In a predictable natural selection process, herbicides select for adaptive alleles that allow weed populations to survive. These resistance alleles may be available immediately from the standing genetic variation within the population or may arise from immigration via pollen or seeds from other populations. Moreover, because all populations are constantly generating new mutant genotypes by de novo mutations, resistant mutants may arise spontaneously in any herbicide-sensitive weed population. Recognizing that the relative contribution of each of these three sources of resistance alleles influences what strategies should be applied to counteract herbicide-resistance evolution, we aimed to add experimental information to the resistance evolutionary framework. Specifically, the objectives of this experiment were to determine the de novo mutation rate conferring herbicide resistance in a natural plant population and to test the hypothesis that the mutation rate increases when plants are stressed by sublethal herbicide exposure. We used grain amaranth (Amaranthus hypochondriacus L.) and resistance to acetolactate synthase (ALS)-inhibiting herbicides as a model system to discover spontaneous herbicide-resistant mutants. After screening 70.8 million plants, however, we detected no spontaneous resistant genotypes, indicating the probability of finding a spontaneous ALS-resistant mutant in a given sensitive population is lower than 1.4 × 10−8. This empirically determined upper limit is lower than expected from theoretical calculations based on previous studies. We found no evidence that herbicide stress increased the mutation rate, but were not able to robustly test this hypothesis. The results found in this study indicate that de novo mutations conferring herbicide resistance might occur at lower frequencies than previously expected.

Field experiments were conducted in 2016 and 2017 in Champaign County, IL, to study a waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] population (CHR) resistant to 2,4-D and 4-hydroxyphenylpyruvate dioxygenase (HPPD)-, photosystem II–, acetolactate synthase (ALS)-, and protoporphyrinogen oxidase–inhibiting herbicides. Two field experiments were designed to investigate the efficacy of very-long-chain fatty-acid (VLCFA)-inhibiting herbicides, including a comparison of active ingredients at labeled use rates and a rate titration experiment. Amaranthus tuberculatus density and control were evaluated at 28 and 42 d after treatment (DAT). Nonencapsulated acetochlor, alachlor, and pyroxasulfone provided the greatest PRE control of CHR (56% to 75%) at 28 DAT, while metolachlor, S-metolachlor, dimethenamid-P, and encapsulated acetochlor provided less than 27% control. In the rate titration study, nonencapsulated acetochlor controlled CHR more than equivalent field use rates of S-metolachlor. Subsequent dose–response experiments with acetochlor, S-metolachlor, dimethenamid-P, and pyroxasulfone in the greenhouse included three multiple herbicide–resistant (MHR) A. tuberculatus populations: CHR-M6 (progeny generated from CHR), MCR-NH40 (progeny generated from Mclean County, IL), and ACR (Adams County, IL), in comparison with a sensitive population (WUS). Both CHR-M6 and MCR-NH40 are MHR to atrazine and HPPD, and ALS inhibitors and demonstrated higher survival rates (LD50) to S-metolachlor, acetochlor, dimethenamid-P, or pyroxasulfone than ACR (atrazine resistant but HPPD-inhibitor sensitive) and WUS. Based on biomass reduction (GR50), resistant to sensitive (R:S) ratios between CHR-M6 and WUS were 7.5, 6.1, 5.5, and 2.9 for S-metolachlor, acetochlor, dimethenamid-P, and pyroxasulfone, respectively. Values were greater for MCR-NH40 than CHR-M6, and ACR was the most sensitive to all VLCFA inhibitors tested. Complete control of all populations was achieved at or below a field use rate of acetochlor. In summary, field studies demonstrated CHR is not controlled by several VLCFA-inhibiting herbicides. Greenhouse dose–response experiments corroborated field results and generated R:S ratios (LD50) ranging from 4.5 to 64 for CHR-M6 and MCR-NH40 among the four VLCFA-inhibiting herbicides evaluated.

Late watergrass [Echinochloa phyllopogon (Stapf) Koso-Pol.] is one of the most persistent weeds in rice fields and shows resistance to some acetolactate synthase (ALS)-inhibiting herbicides, such as penoxsulam. Previous studies of E. phyllopogon’s herbicide resistance have focused on non–target site resistance mechanisms. In this study, E. phyllopogon populations from Heilong Jiang Province, China, that were possibly resistant to penoxsulam were used to identify the target site–based mechanisms of resistance. Population HSRH-520 showed a 25.4-fold higher resistance to penoxsulam than the sensitive population, HSRH-538. HSRH-520 was resistant to other ALS inhibitors, with resistance indexes ranging from 17.1 to 166. Target-gene sequence analysis revealed two different ALS genes in E. phyllopogon; a Pro-197-Ser substitution occurred in the ALS-2 gene of HSRH-520. In vitro activity assays revealed that the penoxsulam concentrations required to inhibit 50% of the ALS activity were 13.7 times higher in HSRH-520 than in HSRH-538. Molecular-docking tests showed that the Pro-197-Ser mutation reduced the binding affinity between ALS and ALS inhibitors belonging to the triazolopyrimidine, sulfonylaminocarbonyltriazolinone, and sulfonylurea families, and there were almost no effects on binding affinity when the ALS inhibitors were of the pyrimidinylthiobenzoate and imidazolinone families. Overall, the results indicated and verified that the Pro-197-Ser mutation leads to increased ALS activity by reducing the binding affinity of the inhibitor and ALS. This is the first report on the Pro-197-Ser mutation in the complete ALS gene of E. phyllopogon and will aid future research of target site–based resistance mechanisms of E. phyllopogon to ALS inhibitors.

Japanese foxtail (Alopecurus japonicus Steud.) is an invasive grass weed that severely threatens the production of wheat (Triticum aestivum L.) and canola (Brassica napus L.) crops in eastern Asia. Mesosulfuron-methyl is a highly efficient acetolactate synthase (ALS)-inhibiting herbicide widely used for control of this species in China. However, in recent years, some A. japonicus populations have evolved resistance to mesosulfuron-methyl by different amino acid substitutions (AASs) within the ALS gene. In the current study, 11 populations of A. japonicus were collected from Anhui Province, China, where the wheat fields were severely infested with this weed. Based on single-dose screening, eight of these populations evolved resistance to mesosulfuron-methyl, and gene sequencing revealed three AASs located in codon 197 or 574 of the ALS gene in the different resistant populations. Subsequently, three typical populations, AH-1, AH-4, and AH-10 with Trp-574-Leu, Pro-197-Thr, and Pro-197-Ser mutations, respectively, in ALS genes were selected to characterize their cross-resistance patterns to ALS inhibitors. Compared with the susceptible population AH-S, AH-1 showed broad-spectrum cross-resistance to sulfonylureas (SUs), imidazolinones (IMIs), triazolopyrimidines (TPs), and sulfonyl-aminocarbonyl-triazolinones (SCTs); whereas AH-4 and AH-10 were resistant to SUs, TPs, and SCTs but sensitive to IMIs. Moreover, all three resistant populations were sensitive to both photosystem II inhibitor isoproturon and 4-hydroxyphenylpyruvate dioxygenase inhibitor QYM201 (1-(2-chloro-3-(3-cyclopropyl-5-hydroxy-1-methyl-1H-pyrazole-4-carbonyl)-6-(trifluoromethyl)phenyl)piperidin-2-one). Based on the current state of knowledge, this study is the first report of A. japonicus evolving cross-resistance to ALS-inhibiting herbicides due to a Pro-197-Ser mutation in the ALS gene.

Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.

Waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] and Palmer amaranth (Amaranthus palmeri S. Watson) are troublesome weeds of row-crop production in the United States. Their dioecious reproductive systems ensure outcrossing, facilitating rapid evolution and distribution of resistances to multiple herbicides. Little is known, however, about the genetic basis of dioecy in Amaranthus species. In this work, we use restriction site–associated DNA sequencing (RAD-Seq) to investigate the genetic basis of sex determination in A. tuberculatus and A. palmeri. For each species, approximately 200 plants of each sex were sampled and used to create RAD-Seq libraries. The resulting libraries were separately bar-coded and then pooled for sequencing with the Illumina platform, yielding millions of 64-bp reads. These reads were analyzed to identify sex-specific and sex-biased sequences. We identified 345 male-specific sequences from the A. palmeri data set and 2,754 male-specific sequences in A. tuberculatus. An unexpected 723 female-specific sequences were identified in a subset of the A. tuberculatus females; subsequent research, however, indicated female specificity of these markers was limited to the population from which they were identified. Primer sets designed to specifically amplify male-specific sequences were tested for accuracy on multiple, geographically distinct populations of A. tuberculatus and A. palmeri, as well as other Amaranthus species. Two primer sets for A. palmeri and four primer sets for A. tuberculatus were each able to distinguish between male and female plants with at least 95% accuracy. In the near term, sex-specific markers will be useful to the A. tuberculatus and A. palmeri research communities (e.g., to predict sex for crossing experiments). In the long-term, this research will provide the foundational tools for detailed investigations into the molecular biology and evolution of dioecy in weedy Amaranthus species.

Glyphosate-resistant junglerice [Echinochloa colona (L.) Link] is a problematic weed in mungbean [Vigna radiata (L.) R. Wilczek] crops in Australia. Due to limited herbicide options in mungbean, there is an increased interest in developing integrated management strategies for the sustainable control of E. colona. Pot experiments were conducted in a screenhouse in 2017 and 2018 by growing E. colona plants (glyphosate-resistant [GR] and glyphosate-susceptible [GS] biotypes) alone (1 plant pot−1) and in competition with 4 and 8 mungbean plants pot−1. Both biotypes were developed from a single population using the clone method. The growth and seed production of both GR and GS biotypes were similar in response to mungbean competition. Averaged over biotypes, there was a reduction in the growth and seed production of E. colona as crop plants increased. Compared with the weed plants grown alone, crop interference reduced E. colona height by 17% to 19%, tiller numbers by 69% to 82%, total shoot biomass by 85% to 91%, and inflorescence numbers by 74% to 91%. When E. colona was grown with 8 mungbean plants pot−1, leaf weight ratio increased by 42% compared with plants grown alone. Compared with weed plants grown alone, mungbean interference (4 and 8 plants pot−1) reduced weed seed production by 85% to 95%. These reductions were similar for both biotypes (GR and GS), suggesting that there was no fitness penalty associated with resistance. The results of this study suggest that mungbean interference can reduce E. colona growth and seed production, but it should not be considered as a stand-alone strategy to manage E. colona and similar species in mungbean. These results also highlight the need for integrating crop competition with other management strategies to achieve complete and sustainable management of this weed.

Field studies were conducted in 2016 and 2017 in Clinton, NC, to determine the interspecific and intraspecific interference of Palmer amaranth (Amaranthus palmeri S. Watson) or large crabgrass [Digitaria sanguinalis (L.) Scop.] in ‘Covington’ sweetpotato [Ipomoea batatas (L.) Lam.]. Amaranthus palmeri and D. sanguinalis were established 1 d after sweetpotato transplanting and maintained season-long at 0, 1, 2, 4, 8 and 0, 1, 2, 4, 16 plants m−1 of row in the presence and absence of sweetpotato, respectively. Predicted yield loss for sweetpotato was 35% to 76% for D. sanguinalis at 1 to 16 plants m−1 of row and 50% to 79% for A. palmeri at 1 to 8 plants m−1 of row. Weed dry biomass per meter of row increased linearly with increasing weed density. Individual dry biomass of A. palmeri and D. sanguinalis was not affected by weed density when grown in the presence of sweetpotato. When grown without sweetpotato, individual weed dry biomass decreased 71% and 62% from 1 to 4 plants m−1 row for A. palmeri and D. sanguinalis, respectively. Individual weed dry biomass was not affected above 4 plants m−1 row to the highest densities of 8 and 16 plants m−1 row for A. palmeri and D. sanguinalis, respectively.

Row-middle weed control in Florida vegetable production is challenging and often necessitates several PRE and POST herbicide applications. Coordinating POST spray applications with emergence timings should increase herbicide efficacy by targeting susceptible growth stages. Most published emergence models were developed in temperate climates, and adapting them to subtropical climates can be complex and requires reductionist insights into seed ecology, particularly germination and dormancy. The study objective was to examine the influence of temperature and osmotic potential on seed germination of carpetweed (Mollugo verticillata L.), Carolina geranium (Geranium carolinianum L.), eclipta [Eclipta prostrata (L.) L.], and goosegrass [Eleusine indica (L.) Gaertn.]. Mollugo verticillata seed germination was positively photoblastic, with increased germination at high temperatures (≥35 C), more so with high fluctuating temperatures (35/20 and 35/25 C), and occurred at osmotic potentials as low as −0.5 MPa. Geranium carolinianum seed germinated between 10 and 20 C in light or darkness and at osmotic potentials as low as −0.4 MPa. Eclipta prostrata seed germination was entirely positively photoblastic, occurring optimally between 15 and 25 C and at osmotic potentials as low as −1 MPa. Eleusine indica seed germination demonstrated some degree of positive photoblasticity, with greater germination in the light, peak germination at 35 C, and germination occurring at osmotic potentials as low as −0.5 MPa. Described germination ecology for selected species will provide insights for building ecology-based growing degree-day accounting restrictions for empirically derived emergence models.

Weedy rice (Oryza spp.) is considered one of the main weeds in cultivated rice (Oryza sativa L.) around the world, having a great impact on both yield and quality of crop rice. Recent studies have characterized the range of morphological and genetic diversity in weedy rice from different locations and have revealed that there is often great morphological diversity within growing regions. No systematic attempt to characterize phenotypic diversity of weedy rice in Colombia, where this group of weeds greatly affects rice production, has yet been carried out. This study seeks (1) to establish the range of variation in various morphological characters for weedy rice collected in the five production zones of Colombia and to compare these with commercial varieties and landraces sown in the country, (2) to determine the association between weedy rice morphotypes and rice production areas in the country, and (3) to assess whether any association exists between morphology and recently discovered genetic groupings for weedy rice in Colombia. Based on a sampling of rice production areas in Colombia and evaluation of 27 phenotypic traits, a two-step cluster analysis identified four morphological groups for weedy rice in Colombia. These groupings had some limited association with geography and the genetic ancestries of weedy rice. Clustering showed that awn and apiculus color and awn length and presence are the most important predictors in defining morphological groupings. Understanding and classifying the morphological diversity may be helpful in understanding weedy rice origins, evolution, and potential management practices.

Barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] is one of the most troublesome and competitive weed species in rice (Oryza sativa L.) grown under conventional flood (FLD) irrigation and is expected to be similarly damaging under alternate-wetting-and-drying (AWD) irrigation. Several indica rice genotypes have been shown to suppress E. crus-galli under FLD management, but very little is known about the nature and potential of weed suppression using AWD irrigation. In this 3-yr field study, we evaluated seven diverse rice genotypes for their weed suppression and grain yield potential under FLD and AWD irrigation. The E. crus-galli dry biomass at midseason was 11% less under AWD compared with FLD. Overall, plots of an indica variety and a hybrid resulted in less E. crus-galli dry biomass under AWD compared with FLD. Grain yield in weed-free AWD plots averaged 12% less than in weed-free FLD plots. Grain yield of the tropical japonica (TRJ) type, ‘Bengal’, was 32% lower under AWD than FLD, whereas grain yields of the two indica genotypes, PI 312777 and ‘Rondo’, and a hybrid were similar in both irrigation systems. Grain yield reduction in E. crus-galli–infested AWD plots averaged greater than 90%. Thus, E. crus-galli greatly reduced the grain yield of all rice genotypes tested in both FLD and AWD systems in this study. Grain yield of the indica and hybrid genotypes was relatively less affected by the AWD treatments compared with the TRJ genotypes, particularly with Bengal, suggesting that the weed-suppressive genotypes, PI 312777 and Rondo, would be better suited to AWD irrigation systems and for inclusion in weed-suppression rice-breeding programs in the southern United States.

Weeds remain the most commonly cited concern of organic farmers. Without the benefit of synthetic herbicides, organic farmers must rely on a host of ecological weed management (EWM) practices to control weeds. Despite EWM’s ability to improve soil quality, the perceived rate of integrated EWM strategy adoption remains low. This low adoption is likely a result of the complexity in designing and evaluating EWM strategies, the tendency for outreach to focus on the risks of EWM strategies rather than their benefits, and a lack of quantitative measures linking the performance of EWM strategies to farmers’ on-farm objectives and practices. Here we report on the development and deployment of an easy-to-use online decision support tool (DST) that aids organic farmers in identifying their on-farm objectives, characterizing the performance of their practices, and evaluating EWM strategies recommended by an expert advisory panel. Informed by the principles of structured decision making, the DST uses multiple choice tasks to help farmers evaluate the short- and long-term trade-offs of EWM strategies, while also focusing their attention on their most important objectives. We then invited organic farmers across the United States, in particular those whose email addresses were registered on the USDA’s Organic Research Integrity Database, to engage the DST online. Results show considerable movement in participants’ (n = 45) preferences from practices focused on reducing weeding costs and labor in the short term to EWM strategies focused on improving soil quality in the long term. Indeed, nearly half of those farmers (48%) who initially ranked a strategy composed of their current practices highest ultimately preferred a better-performing EWM strategy focused on eliminating the weed seedbank over 5 yr.