Potential model weeds to study genomics, ecology, and physiology in the 21st century

Weed Science

Volumn 53, Issue 6, 2005, Pages 929-937

  Chao, Wun S ^a   Horvath, Dave P ^a   Anderson, James V ^a   Foley, Michael E ^a  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Genomics; Model systems; Weed science; Weedy characteristics

Indexed keywords

GENE EXPRESSION; GENOMICS; MODELING; RESEARCH; WEED;

AEGILOPS CYLINDRICA; CIRSIUM ARVENSE; EUPHORBIA ESULA; SOLANUM NIGRUM; SOLANUM PTYCHANTHUM; SORGHUM HALEPENSE;

EID: 33748063645     PISSN: 00431745     EISSN: None     Source Type: Journal    
DOI: 10.1614/WS-04-213R.1     Document Type: Conference Paper

References (93)

1. Alonso-Blanco, C., L. Bentsink, C. J. Hanhart, H.B.E. Vries, and M. Koornneef. 2003. Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana. Genetics 164:711-729.
2. Anderson, G. L., C. W. Prosser, L. E. Wendel, E. S. Delfosse, and R. M. Faust. 2003. The Ecological Areawide Management (TEAM) of leafy spurge program of the United States Department of Agriculture-Agricultural Research Service. Pest Manag. Sci. 59:609-613.
3. Anderson, J. V., W. S. Chao, and D. P. Horvath. 2001. A current review on the regulation of dormancy in vegetative buds. Weed Sci. 49:581-589.
4. Anderson, J. V. and D. G. Davis. 2004. Abiotic stress alters transcript profiles and activity of enzymes involved in glutathione-metabolism in Euphorbia esula. Physiol. Plant. 120:421-433.
5. Anderson, J. V., M. Delseny, M. A. Fregene, et al. 2004. An EST resource for cassava and other species of Euphorbiaceae. Plant Mol. Biol. 56:527-539.
6. Anderson, J. V. and D. P. Horvath. 2001. Random sequencing of cDNAs and identification of mRNAs. Weed Sci. 49:590-597.
7. Anonymous. 2004. Aegilops cylindrical jointed goatgrass-Executive Summary of the National Jointed Goatgrass Research Program CSREES-USDA Special Grant. Available at http://www.jointedgoatgrass.org/.
8. Baker, H. G. 1974. The evolution of weeds. Annu. Rev. Ecol. Syst. 5:1-24.
9. Basu, C., M. D. Halfhill, T. C. Mueller, and C. N. Stewart. 2004. Weed genomics: new tools to understand weed biology. Trends Plant Sci. 9:391-398.
10. Bennett, M. D. and I. J. Leitch. 2003. Plant DNA C-values database. www.kew.org/cval.
11. Bennett, M. D., I. J. Leitch, and L. Hanson. 1998. DNA amounts in two samples of angiosperm weeds. Ann. Bot. 82:121-134.
12. Bishop, G. J. and C. Koncz. 2002. Brassinosteroids and plant steroid hormone signaling. Plant Cell 14:S97-S110.
13. Bowman, J. and Y. Eshed. 2000. Formation and maintenance of the shoot apical meristem. Trends Plant Sci. 5:110-115.
14. Bres-Patry, C., M. Lorieux, G. Clement, M. Bangratz, and A. Ghesquiere. 2001. Heredity and genetic mapping of domestication-related traits in a temperate japonica weedy rice. Theor. Appl. Genet. 102:118-126.
15. CAB International. 2004a. Sorghum halepense. In Crop Protection Compendium. 2004 ed. Wallingford, Great Britain: CAB International. [CD-ROM].
16. CAB International. 2004b. Euphorbia esula [original text by W. Chao and J. V. Anderson]. In Crop Protection Compendium. 2004 ed. Wallingford, Great Britain: CAB International. [CD-ROM].
17. Cai, H. W. and H. Morishima. 2000. Genomic regions affecting seed shattering and seed dormancy in rice. Theor. Appl. Genet. 100:840-846.
18. Chao, W. S. 2002. Contemporary methods to investigate dormancy. Weed Sci. 50:215-226.
19. Chen, L. J., D. S. Lee, Z. P. Song, H. S. Suh, and B. R. Lu. 2004. Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Ann. Bot. 93:67-73.
20. Chen, M. S., G. Presting, W. B. Barbazuk, et al. 2002. An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545.
21. Clark, S. E. 2001. Cell signaling at the shoot meristem. Nat. Rev. Mol. Cell Biol. 2:276-284.
22. Cooper, M. R. and A. W. Johnson. 1984. Poisonous plants in Britain and their effects on animals and man. London: Her Majesty's Stationery Office. 305 p.
23. Debeaujon, I., K. M. Léon-Kloosterziel, and M. Koornneef. 2000. Influence of the testa on seed dormancy, germination, and longevity in Arabidopsis. Plant Physiol. 122:403-413.
24. Debeaujon, I. and M. Koornneef. 2000. Gibberellin requirement for Arabidopsis seed germination is determined both by testa characteristics and embryonic abscisic acid. Plant Physiol. 122:415-424.
25. Defelice, M. S. 2003. The black nightshades, Solanum nigrum L. et al.-poison, poultice, and pie. Weed Technol. 17:421-427.
26. Diarra, A.R.J. and R. E. Talbert. 1985. Interference of red rice (Oryza sativa) with rice (O. sativa). Weed Sci. 33:644-649.
27. Donald, W. W. 1994. The biology of Canada thistle (Cirsium arvense). Rev. Weed Sci. 6:77-101.
28. Donald, W. W. and A. G. Ogg, Jr. 1991. Biology and control of jointed goatgrass (Aegilops cylindrica), a review. Weed Technol. 5:3-17.
29. Dugas, D. V. and B. Barrel. 2004. MicroRNA regulation of gene expression in plants. Curr. Opin. Plant Biol. 7:512-520.
30. Duke, S. O., S. R. Baerson, F. E. Dayan, et al. 2003. U.S. Department of Agriculture-Agricultural Research Service research on natural products for pest management. Pest Manag. Sci. 59:708-717.
31. Finkelstein, R. R., S.S.L. Gampala, and C. D. Rock. 2002. Abscisic acid signaling in seeds and seedlings. Plant Cell 14:515-45.
32. Foley, M. E. 2002. Weeds, seeds, and buds-opportunities and systems for dormancy investigations. Weed Sci. 50:267-272.
33. Footitt, S. and M. A. Cohn. 1995. Seed dormancy in red rice (Oryza sativa). IX. Embryo fructose-2,6-bisphosphate during dormancy breaking and subsequent germination. Plant Physiol. 107:1365-1370.
34. Forcella, F. 2003. U.S. Department of Agriculture-Agricultural Research Service research on pest biology: weeds. Pest Manag. Sci. 59:754-763.
35. Gealy, D. R., D. H. Mitten, and J. N. Rutger. 2003. Gene flow between red rice (Oryza sativa) and herbicide-resistant rice (O-sativa): implications for weed management. Weed Technol. 17:627-645.
36. Gibson, S. I. 2004. Sugar and phytohormone response pathways: navigating a signaling network. J. Exp. Bot. 55:253-264.
37. Goff, S. A., D. Ricke, T.-H. Lan, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100.
38. Gu, X.-Y., S. F. Kianian, and M. E. Foley. 2004. Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics 166:1503-1516.
39. Gu, X.-Y., S. F. Kianian, and M. E. Foley. 2005. Seed dormancy imposed by covering tissues interrelates to shattering and seed morphological characteristics in weedy rice. Crop Sci. 45:948-955.
40. Hartzler, R. G. 2003. Waterhemp-the perfect weed? www.weeds.iastate. edu/mgmt/2003/symposium.shtml. WSSA-North American Weed Management Association Invasive Plant Species Workshop, Kansas City, MO. Feb. 12-13.
41. Hartzler, R. G., B. A. Battles, and D. Nordby. 2004. Effect of common waterhemp (Amaranthus rudis) emergence date on growth and fecundity in soybean. Weed Sci. 52:242-245.
42. Heap, I. 2004. The International Survey of Herbicide Resistant Weeds. www.weedscience.com.
43. Holm, G. L., D. L. Plucknett, J. V. Pancho, and J. P. Herburger. 1977. The World's Worst Weeds: Distribution and Biology. Honolulu, HI: Hawaii University Press.
44. Holm, L. 1969. Weed problems in developing countries. Weed Sci. 17:113-118.
45. Holm, L. G., D. L. Plucknett, J. V. Pancho, and J. P. Herberger. 1991. The World's Worst Weeds: Distribution and Biology. Malabar, FL: Krieger. 609 p.
46. Horak, M. J. and T. M. Loughin. 2000. Growth analysis of four Amaranthus species. Weed Sci. 48:347-355.
47. Horvath, D. P., J. V. Anderson, W. S. Chao, and M. E. Foley. 2003. Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci. 8:534-540.
48. Horvath, D. P. and R. Schaffer. 2003. Urg1, a conserved and previously uncharacterized gene expressed preferentially in growing shoots of Arabidopsis and leafy spurge. Appl. Genomics Proteomics 2:169-179.
49. Hu, F. Y., D. Y. Tao, E. Sacks, et al. 2003. Convergent evolution of perenniality in rice and sorghum. Proc. Natl. Acad. Sci. USA 100:4050-4054.
50. Ishimaru, K., M. Yano, N. Aoki, K. Ono, T. Hirose, S. Y. Lin, L. Monna, T. Sasaki, and R. Ohsugi. 2001. Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. Theor. Appl. Genet. 102:793-800.
51. Jander, G., S. R. Baerson, J. A. Hudak, K. A. Gonzalez, K. J. Gruys, and R. L. Last. 2003. Ethylmethanesulfonate saturation mutagenesis in Arabidopsis to determine frequency of herbicide resistance. Plant Physiol. 131:139-146.
52. Jeschke, M. R., P. J. Tranel, and A. L. Rayburn. 2003. DNA content analysis of smooth pigweed (Amaranthus hybridus) and tall waterhemp (A. tuberculatus): implications for hybrid detection. Weed Sci. 51:1-3.
53. Jia, Y., Y.-Q. Gu, D. P. Horvath, J. V. Anderson, and W. S. Chao. 2005. Subtractive hybridization as a tool for genes involved in dormancy and growth in underground adventitious buds of leafy spurge (Euphorbia esula). Annual Meeting of the Weed Science Society of America. Honolulu, HI. Feb. 7-10.
54. Jordon-Thaden, I. E. and S. M. Louda. 2003. Chemistry of Cirsium and Carduus: a role in ecological risk assessment for biological control of weeds? Biochem. Syst. Ecol. 31:1353-1396.
55. Koornneef, M., L. Bentsink, and H. Hilhorst. 2002. Seed dormancy and germination. Curr. Opin. Plant Biol. 5:33-36.
56. Lampe, K. F. and M. A. McCann. 1985. AMA Handbook of Poisonous and Injurious Plants. Chicago: American Medical Association. 432 p.
57. Leguizamon, E. S. 1986. Seed survival and patterns of seedling emergence in Sorghum halepense (L.) Pers. Weed Res. 26:397-403.
58. Leon, P. and J. Sheen. 2003. Sugar and hormone connections. Trends Plant Sci. 8:110-116.
59. Leon, R. G. and M.D.K. Owen. 2003. Regulation of weed seed dormancy through light and temperature interactions. Weed Sci. 51:752-758.
60. Leopold, A. C., R. Glenister, and M. A. Cohn. 1988. Relationship between water content and afterripening in red rice. Physiol. Plant. 74:659-662.
61. Louda, S. M., D. Kendall, J. Connor, and D. Simberloff. 1997. Ecological effects of an insect introduced for the biological control of weeds. Science 277:1088-1090.
62. Lym, R. G., S. J. Nissen, M. L. Rowe, D. J. Lee, and R. A. Masters. 1996. Leafy spurge (Euphorbia esula) genotype affects gall midge (Spurgia esulae) establishment. Weed Sci. 44:629-633.
63. Madsen, S. B. 1962. Germination of buried and dry stored seeds III, 1934-1960. Proc. Int. Seed Testing Assoc. 27:920-928.
64. Meyerowitz, E. M. 2001. Prehistory and history of Arabidopsis research. Plant Physiol. 125:15-19.
65. Meyerowitz, E. M. and R. E. Pruitt. 1985. Arabidopsis thaliana and plant molecular genetics. Science 229:1214-1218.
66. Meyers, B. C., D. W. Galbraith, T. Nelson, and V. Agrawal. 2004. Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol. 135:637-652.
67. Minorsky, P. V. 2003. Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol. 132:404-409.
68. Monaghan, N. 1979. The biology of johnsongrass (Sorghum halepense). Weed Res. 19:261-267.
69. Moore, R. J. 1975. The biology of Canadian weeds. 13. Cirsium arvense (L.) Scop. Can. J. Plant Sci. 55:1033-1048.
70. Nishimura, C. C., Y. Ohashi, S. Sato, T. Kato, S. Tabata, and C. Ueguchia. 2004. Histidine kinase homologs that act as cytokinin receptors possess overlapping functions in the regulation of shoot and root growth in Arabidopsis. Plant Cell 16:1365-1377.
71. Nordby, D. E. and R. G. Hartzler. 2004. Influence of corn on common waterhemp (Amaranthus rudis) growth and fecundity. Weed Sci. 52:255-259.
72. Ogg, A. G., B. S. Rogers, and E. E. Schilling. 1981. Characterization of black nightshade (Solanum nigrum) and related species in the United States. Weed Sci. 29:27-32.
73. Paterson, A. H., K. F. Schertz, Y.-R. Lin, S.-C. Liu, and Y.-L. Chang. 1995. The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers. Proc. Natl. Acad. Sci. USA 92:6127-6131.
74. Pratt, D. B. and L. G. Clark. 2001. Amaranthus rudis and A. tuberculatus-one species or two? J. Torrey Bot. Soc. 128:282-296.
75. Rensink, W. A. and C. R. Buell. 2004. Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiol. 135:622-629.
76. Richards, D. E., K. E. King, T. Ait-ali, and N. P. Harberd. 2001. How gibberellin regulates plant growth and development: a molecular genetic analysis of gibberellin signaling. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52:67-88.
77. Roux, F., J. Gasquez, and X. Reboud. 2004. The dominance of the herbicide resistance cost in several Arabidopsis thaliana mutant lines. Genetics 166:449-460.
78. Sauer, J. D. 1955. Revision of the dioecious amaranths. Madroño 13:5-46.
79. Schulz-Schaeffer, J. and S. Gerhardt. 1987. Cytotaxonomic analysis of the Euphorbia spp. ("leafy spurge") complex. Biol. Zentbl. 106:429-438.
80. Schulz-Schaeffer, J. and S. Gerhardt. 1989. Cytotaxonomic analysis of the Euphorbia spp. ("leafy spurge") complex. II. Comparative study of the chromosome morphology. Biol. Zentbl. 108:69-76.
81. Seefeldt, S. S., R. Zemetra, F. L. Young, and S. S. Jones. 1998. Production of herbicide-resistant jointed goatgrass (Aegilops cylindrica) × wheat (Triticum aestivum) hybrids in the field by natural hybridization. Weed Sci. 46:632-634.
82. Seibert, A. C. and R. B. Pearce. 1993. Growth analysis of weed and crop species with reference to seed weight. Weed Sci. 41:52-56.
83. Skinner, D. L., A. H. Paterson, W. K. Vencill, and H. Ma. 2003. Cloning and characterization of rhizome-specific genes. Poster 443, Plant and Animal Genomes XI Conference. January 11-15, 2003. Town & Country Convention Center, San Diego, CA. http://www.intl-pag.org/11/abstracts/P5d_P443_XI.html.
84. Skinner, K., L. Smith, and P. Rice. 2000. Using noxious weed lists to prioritize targets for developing weed management strategies. Weed. Sci. 48:640-644.
85. Steber, C. M. and P. McCourt. 2001. A role for brassinosteroids in germination in Arabidopsis. Plant Physiol. 125:763-769.
86. Temnykh, S., G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. McCouch. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11:1441-1452.
87. Turner, J. G., C. Ellis, and A. Devoto. 2002. The jasmonate signal pathway. Plant Cell 14:5153-164.
88. Wang, K. L.-C., H. Li, and J. R. Ecker. 2002. Ethylene biosynthesis and signaling networks. Plant Cell 14:5131-151.
89. Weinig, C., J. R. Stinchcombe, and J. Schmitt. 2003. Evolutionary genetics of resistance and tolerance to natural herbivory in Arabidopsis thaliana. Evol. Int. J. Org. Evol. 57:1270-1280.
90. Westbrooks, R. L. 1998. Invasive plants, changing the landscape of America: fact Book. Federal Interagency Committee for the Management of Noxious and Exotic Weeds (FICMNEW). Washington, D.C. Pp. 4-5, 16-17.
91. Wu, J. Z., T. Maehara, T. Shimokawa, et al. 2002. A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14:525-535.
92. Yu, J., S. N. Hu, J. Wang, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92.
93. Zemetra, R. S., J. Hansen, and C. A. Mallory-Smith. 1998. Potential for gene transfer between wheat (Triticum aestivum) and jointed goatgrass (Aegilops cylindrical. Weed Sci. 46:313-317.