National Forage Seed Production Research Center

In many plant species, seed dormancy is broken by cold stratification, a pre-chilling treatment of fully imbibed seeds. Although the ecological importance of seed response to cold temperature is well appreciated, the mechanisms underlying the physiological changes during cold stratification is unknown. Here we show that the GATA zinc finger protein expressed in Arabidopsis seeds during cold stratification plays a critical role in germination. Characterization of an enhancer-trap population identified multiple lines that exhibited beta-glucuronidase (GUS) expression in the micropylar end of the seed (named Blue Micropylar End, BME lines). One of these lines, BME3, had a T-DNA insertion site in the 5' upstream region of a GATA-type zinc finger transcription factor gene (termed BME3-ZF). The BME3-ZF mRNA accumulated in seeds during cold stratification. Characterization of the BME3-ZF promoter indicated that this gene was activated specifically in the embryonic axis, which was still enclosed by the endosperm. The zinc finger gene knockout plants produced seeds exhibiting deeper dormancy, which showed reduced response to cold stratification. The ungerminated knockout seeds exhibited testa rupture, but failed to penetrate the endosperm layer. Application of gibberellic acid (GA3) rescued impaired germination of knockout seeds without cold stratification, indicating that the normal GA signal transduction pathway is present in the knockout mutants. Expression of GA20-oxidase and GA3-oxidase genes was greatly reduced in the knockout seeds, suggesting the potential involvement of the zinc finger protein in GA biosynthesis. These results suggest that the GATA zinc finger protein is a positive regulator of seed germination.

Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.

Soil organic matter (SOM) supports the Earth's ability to sustain terrestrial ecosystems, provide food and fiber, and retains the largest pool of actively cycling carbon. Over 75% of the soil organic carbon (SOC) in the top meter of soil is directly affected by human land use. Large land areas have lost SOC as a result of land use practices, yet there are compensatory opportunities to enhance productivity and SOC storage in degraded lands through improved management practices. Large areas with and without intentional management are also being subjected to rapid changes in climate, making many SOC stocks vulnerable to losses by decomposition or disturbance. In order to quantify potential SOC losses or sequestration at field, regional, and global scales, measurements for detecting changes in SOC are needed. Such measurements and soil-management best practices should be based on well established and emerging scientific understanding of processes of C stabilization and destabilization over various timescales, soil types, and spatial scales. As newly engaged members of the International Soil Carbon Network, we have identified gaps in data, modeling, and communication that underscore the need for an open, shared network to frame and guide the study of SOM and SOC and their management for sustained production and climate regulation.

We studied whole-tree C allocation with special emphasis on the quantification of C allocation to roots and root respiration. To document seasonal patterns of C allocation, 2-year-old hybrid poplar trees greater than 3 m tall were labeled with (14)CO(2) in a large Plexiglas chamber in the field, in July and September. Climate and CO(2) concentration were controlled to track ambient conditions during labeling. Individual tree canopy CO(2) assimilation averaged 3.8 micromol CO(2) m(-2) s(-1) (12.9 g C day(-1) tree(-1)) in July and 6.2 micromol CO(2) m(-2) s(-1) (9.8 g C day(-1) tree(-1)) in September. Aboveground dark respiration was 12% of net daytime C fixation in July and 15% in September. Specific activity of root-soil respiration peaked 2 days after labeling and stabilized to less than 5% of maximum 2 weeks later. Low specific activity of root-soil respiration and a labeled pool of root C demonstrated that current photosynthate was the primary source of C for root growth and maintenance during the growing season. Root respiration averaged 20% of total soil respiration in both July and September based on the proportion of labeled C respired to labeled C fixed. In July, 80% of the recovered (14)C was found above ground and closely resembled the weight distribution of the growing shoot. By September, 51% of the recovered (14)C was in the root system and closely resembled the weight distribution of different size classes of roots. The finding that the distribution of biomass and (14)C were similar verified that the C introduced during labeling followed normal seasonal translocation pathways. Results are compared to smaller scale labeling studies and the suitability of the approach for studying long-term C fluxes is discussed.

Journal Article A rapid one-tube genomic DNA extraction process for PCR and RAPD analyses Get access J. J. Steiner, J. J. Steiner * National Forage Seed Production Research Center, USDA-ARS, 3450 SW Campus WayCorvallis, OR 97331, USA * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar C. J. Polemba, C. J. Polemba National Forage Seed Production Research Center, USDA-ARS, 3450 SW Campus WayCorvallis, OR 97331, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. G. Fjellstrom, R. G. Fjellstrom National Forage Seed Production Research Center, USDA-ARS, 3450 SW Campus WayCorvallis, OR 97331, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar L. F. Elliott L. F. Elliott National Forage Seed Production Research Center, USDA-ARS, 3450 SW Campus WayCorvallis, OR 97331, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 23, Issue 13, 11 July 1995, Pages 2569–2570, https://doi.org/10.1093/nar/23.13.2569-a Published: 11 July 1995 Article history Received: 24 March 1995 Accepted: 18 May 1995 Published: 11 July 1995

Abstract Despite the fundamental importance of soil temperature for Earth's carbon and energy budgets, ecosystem functioning, and agricultural production, studies of climate change impacts on soil processes have mainly relied on air temperatures, assuming they are accurate proxies for soil temperatures. We evaluated changes in soil temperature, moisture, and air temperature predicted over the 21st century from 14 Earth system models. The model ensemble predicted a global mean soil warming of 2.3 ± 0.7 and 4.5 ± 1.1 °C at 100‐cm depth by the end of the 21st century for RCPs 4.5 and 8.5, respectively. Soils at 100 cm warmed at almost exactly the same rate as near‐surface (~1 cm) soils. Globally, soil warming was slightly slower than air warming above it, and this difference increased over the 21st century. Regionally, soil warming kept pace with air warming in tropical and arid regions but lagged air warming in colder regions. Thus, air warming is not necessarily a good proxy for soil warming in cold regions where snow and ice impede the direct transfer of sensible heat from the atmosphere to soil. Despite this effect, high‐latitude soils were still projected to warm faster than elsewhere, albeit at slower rates than surface air above them. When compared with observations, the models were able to capture soil thermal dynamics in most biomes, but some failed to recreate thermal properties in permafrost regions. Particularly in cold regions, using soil warming rather than air warming projections may improve predictions of temperature‐sensitive soil processes.

Plants respond to various stresses by expressing distinct sets of genes. The effects of multiple stresses on plants and their interactions are not well understood. We have discovered that salt stress causes the accumulation of proteinase inhibitors and the activation of other wound-related genes in tomato (Lycopersicon esculentum) plants. Salt stress was also found to enhance the plant's response to wounding locally and systemically. The tomato mutant (def-1), which has an impairment in the octadecanoid pathway, displayed a severe reduction in the accumulation of proteinase inhibitors under salt stress, indicating that salt stress-induced accumulation of proteinase inhibitors was jasmonic acid dependent. The analysis of salt stress in another tomato mutant, spr-1, which carries a mutation in a systemin-specific signaling component, and transgenic tomato plants that express an antisense-prosystemin cDNA, showed that prosystemin activity was not required for the salt-induced accumulation of proteinase inhibitors, but was necessary to achieve maximal levels. These results suggest that a prosystemin independent- but jasmonic acid-dependent pathway is utilized for proteinase inhibitor accumulation in response to salt stress.

Disease predictive systems are intended to be management aids. With a few exceptions, these systems typically do not have direct sustained use by growers. Rather, their impact is mostly pedagogic and indirect, improving recommendations from farm advisers and shaping management concepts. The degree to which a system is consulted depends on the amount of perceived new, actionable information that is consistent with the objectives of the user. Often this involves avoiding risks associated with costly disease outbreaks. Adoption is sensitive to the correspondence between the information a system delivers and the information needed to manage a particular pathosystem at an acceptable financial risk; details of the approach used to predict disease risk are less important. The continuing challenge for researchers is to construct tools relevant to farmers and their advisers that improve upon their current management skill. This goal requires an appreciation of growers' decision calculus in managing disease problems and, more broadly, their overall farm enterprise management.

Seed priming can markedly increase the germination rate of pepper ( Capsicum annuum L) seed, but has not always been accompanied by improvements in field emergence rates or percentages. Furthermore, optimal priming conditions may vary among cultivars and even seed lots of a given species. The objective of this study was to evaluate the influence of a standard seed priming procedure on the laboratory germination and field emergence of a large number of pepper seed lots. Forty‐two (1986 study) or 30 (1987 study) lots of ‘Yolo Wonder’ and ‘Anaheim’ pepper (all >80% viability) were primed for 7 d at 25 °C on blotters saturated with 30 g KNO 3 kg ‐1 H 2 O solution, rinsed, and dried. Control (untreated) and primed seeds were then germinated in the laboratory at 20 °C or planted in field emergence trials at two locations (Davis and Fresno, CA) in yr. Priming slightly reduced final laboratory germination percentages, but also decreased the mean times to germination (MTG) 71 to 78%. Field emergence percentages generally were unaffected by priming, but mean times to emergence (MTE) were reduced 8 to 29%. There was a strong interaction between seed lots and priming response, with the slowly germinating lots exhibiting the greatest benefit from priming. In both the laboratory and field, the reduction in time to germination or emergence due to priming was linearly related to the initial MTG or MTE. A quadratic relationship between the MTG and MTE of control seeds extrapolated through the same data for primed seeds. Thus, while laboratory germination percentages were a relatively poor predictor of field emergence percentages for these relatively high‐quality seed lots, laboratory MTG was highly correlated with field MTE in two of three field trials. Although seed lots differed in the magnitude of their response to a standard priming treatment, all lots exhibited markedly improved rates of germination and emergence after priming.

Biochar cation exchange capacity (CEC) is a key property central to better retention of soil nutrients and reduction of fertilizer runoff. This paper reports a breakthrough process to improve biochar CEC value by a factor of nearly 10 through biochar surface oxygenation by ozonization. The CEC value of the untreated biochar was measured to be anywhere between 14 and 17 cmol/kg. A 90 min dry ozonization treatment resulted in an increased biochar CEC value of 109–152 cmol/kg. Simultaneously, the biochar ozonization process resulted in a reduction of biochar pH from 9.82 to as low as 3.07, indicating the formation of oxygen-functional groups including carboxylic acids on biochar surfaces. Using the technique of X-ray photoelectron spectroscopy (XPS), the formation of oxygen-functional groups including carboxylic acids on biochar surfaces have been observed at a nanometer molecular scale following the ozonization treatment. The molar O/C ratio (0.31:1) on ozonized biochar surface as analyzed by XPS was indeed significantly higher than that (0.16:1) of the control biochar surface. The molar O/C ratio from the elemental analysis data also showed an increase from the nonozonized sample (0.077:1) to the dry-ozonized sample (0.193:1). Fourier-transform infrared (FTIR) spectroscopy analysis also showed an increase in the content of oxygen-functional groups in the form of carbonyl groups on biochar surfaces upon ozonization, which can also produce certain amount of oxygenated biochar molecular fragments that may be solubilized by liquid water, potentially leading to greater effects upon application of biochar in soil.

Biochar may be a tool for mine spoil remediation; however, its mechanisms for achieving this goal remain unclear. In this study, Miscanthus (Miscanthus giganteus) biochar was evaluated for its ability to reclaim acidic mine spoils (pH < 3) through reducing metal availability, improving soil microbial enzymatic activity, and initial growth of grass seedlings. Biochar was applied at 0, 1, 2.5 and 5% (w/w) along with lime/no lime and fertilizer additions. Blue Wildrye (Elymus glaucus cv. ‘Elkton’) was planted and later the shoots and roots were collected and metal concentrations determined. Afterwards, each pot was leached with deionized water, and the leachate analyzed for pH, electrical conductivity (EC), dissolved organic carbon (DOC) and soluble metal concentrations. After drying, the spoil was extracted with 0.01 M CaCl2 and Mehlich 3 (M3) to determine extractable Al, Cu, and Zn concentrations. Additionally, microbial activity was measured using a fluorescent β-glucosidase and N-acetyl-β-d-glucosaminidase assay. Spoil treated with lime and biochar had significantly greater pH and EC values. Significantly greater β-glucosidase activity occurred only in the 5% biochar plus lime treatment, while N-acetyl-β-d-glucosaminidase activities were not altered. Metal concentrations in rye shoot and roots were mixed. Lime additions significantly reduced extractable metal concentrations. Increasing biochar rates alone significantly reduced leachate DOC concentrations, and subsequently reduced leachable metal concentrations. Surprisingly, miscanthus biochar, by itself, was limited at mitigation, but when combined with lime, the combination was capable of further reducing extractable metal concentrations and improving β-glucosidase enzyme activity.

microRNAs (miRNAs) are small, single-stranded RNAs that down-regulate target genes at the post-transcriptional level. miRNAs regulate target genes by guiding mRNA cleavage or by repressing translation. miRNAs play crucial roles in a broad range of developmental processes in plants. Multiple miRNAs are present in germinating seeds and seedlings of Arabidopsis, some of which are involved in the regulation of germination and seedling growth by plant hormones such as abscisic acid (ABA) and auxin. The involvement of miRNAs in ABA responses is not limited to the early stages of plant development but seems to be important for general stress responses throughout the plant life cycle. This Darwin review summarizes recent progress in miRNA research focusing on seed and stress biology, two topics which were of interest to Charles Darwin.

Abstract: In optimization problems with at least two conflicting objectives, a set of solutions rather than a unique one exists because of the trade‐offs between these objectives. A Pareto optimal solution set is achieved when a solution cannot be improved upon without degrading at least one of its objective criteria. This study investigated the application of multi‐objective evolutionary algorithm (MOEA) and Pareto ordering optimization in the automatic calibration of the Soil and Water Assessment Tool (SWAT), a process‐based, semi‐distributed, and continuous hydrologic model. The nondominated sorting genetic algorithm II (NSGA‐II), a fast and recent MOEA, and SWAT were called in FORTRAN from a parallel genetic algorithm library (PGAPACK) to determine the Pareto optimal set. A total of 139 parameter values were simultaneously and explicitly optimized in the calibration. The calibrated SWAT model simulated well the daily streamflow of the Calapooia watershed for a 3‐year period. The daily Nash‐Sutcliffe coefficients were 0.86 at calibration and 0.81 at validation. Automatic multi‐objective calibration of a complex watershed model was successfully implemented using Pareto ordering and MOEA. Future studies include simultaneous automatic calibration of water quality and quantity parameters and the application of Pareto optimization in decision and policy‐making problems related to conflicting objectives of economics and environmental quality.

Abstract Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil‐to‐atmosphere CO 2 flux, commonly though imprecisely termed soil respiration ( R S ), is one of the largest carbon fluxes in the Earth system. An increasing number of high‐frequency R S measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems as well. Such high frequency data are an invaluable resource for understanding GHG fluxes, but lack a central database or repository. Here we describe the lightweight, open‐source COSORE (COntinuous SOil REspiration) database and software, that focuses on automated, continuous and long‐term GHG flux datasets, and is intended to serve as a community resource for earth sciences, climate change syntheses and model evaluation. Contributed datasets are mapped to a single, consistent standard, with metadata on contributors, geographic location, measurement conditions and ancillary data. The design emphasizes the importance of reproducibility, scientific transparency and open access to data. While being oriented towards continuously measured R S , the database design accommodates other soil‐atmosphere measurements (e.g. ecosystem respiration, chamber‐measured net ecosystem exchange, methane fluxes) as well as experimental treatments (heterotrophic only, etc.). We give brief examples of the types of analyses possible using this new community resource and describe its accompanying R software package.

Xanthomonas leaf blight of onion (Allium cepa), caused by Xanthomonas axonopodis pv. allii, continues to be a challenging and yield-threatening disease in Colorado and other regions of onion production worldwide. Studies were conducted to develop management strategies for this disease that are equally effective and more sustainable than the current practices of making multiple applications of copper bactericides. Mixtures of bacteriophages and the plant defense activator, acibenzolar-S-methyl, were evaluated under field and greenhouse conditions for their abilities to reduce Xanthomonas leaf blight severity. Bacteriophage populations in the phyllosphere of onion were monitored over time. Bacteriophage populations persisted on onion leaves for at least 72 to 96 h under field and greenhouse conditions, respectively. Under field conditions at one location, biweekly or weekly applications of bacteriophages reduced disease severity by 26 to 50%, which was equal to or better than weekly applications of copper hydroxide plus mancozeb. Acibenzolar-S-methyl also successfully reduced disease severity by up to 50% when used alone preventatively or followed by biweekly bacteriophage applications. Reductions in disease severity generally were not associated with improvements in onion bulb size or yield. Integration of bacteriophage mixtures with acibenzolar-S-methyl appears to be a promising strategy for managing Xanthomonas leaf blight of onion, and could reduce grower reliance on conventional copper bactericide applied with ethylenebisdithiocarbamate fungicides.

To study the effects of cytokinin O-glucosylation in monocots, maize (Zea mays L.) transformants harbouring the ZOG1 gene (encoding a zeatin O-glucosyltransferase from Phaseolus lunatus L.) under the control of the constitutive ubiquitin (Ubi) promoter were generated. The roots and leaves of the transformants had greatly increased levels of zeatin-O-glucoside. The vegetative characteristics of hemizygous and homozygous Ubi:ZOG1 plants resembled those of cytokinin-deficient plants, including shorter stature, thinner stems, narrower leaves, smaller meristems, and increased root mass and branching. Transformant leaves had a higher chlorophyll content and increased levels of active cytokinins compared with those of non-transformed sibs. The Ubi:ZOG1 plants exhibited delayed senescence when grown in the spring/summer. While hemizygous transformants had reduced tassels with fewer spikelets and normal viable pollen, homozygotes had very small tassels and feminized tassel florets, resembling tasselseed phenotypes. Such modifications of the reproductive phase were unexpected and demonstrate a link between cytokinins and sex-specific floral development in monocots.

The herbicide-binding region of the chloroplast psbA gene from a total of 20 biotypes of Poa annua L resistant and susceptible to metribuzin and diuron was selectively amplified using PCR. Sequence analysis of the fragment from six herbicide-resistant biotypes of P annua exhibited a substitution from valine to isoleucine at position 219 of the D1 protein encoded by the psbA gene. This is the same mutation as reported for Chlamydomonas and Synechococcus through site-directed mutagenesis and in cell cultures of Chenopodium rubrum L. To our knowledge this is the first report of a higher plant exhibiting resistance in the field to photosystem II inhibitors due to a psbA mutation other than at position 264. The existence of additional biotypes of P annua resistant to diuron or metribuzin but lacking mutation in the herbicide-binding region indicates that resistance to these herbicides can also be attained by other mechanisms. © 2000 Society of Chemical Industry

The series of papers introduced by this one address a range of statistical applications in plant pathology, including survival analysis, nonparametric analysis of disease associations, multivariate analyses, neural networks, meta-analysis, and Bayesian statistics. Here we present an overview of additional applications of statistics in plant pathology. An analysis of variance based on the assumption of normally distributed responses with equal variances has been a standard approach in biology for decades. Advances in statistical theory and computation now make it convenient to appropriately deal with discrete responses using generalized linear models, with adjustments for overdispersion as needed. New nonparametric approaches are available for analysis of ordinal data such as disease ratings. Many experiments require the use of models with fixed and random effects for data analysis. New or expanded computing packages, such as SAS PROC MIXED, coupled with extensive advances in statistical theory, allow for appropriate analyses of normally distributed data using linear mixed models, and discrete data with generalized linear mixed models. Decision theory offers a framework in plant pathology for contexts such as the decision about whether to apply or withhold a treatment. Model selection can be performed using Akaike's information criterion. Plant pathologists studying pathogens at the population level have traditionally been the main consumers of statistical approaches in plant pathology, but new technologies such as microarrays supply estimates of gene expression for thousands of genes simultaneously and present challenges for statistical analysis. Applications to the study of the landscape of the field and of the genome share the risk of pseudoreplication, the problem of determining the appropriate scale of the experimental unit and of obtaining sufficient replication at that scale.

Xanthomonas leaf blight (Xanthomonas axonopodis pv. allii) is a yield-limiting disease of onion (Allium cepa) in the western United States. Frequent applications of copper-based bactericides amended with an ethylenebisdithiocarbamate fungicide (e.g., maneb or mancozeb, class B2 carcinogens) provide some disease suppression, but strategies to reduce conventional bactericide use are needed to minimize grower costs, environmental impact, and public exposure to class B2 pesticides. Applications of acibenzolar-S-methyl reduced in planta and epiphytic populations of X. axonopodis pv. allii as effectively as applications of copper hydroxide-mancozeb in growth chamber studies. Under field conditions, four weekly applications of acibenzolar-S-methyl reduced severity of Xanthomonas leaf blight as or more effectively than 9 to 12 weekly applications of copper hydroxide or copper hydroxide-mancozeb. Acibenzolar-S-methyl applications did not increase bulb yield or grade compared with copper bactericide treatments. However, bulb yield was reduced 22 to 27% when 10 weekly applications of acibenzolar-S-methyl were made in the absence of disease. Application of a commercial formulation of both Pantoea agglomerans strain C9-1 and Pseudomonas fluorescens strain A506 reduced severity of Xanthomonas leaf blight in field experiments. Weekly copper hydroxide applications starting 1 to 2 weeks before bulb initiation were as effective as weekly applications started 3 to 4 weeks before bulb initiation, irrespective of the maneb rate used. Integration of acibenzolar-S-methyl and biological control agents with copper hydroxide in a carefully timed spray program may eliminate the use of the class B2 carcinogens maneb and mancozeb on onion without compromising efficacy for management of Xanthomonas leaf blight.

Tall fescue (Lolium arundinaceum) is one of the primary forage and turf grasses in temperate regions of the world. A number of favourable characteristics of tall fescue are enhanced by its seed-transmissible fungal symbiont (endophyte) Epichloë coenophiala. Our approach was to assemble the tall fescue transcriptome, then identify differentially expressed genes (DEGs) for endophyte-symbiotic (E+) vs endophyte-free (E-) clones in leaf blades, pseudostems, crowns and roots. RNA-seq reads were used to construct a tall fescue reference transcriptome and compare gene expression profiles. Over all tissues examined, 478 DEGs were identified between the E+ and E- clones for at least one tissue (more than two-fold; P < 0.0001, 238 E+ > E- and 240 E- > E+), although no genes were differentially expressed in all four tissues. Gene ontology (GO) terms, GO:0010200 (response to chitin), GO:0002679 (respiratory burst during defence response) and GO:0035556 (intracellular signal transduction) were significantly overrepresented among 25 E- > E+ DEGs in leaf blade, and a number of other DEGs were associated with defence and abiotic response. In particular, endophyte effects on various WRKY transcription factors may have implications for symbiotic stability, endophyte distribution in the plant, or defence against pathogens.