The occurrence of glyphosate-resistant weeds has been reported after more than 20 yr of extensive use. Rigid ryegrass that evolved resistance to glyphosate was found in Australia and in California. Glyphosate-resistant rigid ryegrass plants were collected from northern California and selected through generations 8 and 5 to segregate the most resistant (R) and sensitive (S) biotypes. The eighth generation of R and the fifth generation of S biotypes survived 6.72 and died from 0.11 kg ae ha⁻¹ glyphosate, respectively. The objectives of this study were to evaluate the role of metabolism in the observed resistance, to study the effect of glyphosate on the activity of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), and to characterize the EPSPS gene in R and S rigid ryegrass. Neither quantitative nor qualitative difference was observed in the metabolism of ¹⁴C-glyphosate between the biotypes. Activity of constitutive EPSPS decreased more significantly in the S than R biotype in the presence of 5, 50, 500, and 5,000 µM glyphosate. Inhibition of 50% (I₅₀) of the EPSPS activity by glyphosate was more than 90-fold in S compared to R biotype. Decreased EPSPS sensitivity in the R biotype appeared to be a major contributor to glyphosate resistance in rigid ryegrass from California. Fragments of the EPSPS gene containing 1,320 nucleotides were isolated from mRNA of S and R biotypes. A single nucleotide mutation from cytosine (C) to thymine (T) was identified at nucleotide 301 of the truncated EPSPS gene of the R biotype. This mutation changed the amino acid code from proline (Pro) to serine (Ser), which was similar to that reported for the glyphosate-resistant goosegrass from Malaysia and correlated with glyphosate insensitivity of EPSPS.

Nomenclature: Glyphosate; goosegrass, Eleusine indica (L.) Gaertn. ELEIN; rigid ryegrass, Lolium rigidum Gaud. LOLRI

Hydrilla is one of the most serious aquatic weed problems in the United States, and fluridone is the United States Environment Protection Agency (USEPA)-approved herbicide that provides relatively long-term systemic control. Mature (6-wk-old) and young (freshly planted from 10-cm apical shoot apices) hydrilla were grown in 540 L fiberglass vaults under short- (natural 8 to 10 hr light/14 to 16 hr dark photoperiod) or long- (artificially extended 16 h light/8 h dark photoperiod) day greenhouse conditions. Fluridone treatments of 0, 1, 5, and 10 µg L⁻¹ were applied after 2 wk and maintained within each population and photoperiodic regime throughout the study. Short days promoted subterranean turion formation, but this effect was reduced by long days and 5 and 10 µg L⁻¹ fluridone. Fluridone caused a reduction in chlorophyll and carotenoid levels but the effect on anthocyanin content was variable. Short days caused elevated anthocyanin, and this effect was diminished by fluridone. Fluridone reduced the abscisic acid content of mature apical stems and was higher under short days in younger plants. These studies provide further evidence that fluridone can be used as a fall herbicide application to reduce turion production.

Nomenclature: Fluridone; hydrilla, Hydrilla verticillata (L. f.) Royle HYLLI

Croftonweed is a major invasive weed in China and, although of subtropical origin, has invaded into regions with colder climates. Freezing tolerances of nine croftonweed populations from different geographies were studied using a freezing injury index. Physiological responses to freezing temperature were determined to elucidate mechanisms of freezing tolerance. Plants from Baise, Guangxi (BSG), and Qujing, Yunnan (QJY), China, showed the most freezing injury symptoms, whereas plants from Huangguoshu, Guizhou (HGG), China, displayed the least. Under freezing stress, physiological changes, including increases in malondialdehyde (MDA) and total soluble protein contents; reductions in total soluble sugar, chlorophyll contents, and ratios of variable chlorophyll fluorescence to maximum chlorophyll fluorescence (Fv : Fm); and fluctuation of superoxide dismutase (SOD) activity, were observed among all nine populations. However, different degrees of physiological responses were found among populations with diverse low-temperature sensitivities. After 4 d of treatment at −5 C, MDA content increased 25-fold in leaves of the sensitive BSG population compared with untreated leaves, whereas a range of 0.8-fold to ∼5.3-fold increase was found in other populations. Total soluble protein content in leaves of the tolerant HGG population increased to the highest value among the nine populations. SOD activity of the freezing-sensitive BSG population decreased 36% of the control, whereas the tolerant HGG population reduced to 70%. Moreover, soluble sugar of the tolerant HGG population decreased 29%, less than the sensitive BSG population (87%). There were fewer declines in the percentages of chlorophyll content and Fv : Fm value in HGG than in BSG (less 44% and 32%). Freezing injury index had significant negative correlations with Fv : Fm values and chlorophyll contents (−0.619 and −0.622, respectively). These results suggest that croftonweed has evolved into different ecotypes with regard to freezing tolerance through physiological adaptation during their invasion of southwest regions of China. The freezing-tolerant croftonweed population would have more chances to invade distant northeastern areas in the future.

Nomenclature: Croftonweed, Eupatorium adenophorum Spreng EUPAD

Control of common lambsquarters with POST applications of glyphosate in glyphosate-resistant crops generally has been effective. In 2002, common lambsquarters plants from Westmoreland County, VA, were identified after not being controlled with a POST glyphosate application in glyphosate-resistant soybean. Plants from this site that survived glyphosate were collected in both 2002 and 2004. The objective of this research was to evaluate the susceptibility of F1 and F2 progeny from these common lambsquarters plants, relative to the susceptibility of common lambsquarters collected in Montgomery County, VA. F1 progeny of the Westmoreland plants from both the 2002 and 2004 collections showed reduced response to glyphosate relative to the Montgomery collection. Vigor reduction of F1 progeny from three 2004 Westmoreland source plants with 0.84 kg ae ha⁻¹ of glyphosate ranged from 66 to 85% at 28 d after treatment (DAT), compared with 89% for the Montgomery collection. Evaluation of four Westmoreland F2 common lambsquarters lines derived from 2002 collections indicated significant differences in glyphosate sensitivity. Fifteen F2 lines were generated from 2004 collections from each of three Westmoreland source plants and from the Montgomery source. For the least sensitive Westmoreland source, vigor reduction ranged from only 24 to 36% across F2 lines in response to 1.68 kg ha⁻¹ of glyphosate at 28 DAT relative to 55 to 100% for the Montgomery source. I₅₀ estimates for fresh weight reduction were 0.91 and 0.32 kg ha⁻¹, for these sources, respectively. Sequential treatments of 0.42, 1.26, and 1.68 kg ha⁻¹ applied at 3-wk intervals to the least susceptible 2004 Westmoreland F2 line resulted in only 37% vigor reduction and no mortality among 360 treated plants.

Nomenclature: Glyphosate; common lambsquarters, Chenopodium album L. CHEAL; soybean, Glycine max L. Merr

Resistance to acetohydroxyacid synthase (AHAS) inhibiting herbicides in populations of eastern black nightshade from Ontario has been linked to an Ala₂₀₅Val substitution in the AHAS enzyme. The aim of this study was to determine the mechanism of inheritance of AHAS inhibitor resistance and the genetic relationships among resistant (R) and susceptible (S) eastern black nightshade populations from Ontario. Homozygous R and S parental populations were crossed and the inheritance was analyzed in F₁ (S × R), reciprocal F₁ (R × S), F₂, and backcross (S × F₁) progenies after application of imazethapyr at 150 g ai ha⁻¹. Compared to parental lines, the progenies were rated as R, intermediate (I), and S phenotypes. All the F₁ progenies were of the I phenotype. The backcross progenies segregated in a 1:1 (S:I) ratio, and the F₂ families segregated in a 1:2:1 (R:I:S) ratio. These results indicate that a single nuclear gene, with incomplete dominance, controls resistance to AHAS-inhibiting herbicides in R population of eastern black nightshade. Random amplified polymorphic DNA (RAPD) markers were screened among 25 R and S populations. The genetic relationship of R and S populations based on RAPD profiles generated from six RAPD primers indicated four groups of populations in which resistance seems to have arisen independently. However, based on similarity coefficients, resistance within three of the groups could have arisen by gene flow. Both similar local selection pressure and gene flow could explain the spread of the Ala₂₀₅Val substitution in R populations of eastern black nightshade in Ontario.

Nomenclature: Imazethapyr; eastern black nightshade, Solanum ptychanthum Dun. SOLPT

Spreading orach is an annual weed that colonizes roadsides, field edges, and increasingly, no-till agricultural fields. It produces dimorphic seeds with different levels of physiological dormancy, but little is known about the germination ecology of the two seed types. Field and controlled-environment studies were conducted to determine seed responses to light and stratification, the pattern of seedling emergence in the field, and the effect of soil water content on the length of cold stratification required to break dormancy for each seed type. The large, brown seeds have three times the mass of the smaller, black seeds, primarily because of a larger embryo, but have a thinner seed coat. Germination of brown and black seeds in petri dishes was 98 and 90%, respectively, after stratification for 3 mo at 5 C, whereas germination of unstratified seeds was 19 and 12%, respectively. Light stimulated germination of both stratified and unstratified black seeds but did not increase germination in stratified brown seeds. Up to 40% of brown seeds germinated in situ during stratification, compared with only 2% for black seeds. Germination in petri dishes and emergence in the field were more rapid for brown seeds than for black seeds. Maximum germination of black seeds occurred after stratification for 2 or 3 mo at 5 C on soil that was waterlogged (pore-water matric potential, ψ  =  0 kPa), wet (ψ  =  −0.38 kPa), or at field capacity (ψ  =  −10 kPa). For shorter periods of stratification, total germination and germination rate of black seeds declined as soil water content decreased from waterlogged to dry (ψ  =  −500 kPa). Seed dimorphism in spreading orach may provide a mechanism to enhance survival in uncertain or variable habitats such as disturbed agricultural fields.

Nomenclature: Spreading orach, Atriplex patula L

Horseweed has become increasingly difficult to control in the San Joaquin Valley (SJV) of California. Resistance to glyphosate may not fully explain the quasi-invasive behavior of this native species. We contrast glyphosate-resistant (GR) and glyphosate-susceptible (GS) horseweed biotypes for vigor during the vegetative stage and for resistance to ozone (O₃). The SJV is impacted by O₃ air pollution, which could be a factor in competitiveness of GR vs. GS. Both biotypes were exposed during the seedling and vegetative stages of rosette development to a range of O₃ concentrations in greenhouse exposure chambers. Leaf injury was evaluated visually and biomass production and allocation destructively. In O₃-free air, the GR biotype exhibited fewer foliar lesions, more vigorous growth, and 40% greater biomass than the GS biotype. The slope of the response to O₃ was greater in the GR than in the GS biotype, implying greater relative sensitivity to O₃. This was due to greater vigor at low O₃, as the biotypes performed similarly at high O₃. The competitive advantage of the GR biotype may be reduced in polluted environments. There appeared to be no linkage between the evolution of resistances to O₃ and to glyphosate.

Nomenclature: Horseweed, Conyza canadensis (L.) Cronq. ERICA

Horseweed has generally been considered a winter annual weed species, but efforts to control horseweed as a winter annual weed in no-till soybean production with glyphosate have routinely failed in southeast Indiana. The objective of this study was to determine emergence timing, plant survival, and fecundity of a glyphosate-resistant (GR) horseweed biotype in the presence or absence of other winter annual weeds or soybean. A field study was conducted from October 2003 to October 2004 and repeated from October 2004 to October 2005 in fields following no-till soybean production. Horseweed emergence was not observed in the fall of 2003. Winter survival of plants that emerged in the fall of 2004 was 20% by late April 2005 and was inversely related to fall rosette size. Horseweed population densities were the highest in mid-May of both years, and over 90% of the plants observed at this time emerged in the spring. Plant survival from mid-May to mid-October was 3% and 21% in 2004 and 2005, respectively. Horseweed with flower heads above the soybean canopy by early August had greater late-season survival and produced more seed than plants growing below the canopy. Horseweed with flower heads above the soybean canopy produced an average of 27,200 and 58,320 seeds plant⁻¹ in 2004 and 2005, respectively. Our research indicates that this southeast Indiana horseweed biotype behaves primarily as a summer annual weed and produces significant amounts of seed when uncontrolled in no-till soybean production.

Nomenclature: Glyphosate; horseweed, Conyza canadensis (L.) Cronq. ERICA; soybean, Glycine max (L.) Merr

Increasing the germination potential of dormant seeds in a population over time generally requires afterripening. Research was conducted to study the relationship between temperature and seed moisture content on afterripening of dormant leafy spurge seeds. Germination of nonafterripened seeds was 59 and 36% after 21 d for the Harwood and Fargo populations, respectively. Germination of 85 to 87% and 58 to 62% was obtained for the Harwood and Fargo populations, respectively when afterripened for 12 to 24 wk under the most effective conditions of 30 C and 2.6% seed moisture; increasing the afterripening temperature to 45 C did not increase germination. Germination decreased slightly at 30 C as the seed moisture content increased to 5.6%, but germination still exceeded that of nonafterripened seeds. Afterripening at 30 C with a seed moisture content of ≥9% greatly decreased germinability due to seed ageing. A temperature of 5 C was effective for afterripening when the moisture content was 3.3%, but germination was still slightly less than for the low moisture content seeds afterripened at 30 C. Afterripening seeds with 6 to 13% moisture at 5 C generally did not increase germination compared with the control, but did not result in seed ageing.

Nomenclature: Leafy spurge, Euphorbia esula L. EPHES

Giant sensitiveplant is a dominant weed in many tropical and subtropical countries because it is highly competitive and is difficult to clear by hand. Experiments were conducted to determine the effect of various environmental factors on giant sensitiveplant seed germination and seedling emergence. Light was not required for germination, though germination was stimulated by seed scarification, suggesting that inhibition of germination is mainly due to the seed coat. Germination of scarified seed was not influenced by a range of alternating temperatures. Germination increased by exposure to higher temperatures, such as might occur when vegetation is burnt, as simulated by placing nonscarified seed in an oven for 5 min. Germination increased as exposure temperature was increased from 25 C to 120 C but declined progressively with further increases and there was no germination after exposure to 200 C. Moderate salinity and osmotic stress did not inhibit germination and some seed germinated at 250 mM sodium chloride (55%) and osmotic potential of −1.0 MPa (13%). Germination was greater than 79% over a pH range of 4 to 10. Seedling emergence was 80 to 94% at depths of 0 to 2 cm but decreased progressively at deeper depths, and no seedlings emerged from seed buried at 10 cm. The results of this study identify some of the factors enabling giant sensitiveplant to be a widespread and problematic weed in the humid tropics and provide information that could contribute to its control.

Nomenclature: Giant sensitiveplant, Mimosa invisa Mart. ex Colla MIMIN

Pulse crop management can increase pulse yields and N fixation, but the effects of previous pulse crop management on subsequent crop performance is poorly understood. Field studies were conducted at three locations, in the Parkland region of Alberta, Canada, between 2004 and 2006. Tannin-free faba bean, narrowleaf lupin, and field pea were planted at 0.5, 1.0, 1.5, and 2.0 times the recommended pulse planting density (PPD), with or without barley as a model weed. Faba bean produced the highest seed yields in higher precipitation environments, whereas pea produced the highest seed yields in lower precipitation environments. Lupin seed yields were consistently low. In the absence of weed interference, faba bean, pea, and lupin N-fixation yields ranged from 70 to 223, 78 to 147, and 46 to 173 kg N ha⁻¹, respectively. On average, faba bean produced the highest N-fixation yield. The absence of weed interference and a high PPD increased pulse seed and N-fixation yields. Quality wheat crops were grown on pulse stubble without additional N fertilizer in some site–years. Management practices that increased N fixation resulted in only marginal subsequent wheat yield increases. Subsequent wheat seed yield was primarily influenced by pulse species. Pea stubble produced 11% higher wheat yields than lupin stubble but only 2% higher wheat yields than faba bean stubble. Consistently high wheat yields on pea stubble may be attributed to synchronized N release from decomposing pea residues with subsequent crop N demand and superior non-N rotational benefits.

Nomenclature: Barley, Hordeum vulgare L.; field pea, Pisum sativum L.; narrowleaf lupin, Lupinus angustifolius L.; tannin-free faba bean, Vicia faba L.; wheat, Triticum aestivum L

Physical and chemical methods of managing invasive plants (weeds) create disturbances that paradoxically often promote these species because weeds tend to have traits that confer competitive advantages over desired species in disturbed habitats. A more holistic and sustainable method of managing invasive plants is to design disturbance regimes to favor desired species over weeds. This study investigated how the biomass of a herbicide-tolerant plant, alligator weed, and its competitors respond to different chemical disturbances over a 2-yr period. We compared the response of alligator weed and its monocotyledon competitors to 16 different herbicide treatments in a blocked 4 by 2 by 2 factorial design. Treatments included broad spectrum (nonselective) and dicotyledon specific (selective) herbicides applied at two concentrations (variable depending on herbicide) and two frequency regimes (three or four applications). Belowground biomass of alligator weed in unmanipulated control plots was 10 times greater than aboveground biomass, highlighting the need to reduce belowground material if control is to be achieved. All herbicide treatments reduced belowground alligator weed biomass when compared with controls; however in the short term (8 d after the final treatment), even four applications at the highest listed concentration were not sufficient to eliminate alligator weed from study plots. Over the long term (15 mo after the final treatment), selective herbicide application resulted in a sustained reduction in alligator weed biomass and an increase in monocot biomass.

Nomenclature: Alligator weed, Alternanthera philoxeroides (Mart.) Griseb

Joint action of the effects of atrazine and mesotrione can lead to synergistic herbicidal activity in broadleaf weed species. The objective of these experiments was to determine if specific rates are required to provide synergistic joint activity between mesotrione and atrazine in both triazine-sensitive (TS) and triazine-resistant (TR) redroot pigweed. Herbicide rates were evaluated in TS and TR redroot pigweed in two experiments: a dose response of mesotrione alone and in mixture with a constant rate of atrazine and a dose response of atrazine alone and in mixture with a constant rate of mesotrione. Results from these experiments revealed that synergism was detected in the TS pigweed when 56 g ai ha⁻¹ mesotrione was mixed with 126 g ai ha⁻¹ atrazine. In the TR pigweed, synergism was detected when mesotrione rate at 10 to 56 g ha⁻¹ was mixed with a constant rate of atrazine at 126 g ha⁻¹. Additionally, when mesotrione was held constant at 10 g ha⁻¹, synergism was detected in mixture with atrazine from 31 to 3556 g ha⁻¹ in TR pigweed. Furthermore, in TR pigweed, analysis of slope deviation across the dose-response curves of mesotrione with and without atrazine revealed a divergence that increased in magnitude as the rate of mesotrione increased. In other words, increased synergism was observed with increased mesotrione rate in the TR pigweed, which was also supported by biomass reduction and atrazine-like injury to the leaves. An additional experiment investigated synergism between mesotrione and bromoxynil in both TS and TR pigweed. Mesotrione at 10 g ha⁻¹ was synergistic when paired with bromoxynil from 70 to 210 g ha⁻¹ in both the TS and the TR pigweed.

Nomenclature: Atrazine; bromoxynil; mesotrione; redroot pigweed, Amaranthus retroflexus L. AMARE

Buckwheat residues can suppress both emergence and growth of weeds, but the mechanisms of this suppression are not well understood. The main objectives of this research were to evaluate the possible role of (1) low initial nitrogen (N) availability and (2) fungal pathogens in this suppression for three sensitive weed species: Powell amaranth, shepherd's-purse, and corn chamomile. Growth chamber experiments were conducted comparing weed emergence and growth in bare soil or soil with freshly incorporated buckwheat residue at multiple rates of N fertilization with or without fungicide seed treatment. In the absence of N or fungicide addition, emergence of all weed species was reduced 40 to 70%, and dry weight was reduced 85% in buckwheat residue compared with bare soil. For all three weed species, suppression of growth by buckwheat residue was completely overcome with the addition of N. For shepherd's-purse and corn chamomile (2005 only), suppression of emergence was also overcome with the addition of N. In 2006, treatment of corn chamomile seeds with fungicide resulted in a higher emergence in buckwheat residue than in bare soil. In contrast, suppression of Powell amaranth emergence was not overcome with N fertilization or fungicide treatment. The results suggest that buckwheat-mediated changes in N dynamics account entirely for suppression of weed growth but that the mechanisms responsible for suppression of emergence by buckwheat residue vary by species. Fungal and N effects account for suppression of emergence of corn chamomile and shepherd's-purse, but the mechanism of suppression for Powell amaranth remains obscure.

Nomenclature: Corn chamomile, Anthemis arvensis L. ANTAR; Powell amaranth  =  green pigweed, Amaranthus powellii S. Wats. AMAPO; shepherd's-purse, Capsella bursa-pastoris (L.) Medicus CAPBP; buckwheat, Fagopyrum esculentum Moench

DNA microarrays are one of the new tools of genomics that have become quite commonplace in plant science research within the past decade. Essentially, DNA microarrays are an extension of the more traditional molecular biology technique of northern blotting. Unlike northern blotting, however, in which the expression of a single gene is monitored, DNA microarrays allow for the simultaneous monitoring of thousands of genes—or, in fact, potentially all of an organism's genes—in a single experiment. Most of the currently available plant microarrays are designed for crops species or the model plant, Arabidopsis; however, a microarray for at least one major weed species is currently available. Furthermore, cDNA-based microarrays prepared for one species can be used to investigate gene expression in related species. As the technology is maturing it is becoming much more accessible, and now is the time to begin utilizing microarrays in weed science research. Questions related to herbicide activity are particularly well suited for a microarray approach. Additionally, gene-expression profiling via microarrays can be used to address questions relating to weed biology, weed–crop competition, allelopathy, parasitic weeds, and biological control of weeds.

Nomenclature: Mouse-ear cress; Arabidopsis thaliana (L.) Heynh. ARBTH

Real-time polymerase chain reaction (real-time PCR), also known as quantitative PCR, is used to determine relative gene expression or to quantify exact levels of mRNA in cells or tissues. Before the advent of real-time PCR, the major difficulty associated with traditional quantitative or semiquantitative PCR was to ensure that PCR reactions were quantified within the exponential phase of amplification. Real-time PCR alleviates that problem by detecting and quantifying fluorescent signals after each amplification cycle. Additionally, it does not require running gels and thus is able to produce data in 2 to 3 h. Four different types of chemistries, DNA-binding agents (SYBR Green), hydrolysis probes (TaqMan), hairpin probes (molecular beacons, scorpions), and fluorescent-labeled hybridization probes (Light Cycler), have been commonly used for real-time PCR. Among those chemistries, SYBR Green is the most economical choice. We have used real-time PCR and SYBR Green to examine the expression of a number of leafy spurge genes after growth induction and during normal seasonal growth. Because no reliable endogenous reference genes have been identified in leafy spurge, we performed PCR without an endogenous reference gene and analyzed messenger RNA (mRNA) expression based on the threshold cycle (C_T) value of amplification. Excluding an endogenous reference gene from that data analysis was rather straightforward and reliable if RNA was properly prepared and quantified. Given that genomic tools, such as expressed sequence tags (ESTs), and their expression profiles are lacking for most weedy species, avoiding the use of endogenous reference genes in real-time PCR simplifies the optimization process and reduces the cost tremendously. However, we found that using a passive reference dye (ROX) to normalize non-PCR–related fluctuations in fluorescent signal is desirable.

Nomenclature: Leafy spurge, Euphorbia esula L. EPHES

An overview of bioinformatics is presented with an emphasis on describing a set of tools, databases, and ontologies useful to the weed science community. These tools can be used to identify genes whose product may be the target site of a herbicide or in the degradation pathway of a xenobiotic. They may identify receptors responsible for pathogen recognition or enzymes in the metabolic pathway for allelopathic compounds. Whatever the gene of interest, bioinformatics allows researchers to assemble complete or partial genes from expressed sequence tags (ESTs), complete cDNAs, or complete genomes and then translate them into their corresponding amino acid sequences. Similarity searches can be used to find other proteins with homology to the gene of interest, which can provide clues to its function from the annotation of these database hits. The use of protein domain databases can also provide insight into the functional capabilities of the protein in question and delineate those portions essential for activity. Enzyme Commission (EZ) numbers or gene ontology (GO) descriptors allow placement of the protein within the larger network context of a biological system. These capabilities allow the scientist to probe deeper into the function of their protein of interest to gain a novel understanding of the biology.

Genome sequencing of many model systems, including the human, yeast, Arabidopsis, and rice genomes, has been completed. As a complement to genomic techniques, proteomics has emerged to study the composition, structure, function, and interaction of the expressed proteins or proteome in a given cell, tissue, or organism. During the past several years, tremendous progress has been made with proteomic techniques in human and yeast, but progress has been slower in plants due to several factors. Proteomic techniques have been used in plants, especially in agriculturally important crops and weeds, to understand mechanisms of herbicide tolerance and weed resistance. Proteomic techniques, starting from protein extraction to protein identification, have been developed and advanced for large-scale proteomics studies, but limitations and problems for these techniques still exist for plant proteomics. Further technological improvements are needed to enhance quantitative and comparative large-scale proteomics studies. Applications of these techniques may help weed scientists to understand stress tolerance in crops and investigate weediness traits further. Proteomic techniques have unique strengths but also offer several challenges. Together with transcriptomics and metabolomics, these techniques for analyzing global patterns of gene expression offer new and novel techniques for better understanding biological questions of interest to weed scientists in the future.

Nomenclature: Arabidopsis, Arabidopsis thaliana (L.) Heynh; rice, Oryza sativa L; yeast, Saccharomyces cerevisiae

Genome sequences and genome-wide transcript profiles are becoming increasingly available, opening a way to use this information in analyzing how groups of genes are connected in pathways or “regulons” that might explain how organisms accomplish the integration on an organismal level. We have begun to explore the large datasets that are available for transcripts of the best characterized plant model, Arabidopsis thaliana, setting up a gene network using clustering methods. A network, based on the Graphical Gaussian Model (GGM), describes coregulation of genes under a variety of external factors: abiotic, biotic, and chemical treatments. In its present structure, the network reveals coregulation for more than 7,000 genes in the Arabidopsis genome. The network appears to be particularly suited to reveal the regulatory structure of biochemical pathways and environmental stress responses. Examples describe network predictions centered on a trehalose-6-phosphate phosphatase, an Arabidopsis response regulator and EPSPS. Results from the statistical analysis and bioinformatics of large data sets provide hypotheses that must be checked by additional studies. However, networks, which should be expanded from transcripts to also include proteins and metabolites, can be expected to explain not only how the Arabidopsis gene network is structured, but also provide insight in how similar networks in weed species might deviate or show correspondence and overlap.

Nomenclature: Arabidopsis, Arabidopsis thaliana (L.) Heynh

Genetic markers have been used in horticulture and conservation biology to identify breeding lines, assess genetic diversity, and examine gene flow. In weed science, analysis of genetic markers is not as common, as the focus often lies in the development of control methods. This is unfortunate, because advances in genetic marker techniques may lead to innovative methods in controlling weedy plants. Microsatellites, random amplified polymorphic DNA (RAPDs), intersimple sequence repeats (ISSRs), amplified fragment length polymorphisms (AFLPs), DNA sequences, single nucleotide polymorphisms (SNPs), and derived cleaved amplified polymorphic sequences (dCAPS) have been used in studying genetics of weedy plants. Beyond assessing genetic diversity of weeds, markers have been used to examine gene flow, patterns of dispersal, ploidy levels, and relationships of weedy and nonweedy species, as well as identifying founder populations. Identification of closely related species may indicate the potential for hybridization, cross reactivity of chemical applications, or nontarget biological control effects. Furthermore, markers have been used in identification of mutations conferring herbicide resistance and identification of regions correlating fitness of weedy and hybrid plants in new habitats. Knowledge from genetic markers provides fundamental information that can be used in advancing chemical and biological control in weed management. This article serves as a review of these marker types and their application to weed science.

Purple deadnettle is an obligate winter annual weed and an alternate host of soybean cyst nematode (SCN). Field experiments were conducted using microplots to determine (1) the effect of purple deadnettle planting date and (2) the effect of purple deadnettle removal time on SCN egg population density in continuous no-tillage soybean. A population change factor (PCF) to assess treatment effects on SCN population densities was calculated by dividing the SCN population density at each sampling time (Pf) by the initial population density before treatments were applied (Pi). In the planting date experiment, purple deadnettle seeded on October 3, 11, and 18 resulted in PCF values ranging from 7.28 to 11.41, which were three- to fivefold higher than the PCF values for the weed-free control or purple deadnettle seeded on September 6, 20, and 27. Self-thinning of purple deadnettle seeded in September may have resulted in higher levels of SCN mortality compared to later seeding dates. In the removal time experiment, purple deadnettle removal at 2 and 4 wk after emergence (WAE) resulted in PCF values of 1.19 and 1.54, respectively, which were similar to the PCF for the weed-free control. In contrast, PCF values for purple deadnettle removal times of 6 WAE or later ranged from 2.46 to 5.44. Field and greenhouse experiments provided evidence that completion of the SCN life cycle on purple deadnettle was prevented if the weed was removed before the accumulation of 380 soil degree days within the 5 to 30 C range. Results from the removal study also suggested that completion of the first SCN generation on purple deadnettle in the fall was the primary factor causing increases in egg population density, since PCF values did not continue to increase significantly beyond the 6 WAE removal time.

Nomenclature: Purple deadnettle, Lamium purpureum L. LAMPU; soybean, Glycine max L. Merr; soybean cyst nematode, Heterodera glycines