Evolutionary genomics of weedy rice in the USA

Journal of Integrative Plant Biology

Volumn 49, Issue 6, 2007, Pages 811-816

  Olsen, Kenneth M ^a   Caicedo, Ana L ^b   Jia, Yulin ^c  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

^c USDA ARS Dale Bumpers National Rice Research Center   (United States)

Author keywords

Crop weed introgression; De domestication; Oryza sativa; Weed evolution; Weedy rice

Indexed keywords

COMPETITION (ECOLOGY); CROP PRODUCTION; CROP YIELD; CULTIVAR; GENETIC ANALYSIS; GENOMICS; HYBRIDIZATION; PHENOTYPE; RICE; WEED;

NORTH AMERICA; UNITED STATES;

JAPONICA; ORYZA; ORYZA RUFIPOGON; ORYZA SATIVA;

EID: 34347252658     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1744-7909.2007.00506.x     Document Type: Review

References (36)

1. Arrieta-Espinoza G, Sanchez E, Vargas S, Lobo J, Quesada T, Espinoza AM (2005). The weedy rice complex in Costa Rica. I. Morphological study of relationships between commercial rice varieties, wild Oryza relatives and weedy types. Genet. Res. Crop Evol. 52, 575-587.
2. Bres-Patry C, Bangratz M, Ghesquiere A (2001). Genetic diversity and population dynamics of weedy rice in Camargue area. Genet. Selection Evol. 33 (Suppl. 1), S425-S440.
3. Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL (2002). The cost of inbreeding i. Arabidopsis. Nature 416, 531-534.
4. Childs N (2005). Recap of the 2004/2005 U.S. Rice Market. In: Evans M, ed. Rice Situation and Outlook Yearbook. Economic Research Service, US Department of Agriculture, Published electronically (http://www.ers.usda.gov). pp. 43-73.
5. Cho YC, Chung TY, Suh, HS (1995). Genetic characteristics of Korean weedy rice (Oryza sativa L.) by RFLP analysis. Euphytica 86, 103-110.
6. Craigmiles JP (1978). Introduction. In: Eastin EF, ed. Rice Research and Control. Texas Agricultural Experiment Station Bulletin. State of Texas Publications Press, College Station, TX. pp. 5-6.
7. Ellstrand NC, Prentice HC, Hancock JF (1999). Gene flow and introgression from domesticated plants into their wild relatives. Annu. Rev. Ecol. Syst. 30, 539-563.
8. Estorninos LE, Gealy DR, Gbur EE, Talbert RE, McClelland MR (2005). Rice and red rice interference. II. Rice response to population densities of three red rice (Oryza sativa) ecotypes. Weed Sci. 53, 683-689.
9. Food and Agricultural Organization of the United Nations (2003). FAO statistical data (on-line). http://faostat.fao.org.
10. Fay JC, Wu CI (2000). Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413.
11. Federici MT, Vaughan D, Tomooka N, Kaga A, Wang XW, Doi K et al. (2001). Analysis of Uruguayan weedy rice genetic diversity using AFLP molecular markers. Electronic J. Biotechnol. 4, 131-145.
12. Ferrero A (2001). Biology and control of red rice (Oryza sativa L. var. sylvatica) infesting European fields. In: Chataigner J, ed. Medoyrzae-Interregional Cooperative Research Network on Rice in the Mediterranean Climate, Issue 9. FAO-CIHEAM-Institut Agronomique Mediterranéen, Montellier, France. pp. 2-4.
13. Gao H, Bustamante CD (2007). Instruct: A Bayesian clustering approach for joint inference of population structure and selfing rates from multi-locus genotype data. http://www.intl-pag.org/15/abstracts/ PAG15_W02_11.html.
14. Gealy DR (2005). Gene movement between rice (Oryza sativa) and weedy rice (Oryza sativa: A US Temperate Rice Perspective. In: Gressel J, ed. Crop Ferality and Volunteerism. CRC Press, Boca Raton. pp. 323-354.
15. Gealy DR, Tai TH, Sneller CH (2002). Identification of red rice, rice, and hybrid populations using microsatellite markers. Weed Sci. 50, 333-339.
16. Gealy DR, Yan W, Eizanga G, Moldenhauer K, Redus M (2004). Insights into the Parentage of Rice/Red Rice Crosses Using SSR Analysis of US Rice Cultivars and Red Rice Populations. Rice Technology Working Group 30. US Department of Agriculture, Beaumont, TX. pp. 179.
17. Goff SA, Ricke D, Lan TH, Presting G, Wang RL, Dunn M et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296, 92-100.
18. Hudson RR, Kreitman M, Aguade M (1987). A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-159.
19. Langevin, SA, Clay K, Grace JB (1990). The incidence and effects of hybridization between cultivated rice and its related weed red rice (Oryza sativa L.). Evolution 44, 1000-1008.
20. LingHwa T, Morishima H (1997). Genetic characterization of weedy rices and the inference on their origins. Breeding Sci. 47, 153-160.
21. Londo JP (2006). Genetic and Physiological Variation in Cultivated and Wild Rice: Domestication, Phylogeography, and Aluminum Stress Resistance. PhD thesis, Washington University, St Louis.
22. Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (2006). Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice. Oryza sativa. Proc. Natl. Acad. Sci. USA 103, 9578-9583.
23. Lu BR, Snow AA (2005). Gene flow from genetically modified rice and its environmental consequences. Bioscience 55, 669-678.
24. Lu H, Redus MA, Coburn JR, Rutger NA, McCouch SR, Tai TH (2005). Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis. Crop Sci. 45, 66-76.
25. Mackill DJ, McKenzie KS (2003). Origin and characteristics of US rice cultivars. In: Smith CW, ed. Rice: Origin, History, Technology, and Production. John Wiley & Sons, Hoboken, NJ. pp. 87-100.
26. McClung AM, Marchetti MA, Webb BD, Bollich CN (1998). Registration of Jasmine 85 rice. Crop Sci. 38, 896.
27. Moldenhauer KAK, Gibbons JH, McKenzie KS (2004). Rice varieties. In: Champagne ET, ed. Rice: Chemistry and Technology. American Association of Cereal Chemists, Inc., St Paul, MN. pp. 49-75.
28. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
29. Rajguru SN, Burgos NR, Shivrain VK, Stewart JM (2005). Mutations in the red rice ALS gene associated with resistance to imazethapyr. Weed Sci. 53, 567-577.
30. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA et al. (2002). Genetic structure of human populations. Science 298, 2381-2385.
31. Suh HS, Sato YI, Morishima H (1997). Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers. Theor. Appl. Genet. 94, 316-321.
32. Tajima F (1989a). Statistical method for testing the neutral mutation hypothesis by DNA. Genetics 123, 585-595.
33. Tajima F (1989b). The effect of change in population size on DNA polymorphism. Genetics 123, 597-601.
34. Vaughan LK, Ottis BV, Prazak-Havey AM, Bormans CA, Sneller C, Chandler JM et al. (2001). Is all red rice found in commercial rice reall. Oryza sativa? Weed Sci. 49, 468-476.
35. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y et al. (2002). A comprehensive rice transcript map containing 6591 expressed sequence tagged sites. Plant Cell 14, 525-535.
36. Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92.