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Evolution of Weediness and Invasiveness: Charting the Course for Weed Genomics

Published online by Cambridge University Press:  20 January 2017

C. Neal Stewart Jr. ,
Patrick J. Tranel ,
David P. Horvath ,
James V. Anderson ,
Loren H. Rieseberg ,
James H. Westwood ,
Carol A. Mallory-Smith ,
Maria L. Zapiola  and
Katrina M. Dlugosch
C. Neal Stewart Jr.*
Affiliation:
Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996
Patrick J. Tranel
Affiliation:
Department of Crop Sciences, University of Illinois, Urbana, IL 61801
David P. Horvath
Affiliation:
U.S. Department of Agriculture–Agricultural Research Service, Fargo, ND 58105
James V. Anderson
Affiliation:
U.S. Department of Agriculture–Agricultural Research Service, Fargo, ND 58105
Loren H. Rieseberg
Affiliation:
Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
James H. Westwood
Affiliation:
Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061
Carol A. Mallory-Smith
Affiliation:
Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
Maria L. Zapiola
Affiliation:
Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
Katrina M. Dlugosch
Affiliation:
Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
*
Corresponding author's E-mail: nealstewart@utk.edu
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Abstract

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The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but no Arabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources.

Keywords

BioinformaticsDNA sequencinggene expressiongenetic transformationgenomicssystems biologyweed biology
Type
Physiology, Chemistry, and Biochemistry
Information
Weed Science , Volume 57 , Issue 5 , October 2009 , pp. 451 - 462
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
Copyright © Weed Science Society of America

References

Literature Cited

Anderson, J. V. 2008. Emerging technologies: an opportunity for weed biology research. Weed Sci. 56:281–282.Google Scholar
Anderson, J. V., Delseny, M., Fregene, M. A., et al. 2004. An EST resource for cassava and other species of Euphorbiaceae. Plant Mol. Biol. 56:527–539.Google Scholar
Anderson, J. V., Horvath, D. P., Chao, W. S., et al. 2007. Characterization of an EST database for the perennial weed leafy spurge: an important resource for weed biology research. Weed Sci. 55:193–203.Google Scholar
Baker, H. G. 1974. The evolution of weeds. Annu. Rev. Ecol. Syst. 5:1–24.Google Scholar
Barker, M. S., Kane, N. C., Kozik, A., Michelmore, R. W., Matvienko, M., Knapp, S. J., and Rieseberg, L. H. 2008. Multiple paleopolyploidizations during the evolution of the Asteraceae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25:2445–2455.Google Scholar
Barbazuk, W. B., Bedell, J. A., and Rabinowicz, P. D. 2005. Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays. 27:839–848.Google Scholar
Barrett, S. C. H., Colautti, R. I., and Eckert, C. G. 2008. Plant reproductive systems and evolution during biological invasion. Mol. Ecol. 17:373–383.Google Scholar
Barrett, S. C. H. 1983. Crop mimicry in weeds. Econ. Bot. 37:255–282.Google Scholar
Basu, C., Halfhill, M. D., Mueller, T. C., and Stewart, C. N. Jr. 2004. Weed genomics: new tools to understand weed biology. Trends Plant Sci. 9:391–398.Google Scholar
Bennett, M. D. and Leitch, I. J. 2003. Plant DNA C-values database. www.kew.org/cval.Google Scholar
Blödner, C., Goebel, C., Feussner, I., Gatz, C., and Polle, A. 2007. Warm and cold parental reproductive environments affect seed properties, fitness, and cold responsiveness in Arabidopsis thaliana progenies. Plant Cell Environ. 30:165–175.Google Scholar
Bodo Slotta, T. A. 2008. What we know about weeds: insights from genetic markers. Weed Sci. 56:322–326.Google Scholar
Bossard, C. C., Randall, J. M., and Hoshovsky, M. C. 2000. Invasive plants of California's wildlands. Berkeley, CA University of California Press, Berkeley. 360.Google Scholar
Broz, A. K., Broeckling, C. D., He, J., Dai, X., Zhao, P. X., and Vivanco, J. M. 2007. A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa . BMC Plant Biol. 7:25. http://www.biomedcentral.com/1471-2229/7/25.Google Scholar
Chao, W. S. 2008. Real-time PCR as a tool to study weed biology. Weed Sci. 56:290–296.Google Scholar
Chao, W. S., Horvath, D. P., Anderson, J. V., and Foley, M. P. 2005. Potential model weeds to study genomics, ecology, and physiology in the 21st century. Weed Sci. 53:929–937.Google Scholar
Charmet, G., Balfourier, F., and Chatard, V. 1996. Taxonomic relationships and interspecific hybridization in the genus Lolium (grasses). Genet. Resour. Crop Evol. 43:319–327.Google Scholar
Church, S. A., Livingstone, K., Lai, Z., Kozik, A., Knapp, S. J., Michelmore, R. W., and Rieseberg, L. H. 2007. Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for EST sequences. J. Mol. Evol. 64:171–180.Google Scholar
Ciannamea, S., Busscher-Lange, J., de Folter, S., Angenent, G. C., and Immink, R. G. H. 2006. Characterization of the vernalization response in Lolium perenne by a cDNA microarray approach. Plant Cell Physiol. 47:481–492.Google Scholar
Devine, M. D. and Shukla, A. 2000. Altered target sites as a mechanism of herbicide resistance. Crop Prot. 19:881–889.Google Scholar
Dlugosch, K. M. and Whitton, J. 2008. Can we stop transgenes from taking a walk on the wild side? Mol. Ecol. 17:1167–1169.Google Scholar
Eckes, P., van Almsick, C., and Weidler, M. 2004. Gene expression profiling, a revolutionary tool in Bayer CropScience herbicide discovery. Pflanzenschutz-Nachr. Bayer. 57:62–77.Google Scholar
Ellstrand, N. C. and Schierenbeck, K. A. 2000. Hybridization as a stimulus for the evolution of invasiveness in plants? Proc. Natl. Acad. Sci. U.S.A. 97:7043–7050.Google Scholar
Emberton, J., Ma, J. X., Yuan, Y. N., SanMiguel, P., and Bennetzen, J. L. 2005. Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res. 15:1441–1446.Google Scholar
Evans, G. M., Rees, H., Snell, C. L., and Sun, S. 1972. The relation between nuclear DNA amount and the duration of the mitotic cycle. Chromosomes Today. 3:24–31.Google Scholar
Gardner, S. N., Gressel, J., and Mangel, M. 1998. A revolving dose strategy to delay the evolution of both quantitative vs. major monogene resistances to pesticides and drugs. Int. J. Pest Manag. 44:161–180.Google Scholar
Gressel, J. 2002. Molecular Biology of Weed Control. New York Taylor and Francis. 504.Google Scholar
Gressel, J. 2008. Genetic Glass Ceilings. Baltimore The Johns Hopkins University Press. 348.Google Scholar
Grime, J. P. 1977. Evidence for the existence of three primary strategies in plants and its relevance to ecological and evolutionary theory. Am. Nat. 111:1169–1194.Google Scholar
Halfhill, M. D., Good, L. L., Basu, C., Burris, J., Main, C. L., Mueller, T. C., and Stewart, C. N. Jr. 2007. Transformation and segregation of GFP fluorescence and glyphosate resistance in horseweed (Conyza canadensis) hybrids. Plant Cell Rep. 26:303–311.Google Scholar
Heimann, B. and Cussans, G. W. 1996. The importance of seeds and sexual reproduction in the population biology of Cirsium arvense—a literature review. Weed Res. (Oxf.) 36:493–503.Google Scholar
Hieter, P. and Boguski, M. 1997. Functional genomics: it's all how you read it. Science. 278:601–602.Google Scholar
Holm, L., Doll, J., Holm, E., Pancho, J. V., and Herberger, J. P. 1997. World Weeds: Natural Histories and Distribution. New York John Wiley and Sons. 1152.Google Scholar
Horvath, D. P. and Clay, S. 2007. Heterologous hybridization of cotton (Gossypium hirsutum) microarrays with velvetleaf (Abutilon theophrasti) reveals physiological responses due to corn competition. Weed Sci. 55:546–557.Google Scholar
Horvath, D. P., Anderson, J. V., Soto-Suárez, M., and Chao, W. S. 2006a. Transcriptome analysis of leafy spurge (Euphorbia esula) crown buds during shifts in well-defined phases of dormancy. Weed Sci. 54:821–827.Google Scholar
Horvath, D. P., Chao, W. S., Suttle, J. C., Thimmipuram, J., and Anderson, J. V. 2008. Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.). BMC Genomics. 9:536.Google Scholar
Horvath, D. P., Gulden, R., and Clay, S. A. 2006b. Microarray analysis of late-season velvetleaf (Abutilon theophrasti) effect on corn. Weed Sci. 54:983–994.Google Scholar
Horvath, D. P., Schaffer, R., and Wisman, E. 2003. Identification of genes induced in emerging tillers of wild oat (Avena fatua) using Arabidopsis microarrays. Weed Sci. 51:503–508.Google Scholar
Hudson, R. R., Kreitman, M., and Aguade, M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics. 116:153–159.Google Scholar
Inderjit, R. M., Callaway, R., and Vivanco, J. M. 2006. Plant biochemistry helps to understand invasion ecology. Trends Plant Sci. 11:574–580.Google Scholar
Jofre-Garfias, A. E., Villegas-Sepúlveda, N., Cabrera-Ponce, J. L., Adame-Alvarez, R. M., Herrera-Estrella, L., and Simpson, J. 1997. Agrobacterium-mediated transformation of Amaranthus hypochondriacus: light- and tissue-specific expression of a pea chlorophyll a/b-binding protein promoter. Plant Cell Rep. 16:847–852.Google Scholar
Johnsen, Ø, Fossdal, C. G., Nagy, N., Mølmann, J., Daehlen, O. G., and Skrøppa, T. 2005. Climatic adaptation in Picea abies progenies is affected by the temperature during zygotic embryogenesis and seed maturation. Plant Cell Environ. 28:1090–1102.Google Scholar
Kane, N. C. and Rieseberg, L. H. 2007. Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus . Genetics. 175:1803–1812.Google Scholar
Kane, N. C. and Rieseberg, L. H. 2008. Genetics and evolution of weedy Helianthus annuus populations: evidence of multiple origins of an agricultural weed. Mol. Ecol. 7:384–394.Google Scholar
Karrenberg, S. and Widmer, A. 2008. Ecologically relevant genetic variation from a non-Arabidopsis perspective. Curr. Opin. Plant Biol. 11:156–162.Google Scholar
Kim, M., Cui, M-L., Cubas, P., Gillies, A., Lee, K., Chapman, M. A., Abbott, R. J., and Coen, E. 2008. Regulatory genes control a key morphological and ecological trait transferred between species. Science. 322:1116–1119.Google Scholar
Lai, Z., Gross, B. L., Zou, Y., Andrews, J., and Rieseberg, L. H. 2006. Microarray analysis reveals differential gene expression in hybrid sunflower species. Mol. Ecol. 15:1213–1227.Google Scholar
Lai, Z., Kane, N. C., Zou, Y., and Rieseberg, L. H. 2008. Natural variation in gene expression between wild and weedy populations of Helianthus annuus . Genetics. 179:1881–1890.Google Scholar
Landry, C. R., Lemos, B., Rifkin, S. A., Dickinson, W. J., and Hartl, D. K. 2007. Genetic properties influencing the evolvability of gene expression. Science. 317:118–121.Google Scholar
Larrinua, I. M. and Belmar, S. B. 2008. Bioinformatics and its relevance to weed science. Weed Sci. 56:297–305.Google Scholar
Lee, R. M. and Tranel, P. T. 2008. Utilization of DNA microarrays in weed science research. Weed Sci. 56:283–289.Google Scholar
Lein, W., Börnke, F., Reindl, A., Ehrhardt, T., Stitt, M., and Sonnewald, U. 2004. Target-based discovery of novel herbicides. Curr. Opin. Plant Biol. 7:219–225.Google Scholar
Liu, X. S. 2007. Getting started in tiling microarray analysis. PLoS Comput. Biol. 3:e183.Google Scholar
Lokko, Y., Anderson, J. V., Rudd, S., et al. 2007. Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. Plant Cell Rep. 26:1605–1618.Google Scholar
Mallory-Smith, C. and Zapiola, M. 2008. Gene flow from glyphosate-resistant crops. Pest. Manag. Sci. 64:428–440.Google Scholar
Malone-Schonenberg, J., Scelonge, C. J., Burrus, M., and Bidney, D. L. 1994. Stable transformation of sunflower using Agrobacterium and split embryonic axis explants. Plant Sci. 103:199–207.Google Scholar
Mardis, E. R. 2008. The impact of next-generation sequencing technology on genetics. Trends Genet. 24:133–141.Google Scholar
McDonald, J. H. and Kreitman, M. 1991. Adaptive protein evolution at the Adh locus in Drosophila . Nature. 351:652–654.Google Scholar
Michelmore, R., Marsh, E., Seely, S., and Landry, B. 1987. Transformation of lettuce Lactuca sativa mediated by Agrobacterium tumefaciens . Plant Cell Rep. 6:439–42.Google Scholar
Narumi, T., Aida, R., Ohmiya, A., and Satoh, S. 2005. Transformation of chrysanthemum with mutated ethylene receptor genes: mDG-ERS1 transgenes conferring reduced ethylene sensitivity and characterization of the transformants. Postharvest Biol. Technol. 37:101–110.Google Scholar
Neale, D. B. and Ingvarsson, P. K. 2008. Population, quantitative and comparative genomics of adaptation in forest trees. Curr. Opin. Plant Biol. 11:149–155.Google Scholar
Patzoldt, W. L., Tranel, P. J., and Hager, A. G. 2005. A waterhemp (Amaranthus tuberculatus) biotype with multiple resistance across three herbicide sites of action. Weed Sci. 53:30–36.Google Scholar
Pimentel, D., Zuniga, R., and Morrison, D. 2005. Update on the environmental and economic costs associated with alien-invasive species in the United States. Ecol. Econ. 52:273–288.Google Scholar
Prentis, P. J., Wilson, J. R. U., Dormontt, E. E., Richardson, D. M., and Lowe, A. J. 2008. Adaptive evolution in invasive species. Trends Plant Sci. 13:288–294.Google Scholar
Raghavan, C., Ong, E. K., Dalling, M., and Stevenson, T. W. 2005. Effect of herbicidal application of 2,4-dichlorophenoxyacetic acid in Arabidopsis . Funct. Integr. Genomics. 5:4–17.Google Scholar
Raghavan, C., Ong, E. K., Dalling, M., and Stevenson, T. W. 2006. Regulation of genes associated with auxin, ethylene and ABA pathways by 2,4-dichlorophenoxyacetic acid in Arabidopsis . Funct. Integr. Genomics. 6:60–70.Google Scholar
Rayburn, A. L., McLoskey, R., Jeschke, T. C., and Tranel, P. J. 2005. Genome size analysis of weedy Amaranthus species. Crop Sci. 45:2557–2562.Google Scholar
Renn, S. C., Aubin-Horth, N., and Hofmann, H. A. 2004. Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics. 5:42.Google Scholar
Sawbridge, T., Ong, E., Binnion, C., et al. 2003. Generation and analysis of expressed sequence tags in perennial ryegrass (Lolium perenne L.). Plant Sci. 165:1089–1100.Google Scholar
Shendure, J. 2008. The beginning of the end for microarrays. Nat. Methods. 5:585–587.Google Scholar
Stevens, P. F. 2007. Angiosperm Phylogeny. Version 8. http://www.mobot.org/MOBOT/research/APweb/. Accessed: January 13, 2008.Google Scholar
Stewart, C. N. Jr. 2009. Weedy and Invasive Plant Genomics. Ames, IA Blackwell Scientific. 254 p.Google Scholar
Stinchcombe, J. R. and Hoekstra, H. E. 2008. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity. 100:158–179.Google Scholar
Taji, T., Seki, M., Satou, M., et al. 2004. Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiol. 135:1697–1709.Google Scholar
Tajima, F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics. 123:85–595.Google Scholar
Tatematsu, K., Ward, S., Leyser, O., Kamiya, Y., and Nambara, E. 2005. Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol. 138:757–766.Google Scholar
Thomas, M. A. and Klaper, R. 2004. Genomics for the ecological toolbox. Trends Ecol. Evol. 19:439–445.Google Scholar
Tranel, P. J. and Trucco, F. The Amaranthus complex: a model for weed genomics. In Stewart, C. N. Jr. Weedy and Invasive Plant Genomics. Ames, IA Blackwell. In press.Google Scholar
Tranel, P. J. and Wright, T. R. 2002. Resistance of weeds to ALS-inhibiting herbicides: what have we learned? Weed Sci. 50:700–712.Google Scholar
VanGessel, M. J. 2001. Glyphosate-resistant horseweed from Delaware. Weed Sci. 49:703–705.Google Scholar
Warwick, S. I. and Stewart, C. N. Jr. 2005. Crops come from wild plants: How domestication, transgenes, and linkage effects shape ferality. Pages 9–30. In Gressel, J. Crop Ferality and Volunteerism. Boca Raton, Florida CRC.Google Scholar
Weiss-Schneeweiss, H., Greilhuber, J., and Schneeweiss, G. M. 2005. Genome size evolution in holoparasitic Orobanche (Orobanchaceae) and related genera. Am. J. Bot. 93:148–156.Google Scholar
Whitelaw, C. A., Barbazuk, W. B., Pertea, G., et al. 2003. Enrichment of gene-coding sequences in maize by genome filtration. Science. 302:2118–2120.Google Scholar
Whitney, K. D., Randell, R. A., and Rieseberg, L. H. 2006. Adaptive introgression of herbivore resistance traits in the weedy sunflower Helianthus annuus . Am. Nat. 167:794–707.Google Scholar
Wiehe, T., Nolte, V., Zivkovic, D., and Schlotterer, C. 2007. Identification of selective sweeps using a dynamically adjusted number of linked microsatellites. Genetics. 175:207–218.Google Scholar
Wood, H. M., Grahame, J. W., Humphray, S., Rogers, J., and Butlin, R. K. 2008. Sequence differentiation in regions identified by a genome scan for local adaptation. Mol. Ecol. 17:3123–3135.Google Scholar
Wright, S. I. and Gaut, B. S. 2005. Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22:506–519.Google Scholar
[WSSA] Weed Science Society of America 2008. Charting the course for weed genomics: the evolution of weediness. WSSA Annual Meeting, February 4–7, 2008, Chicago, Illinois.Google Scholar
Wu, C. A., Lowry, D. B., Cooley, A. M., Wright, K. M., Lee, Y. W., and Willis, J. H. 2008. Mimulus is an emerging model system for the integration of ecological and genomic studies. Heredity. 100:220–230.Google Scholar
Wu, Y-Y., Chen, Q-J., Chen, M., Chen, J., and Wang, X-C. 2005. Salt-tolerant transgenic perennial ryegrass (Lolium perenne L.) obtained by Agrobacterium tumefaciens-mediated transformation of the vacuolar Na+/H+ antiporter gene. Plant Sci. 169:65–73.Google Scholar
Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568–573.Google Scholar
Yu, J., Hu, S., Wang, J., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 296:79–92.Google Scholar
Yuan, J. S., Galbraith, S. Y., Dai, S. Y., Griffin, P., and Stewart, C. N. Jr. 2008. Plant systems biology comes of age. Trends Plant Sci. 13:165–171.Google Scholar
Yuan, J. S., Reed, A., Chen, F., and Stewart, C. N. Jr. 2006. Statistical analysis of real-time PCR data. BMC Bioinformatics. 7:85.Google Scholar
Yuan, J. S., Tranel, P. J., and Stewart, C. N. Jr. 2007. Non-target herbicide resistance: a family business. Trends Plant Sci. 12:6–13.Google Scholar
Zayed, A. and Whitfield, C. W. 2008. A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera . Proc. Natl. Acad. Sci. U.S.A. 105:3421–3426.Google Scholar