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Molecular Mechanisms of Herbicide Resistance

Published online by Cambridge University Press:  20 January 2017

Christophe Délye ,
Arnaud Duhoux ,
Fanny Pernin ,
Chance W. Riggins  and
Patrick J. Tranel
Christophe Délye
Affiliation:
INRA, UMR1347 Agroécologie, F-21000 Dijon, France
Arnaud Duhoux
Affiliation:
INRA, UMR1347 Agroécologie, F-21000 Dijon, France
Fanny Pernin
Affiliation:
INRA, UMR1347 Agroécologie, F-21000 Dijon, France
Chance W. Riggins
Affiliation:
Department of Crop Sciences, University of Illinois, Urbana, IL 61801
Patrick J. Tranel*
Affiliation:
Department of Crop Sciences, University of Illinois, Urbana, IL 61801
*
Corresponding author's E-mail: tranel@illinois.edu
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Resistance to herbicides occurs in weeds as the result of evolutionary adaptation (Jasieniuk et al. 1996). Basically, two types of mechanisms are involved in resistance (Beckie and Tardif 2012; Délye 2013). Target-site resistance (TSR) is caused by changes in the tridimensional structure of the herbicide target protein that decrease herbicide binding, or by increased activity (e.g., due to increased expression or increased intrinsic activity) of the target protein. Nontarget-site resistance (NTSR) is endowed by any mechanism not belonging to TSR, e.g., reduction in herbicide uptake or translocation in the plant, or enhanced herbicide detoxification (reviewed in Délye 2013; Yuan et al. 2007).

Keywords

Allele-specific PCRdCAPSDNA sequencinggene expressionmutationPCRqPCR
Type
Weed Biology and Ecology
Information
Weed Science , Volume 63 , Issue SP1: Special Issue: Research Methods in Weed Science , February 2015 , pp. 91 - 115
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

Alarcón-Reverte, R, Hanley, S, Kaundun, SS, Karp, A, Moss, SR (2013) A SNaPshot assay for the rapid and simple detection of known point mutations conferring resistance to ACCase-inhibiting herbicides in Lolium spp. Weed Res 53:12–20Google Scholar
Andersen, L, Jensen, JL, Ørntoft, TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization applied to bladder and colon cancer data sets. Cancer Res 64:5245–5250Google Scholar
Beckie, HJ, Tardif, FJ (2012) Herbicide cross-resistance in weeds. Crop Prot 35:15–28Google Scholar
Bhargava, A, Shukla, S, Ohri, D (2006) Karyotypic studies on some cultivated and wild species of Chenopodium (Chenopodiaceae). Genet Resour Crop Evol 53:1309–1320Google Scholar
Bubner, B, Baldwin, IT (2004) Use of real-time PCR for determining copy number and zygosity in transgenic plants. Plant Cell Rep 23:263–271Google Scholar
Burgos, NR, Tranel, PJ, Streibig, JC, Davis, VM, Shaner, D, Norsworthy, JK, Ritz, C (2013) Review: confirmation of resistance to herbicides and evaluation of resistance levels. Weed Sci 61:4–20Google Scholar
Bustin, SA, Beaulieu, JF, Huggett, J, Jaggi, R, Kibenge, FSB, Olsvik, PA, Penning, LC, Toeggel, S (2010) MIQE precis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. BMC Mol Biol 11:74Google Scholar
Bustin, SA, Benes, V, Garson, JA, Hellemans, J, Huggett, J, Kubista, M, Mueller, R, Nolan, T, Pfaffl, MW, Shipley, GL, Vandesompele, J, Wittwer, CT (2009) The MIQE guidelines: minimum information for publication of quantitative realtime PCR experiments. Clin Chem 55:611–622Google Scholar
Chaves, AL, Vergara, CE, Mayer, JE (1995) Dichloromethane as an economic alternative to chloroform in the extraction of DNA from plant tissues. Plant Mol Biol Rep 13:18–25Google Scholar
Czechowski, T, Stitt, M, Altmann, T, Udvardi, MK, Scheible, WR (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis thaliana. Plant Physiol 139:5–17Google Scholar
Dayan, FE, Owens, DK, Corniani, N, Silva, FML, Watson, SB, Howell, J, Shaner, DL (2015) Biochemical markers and enzyme assays for herbicide mode of action and resistance studies. Weed Sci 63:23–63Google Scholar
Délye, C (2005) Weed resistance to acetyl coenzyme A carboxylase inhibitors: an update. Weed Sci 53:728–746Google Scholar
Délye, C (2013) Unravelling the genetic bases of non-target-site-based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade. Pest Manag Sci 69:176–187Google Scholar
Délye, C, Boucansaud, K (2008) A molecular assay for the proactive detection of target site-based resistance to herbicides inhibiting acetolactate synthase in Alopecurus myosuroides. Weed Res 48:97–101Google Scholar
Délye, C, Jasieniuk, M, Le Corre, V (2013) Deciphering the evolution of herbicide resistance in weeds. Trends Genet 29:649–658Google Scholar
Délye, C, Matéjicek, A, Gasquez, J (2002) PCR-based detection of resistance to acetyl-CoA carboxylase-inhibiting herbicides in black-grass (Alopecurus myosuroides Huds.) and ryegrass (Lolium rigidum Gaud.). Pest Manag Sci 58:474–478Google Scholar
Délye, C, Michel, S, Bérard, A, Chauvel, B, Brunel, D, Guillemin, JP, Dessaint, F, Le Corre, V (2010) Geographical variation in resistance to acetyl-coenzyme A carboxylase-inhibiting herbicides across the range of the arable weed Alopecurus myosuroides (blackgrass). New Phytol 186:1005–1017Google Scholar
Délye, C, Pernin, F, Michel, S (2011) ‘Universal’ PCR assays detecting mutations in acetyl-coenzyme A carboxylase or acetolactate-synthase that endow herbicide resistance in grass weeds. Weed Res 51:353–362Google Scholar
Dower, WJ, Miller, JF, Ragsdale, CW (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16:6127–6145Google Scholar
Doyle, JJ, Doyle, JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15Google Scholar
Duhoux, A, Délye, C (2013) Reference genes to study herbicide stress response in Lolium sp.: up-regulation of P450 genes in plants resistant to acetolactate-synthase inhibitors. PLOS ONE 8 10.1371/journal.pone.0063576Google Scholar
Gaines, T, Lorentz, L, Maiwald, F, Ott, MC, Perret, P, Yu, Q, Han, H, Busi, R, Strek, H, Beffa, R, Powles, S (2013) Identifying differential expression in non-target-site herbicide resistance genes in Lolium rigidum using high-throughput sequencing. Page 69in Global Herbicide Resistance Challenge. Perth, AustraliaAustralian Herbicide Resistance Initiative [Abstract]Google Scholar
Gaines, TA, Zhang, W, Wang, D, Bukun, B, Chisholm, ST, Shaner, DL, Nissen, SJ, Patzoldt, WL, Tranel, PJ, Culpepper, AS, Grey, TL, Webster, TM, Vencill, WK, Sammons, RD, Jiang, J, Preston, C, Leach, JE, Westra, P (2010) Gene amplification confers glyphosate resistance in Amaranthus palmeri. Proc Natl Acad Sci U S A 107:1029–1034Google Scholar
Gardin, J, Beffa, R, Gouzy, J, Carrère, S, Délye, C (2013) A transcriptomics-based approach enables the first identification of candidate genes involved in non-target-site-based resistance to herbicides in a grass weed (Alopecurus myosuroides). Page 68in Global Herbicide Resistance Challenge. Perth, AustraliaAustralian Herbicide Resistance Initiative [Abstract]Google Scholar
Huang, S, Sirikhachornkit, A, Faris, JD, Su, X, Gill, BS, Haselkorn, R, Gornicki, P (2002) Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses. Plant Mol Biol 48:805–820Google Scholar
Iwakami, S, Uchino, A, Watanabe, H, Yamasuea, Y, Inamura, T (2012) Isolation and expression of genes for acetolactate synthase and acetyl-CoA carboxylase in Echinochloa phyllopogon, a polyploid weed species. Pest Manag Sci 68:1098–1106Google Scholar
Jasieniuk, M, Brûlé-Babel, AL, Morrison, IN (1996) The evolution and genetics of herbicide resistance in weeds. Weed Sci 44:176–193Google Scholar
Kaundun, SS, Cleere, SM, Stanger, CP, Burbidge, JM, Windass, JD (2006) Real-time quantitative PCR assays for quantification of L1781 ACCase inhibitor resistance allele in leaf and seed pools of Lolium populations. Pest Manag Sci 62:1082–1091Google Scholar
Kaundun, SS, Dale, RP, Zelaya, IA, Dinelli, G, Marotti, I, McIndoe, E, Cairns, A (2011) A novel P106L mutation in EPSPS and an unknown mechanism(s) act additively to confer resistance to glyphosate in a South African Lolium rigidum population. J Agric Food Chem 59:3227–3233Google Scholar
Kaundun, SS, Windass, JD (2006) Derived cleaved amplified polymorphic sequence, a simple method to detect a key point mutation conferring acetyl CoA carboxylase inhibitor herbicide resistance in grass weeds. Weed Res 46:34–39Google Scholar
Kwok, S, Chang, SY, Sninsky, JJ, Wang, A (1994) A guide to the design and use of mismatched and degenerate primers. PCR Methods Appl 3:S39–S47Google Scholar
Livak, KJ, Schmittgen, TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt Method. Methods 25:402–408Google Scholar
Mallory-Smith, C, Hall, L, Burgos, N (2015) Experimental methods to study gene flow. Weed Sci 63:12–22Google Scholar
Martin, JA, Wang, Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682Google Scholar
Metzker, ML (2005) Emerging technologies in DNA sequencing. Genome Res 15:1767–1776Google Scholar
Neff, MM, Neff, JD, Chory, J, Pepper, AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387–392Google Scholar
Neff, MM, Turk, E, Kalishman, M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615Google Scholar
Ness, RW, Siol, M, Barrett, SCH (2011) De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC Genomics 12:298Google Scholar
Nolan, T, Hands, RE, Bustin, SA (2006) Quantification of mRNA using real-time RT-PCR. Nat Protoc 1:1559–1582Google Scholar
Ohtsuka, E, Matsuki, S, Ikehara, M, Takahashi, Y, Matsubara, K (1985) An alternative approach to deoxyoligonucleotides as hybridation probes by insertion of deoxyinosine at ambiguous codon positions. J Biol Chem 260:2605–2608Google Scholar
Ozsolak, F, Milos, PM (2010) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87–98Google Scholar
Petit, C, Pernin, F, Heydel, JM, Délye, C (2012) Validation of a set of reference genes to study response to herbicide stress in grasses. BMC Res Notes 5:18Google Scholar
Pettersson, M, Bylund, M, Alderborn, A (2003) Molecular haplotype determination using allele-specific PCR and pyrosequencing technology. Genomics 82:390–396Google Scholar
Pfaffl, MW (2001) A new mathematical model relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45Google Scholar
Pfaffl, MW, Horgan, GW, Dempfle, L (2002) Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30:e36Google Scholar
Pfaffl, MW, Tichopad, A, Prgomet, C, Neuvians, TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol Lett 26:509–515Google Scholar
Radstrom, P, Lofstrom, C, Lovenklev, M (2003) Strategies for overcoming PCR inhibition. Pages 149–161in Dieffenbach, CW, Dveksler, GS, eds. PCR Primer: A Laboratory Manual. Cold Spring HarborCold Spring Harbor Laboratory PressGoogle Scholar
Riggins, CW, Peng, Y, Stewart, CN Jr., Tranel, PJ (2010) Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest Manag Sci 66:1042–1052Google Scholar
Roux, KH (1995) Optimization and troubleshooting in PCR. Genome Res 4:S185–S194Google Scholar
Roux, KH (2009) Optimization and troubleshooting in PCR. Cold Spring Harbor Protoc 1–6, DOI:10.1101/pdb.ip66. http://cshprotocols.cshlp.org/content/2009/4/pdb.ip66. Accessed June 18, 2013Google Scholar
Salas, RA, Dayan, FE, Pan, Z, Watson, SB, Dickson, JW, Scott, RC, Burgos, NR (2012) EPSPS gene amplification in glyphosate-resistant Italian ryegrass (Lolium perenne ssp. multiflorum) from Arkansas. Pest Manag Sci 68:1223–1230Google Scholar
Sanger, F, Nicklen, S, Coulson, AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467Google Scholar
Scarabel, L, Locascio, A, Furini, A, Sattin, M, Varotto, S (2010) Characterisation of ALS genes in the polyploid species Schoenoplectus mucronatus and implications for resistance management. Pest Manag Sci 66:337–344Google Scholar
Sommer, SS, Groszbar, AR, Bottema, CDK (1992) PCR amplification of specific alleles (PASA) is a general method for rapidly detecting known single base-pair changes. Biotechniques 12:82–87Google Scholar
Southern, EM (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517Google Scholar
Thudi, M, Li, Y, Jackson, SA, May, GD, Varshney, RK (2012) Current state-of-art of sequencing technologies for plant genomics research. Brief Funct Genomics 2:3–11Google Scholar
Tindall, KR, Kunkel, TA (1988) Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27:6008–6013Google Scholar
Tranel, PJ, Riggins, CW, Bell, MS, Hager, AG (2011) Herbicide resistances in Amaranthus tuberculatus: a call for new options. J Agric Food Chem 59:5808–5812Google Scholar
Tranel, PJ, Wright, TR (2002) Resistance of weeds to ALS-inhibiting herbicides: what have we learned. Weed Sci 50:700–712Google Scholar
Vandesompele, J, De Preter, K, Pattyn, F, Poppe, B, Van Roy, N, De Paepe, A, Speleman, F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3 10.1186/gb-2002-3-7-research0034Google Scholar
Vigueira, CC, Olsen, KM, Caicedo, AL (2013) The red queen in the corn: agricultural weeds as models of rapid adaptive evolution. Heredity 110:303–311Google Scholar
Wagner, J, Haas, HU, Hurle, K (2002) Identification of ALS inhibitor-resistant Amaranthus biotypes using polymerase chain reaction amplification of specific alleles. Weed Res 42:280–286Google Scholar
Ward, JA, Ponnola, L, Weber, CA (2012) Strategies for transcriptome analysis in nonmodel plants. Am J Bot 99:267–276Google Scholar
Warwick, SI, Xu, R, Sauder, C, Beckie, HJ (2008) Acetolactate synthase target-site mutations and single nucleotide polymorphism genotyping in ALS-resistant kochia (Kochia scoparia). Weed Sci 56:797–806Google Scholar
Yu, Q, Ahmad-Hamdani, MS, Han, H, Christoffers, MJ, Powles, SB (2013) Herbicide resistance-endowing ACCase gene mutations in hexaploid wild oat (Avena fatua): insights into resistance evolution in a hexaploid species. Heredity 110:220–231Google Scholar
Yuan, JS, Tranel, PJ, Stewart, CN Jr. (2007) Non-target-site herbicide resistance: a family business. Trends Plant Sci 12:6–13Google Scholar