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The U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS) has been a leader in weed science research covering topics ranging from the development and use of integrated weed management (IWM) tactics to basic mechanistic studies, including biotic resistance of desirable plant communities and herbicide resistance. ARS weed scientists have worked in agricultural and natural ecosystems, including agronomic and horticultural crops, pastures, forests, wild lands, aquatic habitats, wetlands, and riparian areas. Through strong partnerships with academia, state agencies, private industry, and numerous federal programs, ARS weed scientists have made contributions to discoveries in the newest fields of robotics and genetics, as well as the traditional and fundamental subjects of weed–crop competition and physiology and integration of weed control tactics and practices. Weed science at ARS is often overshadowed by other research topics; thus, few are aware of the long history of ARS weed science and its important contributions. This review is the result of a symposium held at the Weed Science Society of America’s 62nd Annual Meeting in 2022 that included 10 separate presentations in a virtual Weed Science Webinar Series. The overarching themes of management tactics (IWM, biological control, and automation), basic mechanisms (competition, invasive plant genetics, and herbicide resistance), and ecosystem impacts (invasive plant spread, climate change, conservation, and restoration) represent core ARS weed science research that is dynamic and efficacious and has been a significant component of the agency’s national and international efforts. This review highlights current studies and future directions that exemplify the science and collaborative relationships both within and outside ARS. Given the constraints of weeds and invasive plants on all aspects of food, feed, and fiber systems, there is an acknowledged need to face new challenges, including agriculture and natural resources sustainability, economic resilience and reliability, and societal health and well-being.
The Fontan Outcomes Network was created to improve outcomes for children and adults with single ventricle CHD living with Fontan circulation. The network mission is to optimise longevity and quality of life by improving physical health, neurodevelopmental outcomes, resilience, and emotional health for these individuals and their families. This manuscript describes the systematic design of this new learning health network, including the initial steps in development of a national, lifespan registry, and pilot testing of data collection forms at 10 congenital heart centres.
The Murchison Widefield Array (MWA) is an open access telescope dedicated to studying the low-frequency (80–300 MHz) southern sky. Since beginning operations in mid-2013, the MWA has opened a new observational window in the southern hemisphere enabling many science areas. The driving science objectives of the original design were to observe 21 cm radiation from the Epoch of Reionisation (EoR), explore the radio time domain, perform Galactic and extragalactic surveys, and monitor solar, heliospheric, and ionospheric phenomena. All together
programs recorded 20 000 h producing 146 papers to date. In 2016, the telescope underwent a major upgrade resulting in alternating compact and extended configurations. Other upgrades, including digital back-ends and a rapid-response triggering system, have been developed since the original array was commissioned. In this paper, we review the major results from the prior operation of the MWA and then discuss the new science paths enabled by the improved capabilities. We group these science opportunities by the four original science themes but also include ideas for directions outside these categories.
Modern high-throughput molecular and analytical tools offer exciting opportunities to gain a mechanistic understanding of unique traits of weeds. During the past decade, tremendous progress has been made within the weed science discipline using genomic techniques to gain deeper insights into weedy traits such as invasiveness, hybridization, and herbicide resistance. Though the adoption of newer “omics” techniques such as proteomics, metabolomics, and physionomics has been slow, applications of these omics platforms to study plants, especially agriculturally important crops and weeds, have been increasing over the years. In weed science, these platforms are now used more frequently to understand mechanisms of herbicide resistance, weed resistance evolution, and crop–weed interactions. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding weedy traits. Although these techniques can provide robust insights about the molecular functioning of plants, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. Therefore, it is desirable to integrate the different omics technologies to give a better understanding of molecular functioning of biological systems. This multidimensional integrated approach can therefore offer new avenues for better understanding of questions of interest to weed scientists. This review offers a retrospective and prospective examination of omics platforms employed to investigate weed physiology and novel approaches and new technologies that can provide holistic and knowledge-based weed management strategies for future.
Leafy spurge (Euphorbia esula L.) is an invasive perennial weed infesting range and recreational lands of North America. Previous research and omics projects with E. esula have helped develop it as a model for studying many aspects of perennial plant development and response to abiotic stress. However, the lack of an assembled genome for E. esula has limited the power of previous transcriptomics studies to identify functional promoter elements and transcription factor binding sites. An assembled genome for E. esula would enhance our understanding of signaling processes controlling plant development and responses to environmental stress and provide a better understanding of genetic factors impacting weediness traits, evolution, and herbicide resistance. A comprehensive transcriptome database would also assist in analyzing future RNA-seq studies and is needed to annotate and assess genomic sequence assemblies. Here, we assembled and annotated 56,234 unigenes from an assembly of 589,235 RNA-seq-derived contigs and a previously published Sanger-sequenced expressed sequence tag collection. The resulting data indicate that we now have sequence for >90% of the expressed E. esula protein-coding genes. We also assembled the gene space of E. esula by using a limited coverage (18X) genomic sequence database. In this study, the programs Velvet and Trinity produced the best gene-space assemblies based on representation of expressed and conserved eukaryotic genes. The results indicate that E. esula contains as much as 23% repetitive sequences, of which 11% are unique. Our sequence data were also sufficient for assembling a full chloroplast and partial mitochondrial genome. Further, marker analysis identified more than 150,000 high-quality variants in our E. esula L-RNA–scaffolded, whole-genome, Trinity-assembled genome. Based on these results, E. esula appears to have limited heterozygosity. This study provides a blueprint for low-cost genomic assemblies in weed species and new resources for identifying conserved and novel promoter regions among coordinately expressed genes of E. esula.
The discovery of the first electromagnetic counterpart to a gravitational wave signal has generated follow-up observations by over 50 facilities world-wide, ushering in the new era of multi-messenger astronomy. In this paper, we present follow-up observations of the gravitational wave event GW170817 and its electromagnetic counterpart SSS17a/DLT17ck (IAU label AT2017gfo) by 14 Australian telescopes and partner observatories as part of Australian-based and Australian-led research programs. We report early- to late-time multi-wavelength observations, including optical imaging and spectroscopy, mid-infrared imaging, radio imaging, and searches for fast radio bursts. Our optical spectra reveal that the transient source emission cooled from approximately 6 400 K to 2 100 K over a 7-d period and produced no significant optical emission lines. The spectral profiles, cooling rate, and photometric light curves are consistent with the expected outburst and subsequent processes of a binary neutron star merger. Star formation in the host galaxy probably ceased at least a Gyr ago, although there is evidence for a galaxy merger. Binary pulsars with short (100 Myr) decay times are therefore unlikely progenitors, but pulsars like PSR B1534+12 with its 2.7 Gyr coalescence time could produce such a merger. The displacement (~2.2 kpc) of the binary star system from the centre of the main galaxy is not unusual for stars in the host galaxy or stars originating in the merging galaxy, and therefore any constraints on the kick velocity imparted to the progenitor are poor.
Microarray analysis was used to follow changes in gene expression coinciding with seasonal changes in the dormancy status of crown buds of field-grown leafy spurge. Known cold-regulated genes were induced, and numerous gibberellic acid–responsive genes were down-regulated during the transition from paradormancy to endodormancy. Genes involved in photomorphogenesis were induced during endodormancy. Also, ethylene signaling responses were observed during ecodormancy rather than endodormancy. These results provide additional insights into the signals regulating expression of several genes previously associated with transition from paradormancy to growth in root buds.
Previous evidence indicates that changes in well-defined phases of dormancy in underground adventitious buds of leafy spurge in late summer and autumn are regulated by complex sensing and signaling pathways involving aboveground sugar signals. However, little information exists concerning seasonal photosynthesis and carbohydrate partitioning of leafy spurge, although such information would help to elucidate the involvement of sugar in controlling bud dormancy. An outdoor study was conducted over two growing seasons to determine and model seasonal patterns of photosynthesis and aboveground carbohydrate partitioning and their relationship to underground adventitious bud carbohydrate status. Photosynthesis and total nonstructural carbohydrate (TNC) content of aboveground tissues was greatest during vegetative growth. Photosynthesis gradually declined over the growing season, whereas TNC decreased sharply during flowering, followed by a gradual decline between midsummer and autumn. Leaf starch increased dramatically to midsummer before declining sharply throughout late summer and early autumn, whereas sucrose content responded inversely, indicating a mobilization of starch reserves and export of sugars to overwintering belowground sink tissues. Because newly formed underground adventitious buds showed a continuous increase in TNC from midsummer through autumn, export of sugars from aboveground tissues likely contributed to the increase in TNC. These results may facilitate new strategies for biological control of leafy spurge.
In this review, we examine current techniques and recent advances directed toward understanding cellular mechanisms involved in controlling dormancy in vegetative propagules. Vegetative propagules (including stems, rhizomes, tubers, bulbs, stolons, creeping roots, etc.) contain axillary and adventitious buds capable of producing new stems/branches under permissive environments. Axillary and adventitious buds are distinct in that axillary buds are formed in the axil of leaves and are responsible for production of lateral shoots (branches). Adventitious buds refer to buds that arise on the plant at places (stems, roots, or leaves) other than leaf axils. Both axillary and adventitious buds generally undergo periods of dormancy. Dormancy has been described as a temporary suspension of visible growth of any plant structure containing a meristem (Lang et al. 1987). Dormancy can be subdivided into three categories: (1) ecodormancy-arrest is under the control of external environmental factors; (2) paradormancy-arrest is under the control of external physiological factors within the plant; and (3) endodormancy-arrest is under the control of internal physiological factors. One common feature in all of these processes is prevention of growth under conditions where growth should otherwise continue. There is growing evidence that lack of growth is due to blockage of cell division resulting from interactions between the signaling pathways controlling dormancy and those controlling the cell cycle.
Persistence of the soil seed bank requires both dormancy and resistance to seed decay organisms. However, there is little or no information evaluating biochemical responses of dormant weed seeds to pathogens. Wild oat caryopses were incubated with four pathogenic fungal isolates to evaluate the response of the pathogen defense enzyme, polyphenol oxidase (PPO). Caryopsis PPO activity was induced by three Fusarium spp. isolates previously obtained from whole seeds incubated in the field whereas caryopsis PPO activity was decreased by a Pythium isolate. Fusarium avenaceum isolate F.a.1 caused the greatest PPO induction and was studied in more detail. When whole wild oat seeds were incubated on F.a.1, PPO activity was induced in seeds, hulls (lemma and palea), and caryopses. Incubation of whole seeds on F.a.1 gradually induced caryopsis PPO activity over an 8-d period, whereas incubation of caryopses on F.a.1 over a 4-d period caused a greater and more rapid induction of PPO activity. Very little PPO activity could be leached from untreated caryopses, but nearly all of the induced PPO activity in F.a.1-treated caryopses was readily leached when incubated in buffer. In Western blots, both untreated and F.a.1-treated leachates contained a ∼57-kilodalton (kD) protein, putatively the mature and relatively inactive form of PPO. However, lower molecular weight antigenic proteins between ∼52 and ∼25 kD were strongly induced in F.a.1-treated caryopses, with this induction being correlated with the increase in PPO activity. We hypothesize that dormant weed seeds possess biochemical defenses against pathogens and, more specifically, that proteolysis in the presence of fungal pathogens may release an activated form of PPO from the surface of wild oat caryopses and hulls.
Plant model systems have contributed greatly to the dramatic progress in understanding the fundamental aspects of plant biology. Using model weeds will also help facilitate focused funding and research in the weed science community. Criteria for developing model weeds require attention to weedy characteristics that impart economic losses and a wide geographic distribution, attributes that present the potential for political and scientific support. Expressed sequence tag (EST) databases for model weeds are the most practical approach to identifying new genes and obtaining data on the gene expression underlying weedy characteristics. Weeds such as Canada thistle, eastern black nightshade, johnsongrass, jointed goatgrass, leafy spurge, waterhemp, and weedy rice are proposed as model systems.
Leafy spurge is a tenacious perennial weed of the Northern Plains. This plant maintains a perennial growth cycle by controlled production and growth of numerous underground adventitious buds. We are using molecular tools to identify signaling pathways that control underground adventitious bud growth and development in leafy spurge. Toward this end, we have used three techniques to identify genes that are differentially expressed concomitantly with the breaking of quiescence in underground buds of leafy spurge. These techniques include differential display of cDNAs, random cloning and sequencing of genes expressed in growing buds, and microarray technology. To date, we have identified more than 16 genes that are differentially expressed in underground buds of leafy spurge during dormancy break and growth initiation. A detailed expression analysis of these genes will allow them to be grouped by their responses to various signals known to play a role in control of underground bud growth. This information will be used to identify key cis-acting elements involved in the regulation of these genes. How such information on signal transduction processes may be used for developing new weed control strategies by the identification of novel target pathways and development of DNA-based herbicides is presented.
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.
Recommended rates of glyphosate for noncultivated areas destroy the
aboveground shoots of the perennial plant leafy spurge. However, such
applications cause little or no damage to underground adventitious buds
(UABs), and thus the plant readily regenerates vegetatively. High
concentrations of glyphosate, applied under controlled environmental
conditions, have been shown to cause sublethal effects in UABs of leafy
spurge that produce stunted and bushy phenotypes in subsequent generations
of shoots. We treated leafy spurge plants in the field with glyphosate (0,
1.1, 3.4, or 6.7 kg ai ha−1) to determine its effects on
vegetative growth from UABs and on molecular processes. The number of shoots
derived from UABs of glyphosate-treated plants was significantly increased
compared to controls in subsequent years after application, and new shoots
displayed various phenotypical changes, such as stunted and bushy
phenotypes. Quantifying the abundance of a selected set of transcripts in
UABs of nontreated vs. treated plants (0 vs. 6.7 kg ha−1)
indicated that glyphosate impacted molecular processes involved in
biosynthesis or signaling of tryptophan or auxin (ARF4,
CYP79B2, PIN3, TAA1,
TRP6, YUC4), gibberellic acid
(GA1/CPS1, GA2/KS), ethylene
(ACO1, ACS10), cytokinins
(AHP1, AK2, CKX1), and
the cell cycle (CDC2A, CDC2B,
CYCD3;1). Glyphosate-induced effects on vegetative
growth and transcript abundance were persistent for at least 2 yr after
treatment. Determining the molecular mechanisms associated with vegetative
reproduction in leafy spurge following foliar glyphosate-treatment could
identify limiting factors or new targets for manipulation of plant growth
and development in perennial weeds.
Infection by Xanthomonas axonopodis pv. manihotis (Xam) of the perennial rangeland weed leafy spurge was tested to see whether Xam might serve a potential biological control agent for this invasive weed. Although leafy spurge was susceptible to Xam infection, it recovered within 21 d after inoculation (DAI). Microarray resources available for leafy spurge allowed us to follow the physiological and signaling pathways that were altered as leafy spurge was infected and then recovered from Xam infection. The first physiological effect of Xam infection was a down-regulation of photosynthetic processes within 1 DAI. By 7 DAI, numerous processes associated with well-documented pathogenesis responses of plants were observed. Although some pathogenesis responses were still detectable at 21 DAI, other processes associated with meristem development were noted. Ontological analysis of potential signaling systems indicated jasmonic acid plays a significant role in the recovery processes.
Long-term control of leafy spurge with glyphosate requires multiple
applications because the plant reproduces vegetatively from abundant
underground adventitious buds, referred to as crown and root buds.
Determining the molecular mechanisms involved in controlling vegetative
reproduction in leafy spurge following foliar glyphosate treatment could
identify limiting factors or new targets for manipulation of plant growth
and development in invasive perennial species. Thus, we treated leafy spurge
plants with 0 or 2.24 kg ai ha−1 glyphosate to determine its
impact on selected molecular processes in crown buds derived from intact
plants and plants decapitated at the soil surface 7 d after glyphosate
treatment. New shoot growth from crown buds of foliar glyphosate-treated
plants was significantly reduced compared with controls after
growth-inducing decapitation, and had a stunted or bushy phenotype.
Quantification of a selected set of transcripts involved in hormone
biosynthesis and signaling pathways indicated that glyphosate had the most
significant impact on abundance of ENT-COPALYL DIPHOSPHATE
SYNTHETASE 1, which is involved in a committed step for
gibberellin biosynthesis, and auxin transporters including PINs,
PIN-LIKES, and ABC TRANSPORTERS. Foliar
glyphosate treatment also reduced the abundance of transcripts involved in
cell cycle processes, which would be consistent with altered growth patterns
observed in this study. Overall, these results suggest that interplay among
phytohormones such as auxin, ethylene, and gibberellins affect vegetative
growth patterns from crown buds of leafy spurge in response to foliar
Signals from both leaves and apical or axillary meristems of leafy spurge are known to inhibit root bud growth. To test the hypothesis that carbohydrates and growth regulators affect root bud growth, decapitated leafy spurge plants were hydroponically treated with glucose, sucrose, gibberellic acid (GA), abscisic acid (ABA), 1-naphthaleneacetic acid (NAA), 6-benzylaminopurine (BA), and a GA biosynthesis inhibitor, paclobutrazol. Both glucose and sucrose caused suppression of root bud growth at concentrations of 30 mM. The inhibitory effect of sucrose was counteracted by GA at 15 μM. In contrast, BA, ABA, NAA, and paclobutrazol inhibited root bud growth at concentrations as low as 1, 2, 1, and 16 μM, respectively. Sugar and starch levels were also determined in root buds at various times after decapitation. Buds of intact plants contained the highest level of sucrose compared with buds harvested 1, 3, and 5 d after decapitation. To determine how seasonal changes affect root bud dormancy, growth from root buds of field-grown plants was monitored for several years. Root buds of field-grown leafy spurge had the highest level of innate dormancy from October to November, which persisted until a prolonged period of freezing occurred in November or early December. Our data support the hypothesis that carbohydrates may be involved in regulating dormancy status in root buds of leafy spurge.
As a first step toward developing a genomics-based research program to study growth and development of underground adventitious shoot buds of leafy spurge, we initiated a leafy spurge expressed sequence tag (EST) database. From the approximately 2,000 clones randomly isolated from a cDNA library made from a population containing growth-induced underground adventitious shoot buds, we have obtained ESTs for 1,105 cDNAs. Approximately 29% of the leafy spurge EST database consists of expressed genes of unknown identity (hypothetical proteins), and 10% represents ribosomal proteins. The remaining 60% of the database is composed of expressed genes that show BLASTX sequence identity scores of ≥ 80 with known GenBank accessions. Clones showing sequence identity to a Histone H3, a gibberellic acid-responsive gene, Tubulin, and a light-harvesting chlorophyll a/b-binding protein were shown to be differentially expressed in underground adventitious shoot buds of leafy spurge after breaking of dormancy. RNA encoding a putative cyclin-dependent protein kinase (CDK)-activating kinase, a gene associated with cell division, and Scarecrow-like 7, a gene involved in GA signaling, were present at similar levels in dormant and growth-induced underground adventitious shoot buds. These data show how even a small EST database can be used to develop a genomics-based research program that will help us identify genes responsive to or involved in the mechanisms controlling underground adventitious shoot bud growth and development.