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Abstract Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome‐level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single‐Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance‐associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype—a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.

Cover cropping is a soil conservation practice that may reduce the impacts of the economically important pathogen Pseudomonas syringae on crops, including squash (Cucurbita pepo). To date, no studies have directly quantified the effect of rye cover crops on P. syringae populations or on the bacterial community of squash leaves. In this work, we tested the hypothesis that the protective effects of cover cropping on squash may be mediated by cover cropping effects on the plant’s microbiota that, in turn, protect against P. syringae. Using combined 16S sequencing and culture-based approaches, we showed that rye cover cropping protects squash against P. syringae, by decreasing pathogen population size on squash leaves and increasing fruit health and marketability at harvest. We also found evidence of a strong effect of rye cover crops on bacterial communities of the squash phyllosphere. Those findings were more striking early in the growing season. Finally, we identified numerous phyllosphere bacteria belonging to the genera Sphingomonas, Methylobacterium, and Pseudomonas that were promoted by rye cover crops. Overall, our findings suggest that cover cropping is effective for the sustainable management of P. syringae on squash and may provide a reservoir of potential microbial biocontrol agents colonizing the phyllosphere.[Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Green pigweed [Amaranthus powellii S. Wats.] is a competitive, annual, broadleaf weed that can significantly reduce soybean yield due to rapid early growth and biomass production. As a consequence of green pigweed’s high competitiveness with crops, the weed species is generally managed with the use of herbicides; this may, however, lead to the selection of resistance. A green pigweed biotype with resistance to MCPA, mecoprop, dichlorprop-p, aminocyclopyrachlor (synthetic auxins), and imazethapyr (acetolactate synthase-(ALS)-inhibitor) was recently confirmed in Ontario, Canada. Research was conducted to identify alternative effective preemergence (PRE) and postemergence (POST) herbicides for the control of multiple-herbicide-resistant (MHR) green pigweed in Ontario soybean production. Four field trials, two with PRE and two with POST herbicides were conducted near Dresden, Ontario in 2019 and 2020. Visible soybean injury, green pigweed control, density, aboveground biomass, and soybean yield were evaluated following application with 19 PRE herbicide treatments and 12 POST herbicide treatments in separate studies. At 8 wk after application (WAA), pyroxasulfone/flumioxazin applied PRE controlled green pigweed 95% and was the most effective soil-applied herbicide. In the POST study, glyphosate was the most effective herbicide, controlling green pigweed 94% at 8 WAA. Imazethapyr, applied PRE or POST did not control this green pigweed biotype as it is also resistant to ALS-inhibitors. Control with other ALS-inhibiting herbicides as well as with PPO-inhibiting herbicides was variable, and further research is needed to determine the reason for variable control with these herbicides.

Bacterial leaf spot of lettuce, caused by Xanthomonas hortorum pv. vitians, is an economically important disease worldwide. For instance, it caused around 4 million CAD in losses in only a few months during the winter of 1992 in Florida. Because only one pesticide is registered to control this disease in Canada, the development of lettuce cultivars tolerant to bacterial leaf spot remains the most promising approach to reduce the incidence and severity of the disease in lettuce fields. The lack of information about the genetic diversity of the pathogen, however, impairs breeding programs, especially when disease resistance is tested on newly developed lettuce germplasm lines. To evaluate the diversity of X. hortorum pv. vitians, a multilocus sequence analysis was performed on 694 isolates collected in Eastern Canada through the summers of 2014 to 2017 and two isolates in 1996 and 2007. All isolates tested were clustered into five phylogroups. Six pathotypes were identified following pathogenicity tests conducted in greenhouses, but when phylogroups were compared with pathotypes, no correlation could be drawn. However, in vitro production of xanthan and xanthomonadins was investigated, and isolates with higher production of xanthomonadins were generally causing less severe symptoms on the tolerant cultivar Little Gem. Whole-genome sequencing was undertaken for 95 isolates belonging to the pathotypes identified, and de novo assembly made with reads unmapped to the reference strain’s genome sequence resulted in 694 contigs ranging from 128 to 120,795 bp. Variant calling was performed prior to genome-wide association studies computed with single-nucleotide polymorphisms (SNPs), copy-number variants and gaps. Polymorphisms with significant p-values were only found on the cultivar Little Gem. Our results allowed molecular identification of isolates likely to cause bacterial leaf spot of lettuce, using two SNPs identified through genome-wide association study.

Wild buckwheat (Polygonum convolvulus L.) is a problem weed and ALS-inhibitors (e.g., chlorsulfuron) are commonly used for its management. Recently, a population of wild buckwheat (KSW-R) uncontrolled with ALS-inhibitors was found in a wheat field in Kansas, USA. The objectives of this research were to determine the level and mechanism of resistance to chlorsulfuron and cross resistance to other ALS-inhibitors in the KSW-R population. In response to chlorsulfuron rates ranging from 0 to 16x (x = 18 g ai/ha), the KSW-R wild buckwheat was found >100-fold more resistant compared to a known ALS-inhibitor susceptible (KSW-S) wild buckwheat. Also, >90% of KSW-R plants survived field recommended rates of sulfonylurea but not imidazolinone family of ALS-inhibitors. A portion of the ALS gene covering all previously reported mutations known to bestow resistance to ALS-inhibitors was sequenced from both KSW-R and KSW-S plants. The Pro-197-Ser substitution that confers resistance to the sulfonylurea herbicides was found in KSW-R plants. Our results support the evolution of high level of chlorsulfuron resistance as a result of a mutation in the ALS-gene in KSW-R buckwheat. This is the first case of resistance to any herbicides in wild buckwheat in the US.

Potato producers in the Atlantic Canadian provinces of New Brunswick (NB) and Prince Edward Island (PE) rely on the photosystem II-inhibiting herbicide metribuzin for weed management. Recently, potato producers in the region have reported unacceptable common lambsquarters control following an application of metribuzin. Tissue and seed samples were collected from escaped common lambsquarters populations from across the potato producing regions of NB and PE and screened for the Ser264Gly mutation in psbA. Overall, 46% of sampled populations possessed the Ser264Gly mutation across the region. Cross-resistance testing to atrazine, metribuzin and linuron confirmed populations with the Ser264Gly were resistant to triazines and triazinones but remained susceptible to linuron. Dose response analysis determined a moderate level of resistance to metribuzin in common lambsquarters which would not be controlled in producers fields. A field experiment was conducted in Fredericton, NB and Harrington, PE, to determine if currently registered and unregistered products and tank-mixes would control PSII-inhibitor-resistant common lambsquarters in potato. All evaluated products, with the exception of S-metolachlor, provided control equivalent to the weed-free check without compromising potato yield or quality. This study demonstrates that PSII-inhibitor-resistant common lambsquarters are found in Atlantic Canadian potato production systems, but can be controlled with currently registered herbicides and rates with alternative modes of action.

Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.