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.

Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.

Nomenclature: Common waterhemp, Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif AMATU; Tall waterhemp, Amaranthus tuberculatus (Moq.) Sauer var. tuberculatus (Sauer) Costea and Tardif AMATU.

Bispyribac-sodium selectively controls annual bluegrass in creeping bentgrass and perennial ryegrass, which might be attributed to differential metabolism among species. To test this hypothesis, we investigated metabolism of ¹⁴C-bispyribac-sodium in annual bluegrass, creeping bentgrass, and perennial ryegrass. Creeping bentgrass and perennial ryegrass metabolized approximately 50% of the ¹⁴C-bispyribac-sodium after 1 d, while annual bluegrass metabolized less than 20%. Parent herbicide recovered 7 d after treatment in annual bluegrass, creeping bentgrass, and perennial ryegrass was 73, 32, and 39% of total radioactivity per species, respectively. Polar metabolites recovered after 7 d in annual bluegrass, creeping bentgrass, and perennial ryegrass were 24, 59, and 55% of total radioactivity per species, respectively. Half-life of ¹⁴C-bispyribac-sodium in annual bluegrass, creeping bentgrass, and perennial ryegrass was estimated at greater than 7 d, 1 d, and 2 d, respectively. Results support the hypothesis that differential tolerances of these grasses are attributed to herbicide metabolism.

Nomenclature: Bispyribac-sodium; annual bluegrass, Poa annua L.; creeping bentgrass, Agrostis stolonifera L., ‘L-93’; perennial ryegrass, Lolium perenne L., ‘Manhattan 4’.

Soybean is a major crop cultivated in Brazil, and acetolactate synthase (ALS)-inhibiting herbicides are widely used to control weeds in this crop. The continuous use of these ALS-inhibiting herbicides has led to the evolution of herbicide-resistant weeds worldwide. Greater beggarticks is a polyploid species and one of the most troublesome weeds in soybean production since the discovery of ALS-resistant biotypes in 1996. To confirm and characterize the resistance of greater beggarticks to ALS inhibitors, whole-plant bioassays and enzyme experiments were conducted. To investigate the molecular basis of resistance in greater beggarticks the ALS gene was sequenced and compared between susceptible and resistant biotypes. Our results confirmed that greater beggarticks is resistant to ALS inhibitors and also indicated it possesses at least three isoforms of the ALS gene. Analysis of the nucleotide and deduced amino acid sequences among the isoforms and between the biotypes indicated that a single point mutation, G–T, in one ALS isoform from the resistant biotype resulted in an amino acid substitution, Trp₅₇₄Leu. Two additional substitutions were observed, Phe₁₁₆Leu and Phe₁₄₉Ser, in a second isoform of the resistant biotype, which were not yet reported in any other herbicide-resistant ALS gene; thus, their role in conferring herbicide resistance is not yet ascertained. This is the first report of ALS mutations in an important, herbicide-resistant weed species from Brazil.

Nomenclature: Chlorimuron; cloransulam; imazethapyr; pyrithiobac; greater beggarticks, Bidens subalternans DC; soybean, Glycine max (L.) Merr.

The development of fluridone resistance by hydrilla has significantly impacted hydrilla management, and research is ongoing to develop alternate herbicides for effective hydrilla control. We determined the potential cross-resistance in fluridone-resistant hydrilla to other bleaching herbicides norflurazon, mesotrione, and topramezone-methyl. Phytoene, β-carotene, and chlorophyll contents as a function of hydrilla biotype and herbicide treatment were evaluated. Hydrilla shoot tips were collected from fluridone-susceptible (S) and -resistant (R) biotypes and exposed to 5, 25, 50, 75, and 100 µg L⁻¹ of herbicide. The susceptible biotype showed an increase in phytoene and a decrease in β-carotene and chlorophyll contents when treated with 5 µg L⁻¹ fluridone, whereas higher doses of fluridone were required to affect these pigments in the resistant biotype. There was no difference in response by S and R biotypes to mesotrione and topramezone-methyl, with both biotypes showing significant affects on pigment contents at 5 µg L⁻¹. Higher doses of norflurazon were required to affect these pigments in the R compared to the S biotype. The S biotype had EC₅₀ values of 11.7, 12.2, and 4.7 µg L⁻¹, whereas the R biotype had EC₅₀ values of 56.6, 41.1, and 41.7 µg L⁻¹ fluridone for phytoene, β-carotene, and chlorophyll contents, respectively. There was no difference in EC₅₀ for phytoene, β-carotene, and chlorophyll values between the hydrilla biotypes for mesotrione and topramezone-methyl herbicides. In fluridone-susceptible and -resistant hydrilla biotypes, EC₅₀ values for phytoene, β-carotene, and chlorophyll were 12.4 to 11.8, 10.2 to 13.2, and 3.1 to 4.6 µg L⁻¹ mesotrione and 12.6 to 13.5, 13.3 to 11.9, and 4.6 to 5.7 µg L⁻¹ topramezone-methyl, respectively. For norflurazon, S and R biotypes had EC₅₀ values of 33.1, 45.4, and 40.6 µg L⁻¹ and 84.6, 81.0, and 92.7 µg L⁻¹ for phytoene, β-carotene, and chlorophyll, respectively. These studies confirmed negative cross-resistance of fluridone-resistant hydrilla to mesotrione and topramezone-methyl and a positive cross-resistance to norflurazon.

Nomenclature: Fluridone; mesotrione; norflurazon; topramezone-methyl; hydrilla, Hydrilla verticillata (L.f.) Royle HYLLI.

A greenhouse study was conducted to determine the influence of soybean cyst nematode (SCN) –susceptible and –resistant plant combinations on SCN population densities and plant growth. Purple deadnettle, annual ryegrass, SCN-resistant and -susceptible soybean were planted in pots alone or in combination at one plant pot⁻¹. Annual ryegrass and purple deadnettle reduced soybean growth. Pots with SCN-resistant plants had lower numbers of SCN cysts and eggs than pots with SCN-susceptible plants. However, an SCN-susceptible species grown with any of the SCN-resistant plants resulted in higher cyst counts than pots with only SCN-resistant plants. From an SCN management standpoint, this research suggests that there may be no incentive to using annual ryegrass as a cover crop over planting other SCN-resistant crops to reduce SCN population density.

Nomenclature: Purple deadnettle, Lamium purpureum L. LAMPU; annual ryegrass, Lolium multiflorum Lam.; soybean, Glycine max (L.) Merr.; soybean cyst nematode, Heterodera glycines Ichinohe.

Horseweed populations with mixtures of biotypes resistant to glyphosate and acetolactate synthase (ALS)–inhibiting herbicides as well as biotypes with multiple resistance to glyphosate ALS-inhibiting herbicides have been documented in Indiana and Ohio. These biotypes are particularly problematic because ALS-inhibiting herbicides are commonly tank mixed with glyphosate to improve postemergence horseweed control in soybean. The objective of this research was to characterize the growth and seed production of horseweed populations with resistance to glyphosate or ALS-inhibiting herbicides, and multiple resistance to glyphosate ALS-inhibiting herbicides. A four-herbicide by four-horseweed population factorial field experiment was conducted in the southeastern region of Indiana in 2007 and repeated in 2008. Four horseweed populations were collected from Indiana or Ohio and confirmed resistant to glyphosate, ALS inhibitors, both, or neither in greenhouse experiments. The four herbicide treatments were untreated, 0.84 kg ae ha⁻¹ glyphosate, 35 g ai ha⁻¹ cloransulam, and 0.84 kg ae ha⁻¹ glyphosate 35 g ai ha⁻¹ cloransulam. Untreated plants from horseweed populations that were resistant to glyphosate, ALS-inhibiting, or multiple glyphosate ALS-inhibiting herbicides produced similar amounts of biomass and seed compared to populations that were susceptible to those herbicides or combination of herbicides. Furthermore, aboveground shoot mass and seed production did not differ between treated and untreated plants.

Nomenclature: Cloransulam; glyphosate; horseweed, Conyza canadensis L. ERICA; soybean, Glycine max L. Merr.

The knowledge of weed distribution in a field is a key factor to manage weeds effectively. The feasibility of using weed distribution maps for site-specific weed control will largely depend on the stability of the spatial distribution of the populations. Seed banks are the most reliable way of telling the area's weediness, but the effect of regular herbicide applications on its stability is largely unknown. A field experiment was conducted during 3 yr in a winter wheat field under herbicide treatments with the aim of studying the seed bank's spatial distribution of prostrate knotweed and corn poppy and the spatiotemporal stability of their populations. Soil samples were taken each year on the same locations, and seed abundance was measured by germination in greenhouse. Both species accounted for more than 10% of the broad-leaved weed seed bank and they were selected for further analysis. Prostrate knotweed seed-bank density decreased 76% and corn poppy 88% in 3 yr. Spatial distribution was described by spherical isotropic semivariograms. Distance of spatial dependence (range) of prostrate knotweed and corn poppy decreased 33 and 11% respectively, and the spatial variability (sill) decreased 96 and 99%. Yearly spatial seed distribution was compared for each species and no temporal stability was observed over a 3-yr period. The lack of stability was attributed to the important decrease of seed density over time and the increase in the short-range variability (nugget). However, for prostrate knotweed, the location of minima and maxima were roughly the same between years, allowing farmers to extend the period of use of the weed distribution maps. Although spatial distribution of seed banks can be affected by processes that promote fast changes in the densities of weed populations, this fact does not mean that weed distribution maps could not be used in consecutive seasons.

Nomenclature: Corn poppy, Papaver rhoeas L.; prostrate knotweed, Polygonum aviculare L; winter wheat, Triticum aestivum L.

Remote sensing has been used to directly detect and map invasive plants, but has not been used for forest understory invaders because they are obscured by a canopy. However, if the invasive species has a leaf phenology distinct from native forest species, then temporal opportunities exist to detect the invasive. Amur honeysuckle, an Asian shrub that invades North American forests, expands leaves earlier and retains leaves later than native woody species. This research project explored whether Landsat 5 TM and Landsat 7 ETM imagery could predict Amur honeysuckle cover in woodlots across Darke and Preble Counties in southwestern Ohio and Wayne County in adjacent eastern Indiana. The predictive abilities of six spectral vegetation indices and six reflectance bands were evaluated to determine the best predictor or predictors of Amur honeysuckle cover. The use of image differencing in which a January 2001 image was subtracted from a November 2005 image provided better prediction of Amur honeysuckle cover than the use of the single November 2005 image. The Normalized Difference Vegetation Index (NDVI) was the best-performing predictor variable, compared to other spectral indices, with a quadratic function providing a better fit (R²  =  0.75) than a linear function (R²  =  0.65). This predictive model was verified with 15 other woodlots (R²  =  0.77). With refinement, this approach could map current and past understory invasion by Amur honeysuckle.

Nomenclature: Amur honeysuckle, Lonicera maackii (Rupr.) Herder.

Buffalobur is a noxious and invasive weed species native to North America. The influence of environmental factors on seed germination and seedling emergence of buffalobur were evaluated in laboratory and greenhouse experiments. The germination of buffalobur seeds occurred at temperatures ranging from 12.5 to 45 C, with optimum germination attained between 25 and 35 C. Buffalobur seeds germinated equally well under both a 14-h photoperiod and continuous darkness; however, prolonged light exposure (≥ 16 h) significantly inhibited the seed germination. Buffalobur seed is rather tolerant to low water potential and high salt stress, as germination was 28 and 52% at osmotic potentials of −1.1 MPa and salinity level of 160 mM, respectively. Medium pH has no significant effect on seed germination; germination was greater than 95% over a broad pH range from 3 to 10. Seedling emergence was higher (85%) for seeds buried at a soil depth of 2 cm than for those placed on the soil surface (32%), but no seedlings emerged when burial depth reached 8 cm. Knowledge of germination biology of buffalobur obtained in this study will be useful in predicting the potential distribution area and developing effective management strategies for this species.

Nomenclature: Buffalobur, Solanum rostratum Dunal SOLCU.

Variation in primary dormancy among populations of black nightshade and hairy nightshade collected on two dates was investigated. In addition, emergence characteristics of both species were studied during 2 yr with several populations and soil disturbance regimes. Results revealed a variation in the level of primary dormancy among populations and collection dates in black nightshade. However, fresh seeds of hairy nightshade showed no or negligible germinability, indicating a deeper level of dormancy. Emergence was higher in black nightshade than in hairy nightshade in both years, but with significant differences among populations. In addition, various categories regarding the soil temperature requirements for seedling emergence were found within seed batches. This enables the species to extend their emergence timing and therefore escape from climatic extremes or weed control operations. This information can be used to improve weed management strategies by timing weed control measures to larger seedling flushes.

Nomenclature: Black nightshade, Solanum nigrum L., SOLNI; hairy nightshade, Solanum physalifolium Rusby, SOLSA.

The transition period to certified organic production can present a significant weed management challenge for growers. Organic certification requires that prohibited fertilizers and pesticides must not have been used for 36 mo before harvest of the first organic crop. Understanding how organic management practices and initial weed seed-bank densities affect weed population dynamics during the transition period may improve weed management efficacy and adoption of organic practices. We examined how tillage systems (full or reduced) and cover crop species planted during the first transition year (rye or a mixture of timothy and red clover) affect the seedling densities of three common annual weed species, common lambsquarters, velvetleaf, and foxtail spp., during the 3-yr transition period. Weed seeds were applied in a one-time pulse at the beginning of the study at three densities, low, medium, and high (60, 460, and 2,100 seeds m⁻², respectively), and cumulative seedling densities of each species were assessed annually. Treatment factors had variable and species-specific effects on weed seedling densities. In general, the full-tillage system, with an initial cover crop of timothy and red clover, resulted in the lowest density of weed seedlings following seed-bank augmentation. There was little consistent association between the initial densities of applied weed seeds in the weed seed bank at the start of the transition and weed seedling densities at the end of the transition period. This suggests that when multiple crop and weed cultural management practices are employed during the organic transition period, initial failures in weed management may not necessarily lead to persistent and intractable annual weed species management problems following organic certification.

Nomenclature: Common lambsquarters, Chenopodium album L. CHEAL; giant foxtail, Setaria faberi Herrm. SETFA; velvetleaf, Abutilon theophrasti Medik. ABUTH; yellow foxtail, Setaria glauca (L.) Beauv. SETLU; red clover, Trifolium pretense L.; rye, Secale cereal L.; timothy, Phleum pratense L.

Agricultural equipment can disperse weed seeds over large distances. Efforts to minimize or prevent equipment-mediated dispersal should be a key component in any integrated weed management plan. Several experiments were initiated in commercial wild blueberry fields to examine the potential impact of harvesting equipment on weed seed dispersal within and between blueberry fields. Seed loads were examined on harvesting equipment between fields and results suggest that harvesting equipment is a major vector of seed dispersal. Seed loads were 397,000 in 2006 and 194,000 in 2007. Of all seeds located on the harvester, 66 to 79% were located on the belts or affiliated components. In 2006, a second experiment was established to examine within-field seed dispersal. A sampling grid was established over multiple distinct poverty oatgrass patches with seed heads at 44% of all sampling points. Following harvest, seeds were located at 67% of all sampling points. In 2006 and 2007, short-distance secondary dispersal of poverty oatgrass by harvesting equipment was measured. The relationship between distance from patch perimeter and seeds per unit area on the side approached by harvesting equipment and the far side of the patch was adequately modeled with an exponential decay model. Secondary dispersal within blueberry fields by harvesting equipment is inevitable. Dispersal may be reduced by avoiding dense weed patches, or altering harvest timing. Periodic cleaning of harvesting equipment between fields will help prevent the spread of weed seed.

Nomenclature: Poverty oatgrass, Danthonia spicata (L.) Beauv. ex Roemer & J. A. Schultes DANSP; wild blueberry, Vaccinium angustifolium Ait. and Vaccinium myrtilloides Michx.

Microbial metabolites have been identified as a promising class of natural herbicides due to their effective control against weeds and a relatively low environmental impact. Here we report on the potency and crop safety of a natural compound with herbicidal properties, the metabolite SPRI-70014 from Streptomyces griseolus CGMCC 1370. The compound showed excellent herbicidal activities on various broadleaf and gramineous weeds in both greenhouse and field trials. In germination inhibition experiments, SPRI-70014 inhibited the emergence of both root and shoot at 1 mg L⁻¹. At a dose of 31.3 g ai ha⁻¹, SPRI-70014 provided effective control over most broadleaf weeds in greenhouse trials. Observations on absorption and translocation using a cucumber plant model system indicated that SPRI-70014 could be absorbed by the root but only partly by the stem. Field trials showed that SPRI-70014 provided effective control over most weed species tested at a dose of 1,000 g ai ha⁻¹. Crop safety experiments showed that the compound had no harmful effect on peanut or wheat plants at doses up to 2,000 g ai ha⁻¹. These results indicated that this compound could be developed as a potential POST herbicide for control of broadleaf weeds in peanut and wheat fields.

Nomenclature: Cucumber, Cucumis sativus L.; peanut, Arachis hypogaea L.; wheat, Triticum aestivum L.

A fungal pathogen, Helminthosporium gramineum Rabehn f.sp. echinochloae (HGE), has been developed as a mycoherbicidal agent for the control of barnyardgrass in China. Under greenhouse conditions, the effect of the pathogen on disease incidence, mortality, and dry weight reduction of barnyardgrass was tested to determine the potential of this mycoherbicide. Field experiments during 2007 and 2008 showed that the conidia of HGE displayed excellent activity on barnyardgrass and good activity on a few other weed species. The HGE treatment increased the rice yield when compared with the untreated control and had no negative impact on the rice plant. In addition, the progression of HGE infection and the alteration of cellular ultrastructure in infected barnyardgrass were observed by using scanning and transmission electron microscopes. After infection, cell membranes of barnyardgrass leaves were found dramatically changed, and the ultrastructure of cells was severely deformed. This study clearly shows the scope of HGE as a potential mycoherbicide for control of barnyardgrass in agricultural cropping systems and has laid the groundwork for further studies on the mode of infection and the nosogenesis of HGE.

Nomenclature: Helminthosporium gramineum Rabehn f.sp. echinochloae (HGE); barnyardgrass, Echinochloa crus-galli (L.) Beauv.; rice, Oryza sativa L.