H. A. 2005. Identification of rice–red rice crosses in IMI- and non-resistant rice fields of Arkansas. Proc. South. Weed Sci. Soc. 58:211. http://www.weedscience.msstate.edu/swss/.
Gealy, D. R., Yan, W., and Rutger, J. N. 2006. Red rice (Oryza sativa) plant types affect growth, coloration, and flowering characteristics of first and second generation crosses with rice. Weed Technol. 20:839852.
Gramene 2009. A Resource for Comparative Grass Genomics. Release No. 29. http://www.gramene.org. Accessed: June 26, 2009.
[GRIN] Germplasm Resources Information Network 2008. Germplasm Resources Information Network. http://www.ars-grin.gov/npgs/. Accessed: December 31, 2008.
Hoehn, M., Sarre, D., and Henle, K. 2007. The tales of two geckos: does dispersal prevent extinction in recently fragmented populations? Mol. Ecol. 16:32993312.
Kuk, Y. I., Burgos, N. R., and Shivrain, V. K. 2008. Natural tolerance to imazethapyr in red rice (Oryza sativa). Weed Sci. 56:111.
Labate, J. A., Lamkey, K. R., Mitchell, S. E., Kresovich, S., Sullivan, H., and Smith, J. S. C. 2003. Molecular and historical aspects of Corn Belt dent diversity. Crop Sci. 43:8091.
Lee, F. N., Gealy, D. R., and Dilday, R. H. 2000. Differential response of United States Oryza sativa (red rice) accessions to races of Pyricularia grisea . Pages 94101. In Norman, R. J. and Beyrouty, C. A. Arkansas Agricultural Experiment Station, B. R. Wells Rice Research Studies 1999, Series 476. http://www.uark.edu/depts/agripub/Publications.
Liu, K. and Muse, S. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 21:21282129.
Londo, J. P. and Schaal, B. A. 2007. Origins and population genetics of weedy red rice in the USA. Mol. Ecol. 16:45234535.
Lu, H., Redus, M. A., Coburn, J. R., Rutger, J. N., McCouch, S. R., and Tai, T. H. 2005. Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis. Crop Sci. 45:6676.
Moldenhauer, K., Gibbons, J., and McKenzie, K. 2004. Rice varieties. Pages 4975. In Champagn, E. T. Rice: Chemistry and Technology. 3rd ed. St. Paul, MN The American Association of Cereal Chemists. 49–75.
Moldenhauer, K. A. K., Lee, F. N., Norman, R. J., Helms, R. S., Wells, B. R., Dilday, R. H., Rohman, P. C., and Marchetti, M. A. 1990. Registration of Katy rice. Crop Sci. 30:747.
Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. U. S. A. 70:33213323.
Noldin, J. A., Chandler, J. M., Ketchersid, M. L., and McCauley, G. N. 1999b. Red rice (Oryza sativa) biology. II. Ecotype sensitivity to herbicides. Weed Technol. 13:1924.
Noldin, J. A., Chandler, J. M., and McCauley, G. N. 1999a. Red rice (Oryza sativa) biology. I. Characterization of red rice ecotypes. Weed Technol. 13:1218.
Olsen, K. M., Caicedo, A. L., and Jia, Y. 2007. Evolutionary genomics of weedy rice in the USA. J. Integrative Plant Biol. 49:811816.
Patindol, J., Flowers, A., Kuo, M. I., Wang, Y. J., and Gealy, D. 2006. Comparison of physicochemical properties and starch structure of red rice and cultivated rice. J. Agric. Food Chem. 54:27122718.
Peakall, R. and Smouse, P. E. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes. 6:288295.
Pritchard, J. K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945959.
Rogers, J. S. 1972. Measures of genetic similarity and genetic distance. Studies in Genetics VII. Univ. Texas Publ. 7213:145153.
Schneider, S. and Excoffier, L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics. 152:10791089.
Shivrain, V. K., Burgos, N. R., Gealy, D. R., Moldenhauer, K. A. K., and Baquireza, C. J. 2008. Maximum outcrossing rate and genetic compatibility between Red Rice (Oryza sativa) biotypes and ClearfieldTM rice. Weed Sci. 56:807813.
Shivrain, V. K., Burgos, N. R., Rajguru, S. N., Anders, M. M., Moore, J., and Sales, M. A. 2007. Gene flow between ClearfieldTM rice and red rice. Crop Prot. 26:349356.
Sweeney, M. and McCouch, S. 2007. The complex history of the domestication of rice. Ann. Bot. 100:951957. www.aob.oxfordjournals.org.
Sweeney, M. T., Thompson, M. J., Pfeil, B. E., and McCouch, S. 2006. Caught red-handed: Rc Encodes a basic helix–loup–helix protein conditioning red pericarp in rice. Plant Cell. 18:283294.
Thomson, M. J., Septiningsih, E. M., Suwardjo, F., Santoso, T. J., Silitonga, T. S., and McCouch, S. R. 2007. Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers. Theor. Appl. Genet. 114:559568.
van Etten, J., López, M. R. F., Monterroso, L. G. M., and Samayoa, K. M. P. 2008. Genetic diversity of maize (Zea mays L. ssp. mays) in communities of the western highlands of Guatemala: geographical patterns and processes. Genet. Resour. Crop Evol. 55:303317.
Vaughan, L. K., Ottis, B. V., Prazak-Havey, A. M., Bormans, C. A., Sneller, C., Chandler, J. M., and Park, W. D. 2001. Is all red rice found in commercial rice really Oryza sativa? Weed Sci. 49:468476.
Wang, X., Jia, Y., Shu, Q. Y., and Wu, D. 2008. Haplotype diversity at the Pi-ta locus in cultivated rice and its wild relatives. Phytopathology. 98:13051311.
Weir, B. S. 1996. Genetic Data Analysis II: Materials for Discrete Population Genetic Data. Sunderland, MA Sinauer Associates.
Wilson, C. E. and Runsick, S. K. 2007. Trends in Arkansas rice production. Pages 1322. In Norman, R. J., Meullenet, J. F., and Moldenhauer, K. A. K. Research Series 550, B.R. Wells Rice Research Studies 2006. Fayetteville, AR University of Arkansas. http://arkansasagnews.uark.edu/408.htm.
Yuan, J. S., Gealy, D. R., Stoming, T., and Stewart, C. N. Jr. 2006. Identification of genes involved in cold resistance during seed germination and postgermination of rice using comparative proteomics and genomics. In Proceedings of the American Society of Plant Biologists Annual Meeting, Paper No. P09042.
Zhang, W., Linscombe, S., Webster, E., Tan, S., and Oard, J. 2006. Risk assessment of the transfer of imazethapyr herbicide tolerance from Clearfield rice to red rice (Oryza sativa). Euphytica. 152:7586.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Weed Science
  • ISSN: 0043-1745
  • EISSN: 1550-2759
  • URL: /core/journals/weed-science
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords

Type Description Title
PDF
Supplementary materials

Gealy et al. supplementary material
Table S1 and Figures S1-S2

 PDF (346 KB)
346 KB

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed