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Is all red rice found in commercial rice really Oryza sativa?

  • L. Kelly Vaughan (a1), Brian V. Ottis (a2), Ann M. Prazak-Havey (a1), Concetta A. Bormans (a1), Clay Sneller (a3), James M. Chandler and William D. Park (a1)...


All red rice found in commercial rice in the United States has traditionally been classified as Oryza sativa ssp. indica. This assumption was tested by analyzing red rice samples collected from across the southern United States rice belt with 18 simple sequence length polymorphism (SSLP) markers distributed across all 12 chromosomes. The results clearly demonstrate that the traditional classification of red rice is inadequate. Some red rice is closely related to O. sativa ssp. indica cultivated rice. However, other red rice is more closely related to O. sativa ssp. japonica. Most importantly, some red rice samples collected from Arkansas, Louisiana, Mississippi, and Texas form a distinct group that includes a number of Oryza nivara and Oryza rufipogon accessions from the National Small Grains Center. In particular, red rice samples from three states were identified that for all 18 markers are identical to the O. rufipogon accession IRGC 105491. These different classes of red rice are intermingled across the southern U.S. rice belt and within individual production fields. Oryza sativa ssp. indica-like red rice and O. rufipogon-like red rice have been found within a single 9-m2 collection site. While the classification of red rice as O. sativa ssp. indica, O. sativa ssp. japonica, or O. rufipogon using DNA markers is generally in agreement with classification based on simple morphological traits, readily observed morphological traits alone are not sufficient to reliably classify red rice. Because red rice is much more diverse than previously assumed, this diversity must be considered when developing red rice management strategies.


Corresponding author

Corresponding author. Department of Soil and Crop Science, 2474 TAMU, Texas Agricultural Experiment Station, Texas A&M University, College Station, TX 77843-2474;


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Aggarwal, R. K., Brar, D. S., Nandi, S., Huang, N., and Khush, G. S. 1999. Phylogenic relationships among Oryza species revealed by AFLP analysis. Theor. Appl. Genet. 98:13201328.
Beebe, S. E., Ochoa, I., Skroch, P., Nienhuis, J., and Tivang, J. 1995. Genetic diversity among common bean breeding lines developed for Central America. Crop Sci. 35:11781183.
Cho, Y.-C., Chung, T.-Y., and Suh, H.- S. 1995. Genetic characteristics of Korean weedy rice (Oryza sativa L.) by RFLP analysis. Euphytica 86:103110.
Craigmiles, J. P. 1978. Introduction. Pages 56 In Eastin, E. F., ed. Red Rice Research and Control. College Station, TX: Texas Agricultural Experiment Station Bull. B-1270.
Diarra, A., Smith, R. J., and Talbert, R. E. 1985. Growth and morphological characteristics of red rice (Oryza sativa) biotypes. Weed Sci. 3:310314.
Ellstrand, N. C., Prentice, H. C., and Hancock, J. F. 1999. Gene flow and introgression from domesticated plants into their wild relatives. Annu. Rev. Ecol. Syst. 30:539563.
Ge, S., Sang, T., Lu, B., and Hong, D. 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 96:1440014405.
Gizlice, Z., Carter, T. Jr., Gerig, T. M., and Burton, J. W. 1996. Genetic diversity patterns in North American public soybean cultivars based on coefficient of parentage. Crop Sci. 36:753765.
Johns, M. A., Skroch, P., Nienhuis, J., Hinrichsen, P., Bascur, G., and Munoz-Schick, C. 1997. Gene pool classification of common bean landraces from Chile based on RAPD and morphological data. Crop Sci. 37:605613.
Joshi, S. P., Gupta, V. S., Aggarwal, R. K., Ranjekar, P. K., and Brar, D. S. 2000. Genetic diversity and phylogenic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza . Theor. Appl. Genet. 100:13111320.
Khodayari, K., Smith, R. J., and Black, H. J. 1987. Red rice (Oryza sativa) control with herbicide treatments in soybeans (Glycine max). Weed Sci. 35:127129.
Khush, G. S. 1997. Origin, dispersal, cultivation and variation of rice. Plant Mol. Biol. 35:2534.
Kwon, S. L., Smith, R. J., and Talbert, R. E. 1991. Interference of red rice (Oryza sativa) densities in rice (O. sativa). Weed Sci. 39:169174.
Kwon, S. L., Smith, R. J., and Talbert, R. E. 1992. Comparative growth and development of red rice (Oryza sativa) and rice (O. sativa). Weed Sci. 40:5762.
Lago, A. 1982. Characterization of Red Rice (Oryza sativa L.) Phenotypes in Mississippi. Ph.D. dissertation. Mississippi State University, Mississippi State, MS. 143 p.
Langevin, S. A., Clay, K., and Grace, J. B. 1990. The incidence and effects of hybridization between cultivated rice and its related weed red rice (Oryza sativa L.). Evolution 44:10001008.
Li, R., Jiang, T. B., Xu, C. G., Li, X. H., and Wang, X. K. 2000. Relationship between morphological and genetic differentiation in rice (Oryza sativa L.). Euphytica 114:18.
Mackill, D. 1995. Classifying japonica rice cultivars with RAPD markers. Crop Sci. 35:889894.
Martin, C., Juliano, A., Newbury, H. J., Lu, B. R., Jackson, M. T., and Ford-Loyd, B. V. 1997. The use of RAPD markers to facilitate the identification of Oryza species within a germplasm collection. Genet. Res. Crop Evol. 44:175183.
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.
Noldin, J. A., Chandler, J. M., Kertchersid, M. L., and McCauley, G. N. 1999b. Red rice (Oryza sativa) biology. II. Ecotype sensitivity to herbicides. Weed Technol. 13:1924.
Oka, H. I. 1991. Genetic diversity of wild and cultivated rice. Pages 5581 In Khush, G. S. and Toenniessen, G. H., eds. Rice Biotechnology. Wallingford, UK: Biotechnology in Agriculture No. 6. IRRI/CAB Int.
Olufowote, J. O., Xu, Y., Chen, X., Park, W. D., Beachell, H. M., Dilday, R. H., Goto, M., and McCouch, S. R. 1997. Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. Genome 40:370378.
Parker, C. and Dean, M. L. 1976. Control of wild rice in rice. Pestic. Sci. 7:403416.
Parsons, B. J., Newbury, H. J., Jackson, M. T., and Ford-Loyd, B. V. 1997. Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types. Mol. Breed. 3:115125.
Sankula, S., Braverman, M. P., Jodari, F., Linscombe, S. D., and Oard, J. H. 1997. Evaluation of glufosinate on rice (Oryza sativa) transformed with the BAR gene and red rice (Oryza sativa). Weed Technol. 11:7075.
[SAS] Statistical Analysis Systems. 1997. SAS User's Guide Version 5. Version 6.12. Cary, NC: Statistical Analysis Systems Institute.
Shu, H. S., Sato, Y. I., and Morishima, H. 1997. Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes, and RAPD markers. Theor. Appl. Genet. 94:316321.
Skroch, P. W., Nienhuis, J., Beebe, S., Tohme, J., and Pedraza, F. 1998. Comparison of Mexican common bean (Phaseolus vulgaris L.) core and reserve germplasm collections. Crop Sci. 38:488496.
Stachel, M., Lelley, T., Grausgrubber, H., and Vollmann, J. 2000. Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. Theor. Appl. Genet. 100:242248.
Tanksley, S. D. and McCouch, S. R. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:10631066.
Temnykh, S., Park, W. D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Cho, Y. G., Ishii, T., and McCouch, S. R. 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100:697712.
Virk, P. S., Zhu, J., Newbury, H. J., Bryan, G. J., Jackson, M. T., and Ford-Lloyd, B. V. 2000. Effectiveness of different classes of molecular markers for classifying and revealing variation in rice (Oryza sativa) germplasm. Euphytica 112:275284.
Williams, C. E. and Ronald, P. C. 1994. PCR template-DNA isolated quickly from monocot and dicot leaves without tissue homogenization. Nucleic Acids Res. 22:19171918.
Xiao, J., Li, J., Grandillo, S., Ahn, S. N., Yuan, L., Tanksley, S. D., and McCouch, S. R. 1998. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon . Genetics 150:899909.
Zhu, J., Gale, M. D., Quarrie, S., Jackson, M. T., and Bryan, G. J. 1998. AFLP markers for the study of rice biodiversity. Theor. Appl. Genet. 96:602611.



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