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Virginia Cooperative Extension (VCE) has been a reputable source of research-based information for over 100 years. This information is provided through various forms such as field days, demonstrations, volunteer services and written materials in the form of publications. Peer reviewed publications are scholarly works and undergo reviews from experts in the field. Currently there are no VCE publications about native plants and their benefits. Materials from other organizations and such as the Virginia Department of Environmental Quality’s Plant Virginia Natives Campaign regional guides, Department of Conservation and Recreation brochures and the Digital Atlas of Virginia Flora online database have been used in VCE programming efforts. Plant Virginia Natives has been a leader in the movement to raise awareness, demand for native plants throughout the state, and has developed guides for ten regions across Virginia. By increasing the awareness of native plants, pollinators, and wildlife, local ecosystems will benefit greatly. Incorporating native plants into landscapes is especially critical because a review of 16 studies shows that the global population of insects has decreased by 45% in 40 years (Dirzo et al., 2014). Native plants provide essential support for insects. One of the barriers identified to planting more native plants is the lack of knowledge or confidence in people’s knowledge of the subject (Plant RVA Natives Steering Team, 2021). To address the lack of resources from VCE and the need for supplemental education materials, I have developed a three-part publication series on native plants. This series will promote native plants in the landscape by helping homeowners understand what native plants are, their benefits, how to use them in the landscape and how to maintain them for long term sustainability and resilience of landscapes.

Perhaps more than any other ecological discipline, invasion biology has married the practices of basic science and the application of that science. The conceptual frameworks of population regulation, metapopulations, supply-side ecology, and community assembly have all to some degree informed the regulation, management, and prevention of biological invasions. Invasion biology needs to continue to adopt emerging frameworks and paradigms to progress as both a basic and applied science. This need is urgent as the biological invasion problem continues to worsen. The development of metacommunity theory in the last two decades represents a paradigm-shifting approach to community ecology that emphasizes the multi-scale nature of community assembly and biodiversity regulation. Work on metacommunities has demonstrated that even relatively simple processes at local scales are often heavily influenced by regional-scale processes driven primarily by the dispersal of organisms. Often the influence of dispersal interacts with, or even swamps, the influence of local-scale drivers like environmental conditions and species interactions. An emphasis on dispersal and a focus on multi-scale processes enable metacommunity theory to contribute strongly to the advancement of invasion biology. Propagule pressure of invaders has been identified as one of the most important drivers facilitating invasion, so the metacommunity concept, designed to address how dispersal-driven dynamics affect community structure, can directly address many of the central questions of invasion biology. Here we revisit many of the important concepts and paradigms of biological invasions-propagule pressure, biotic resistance, enemy release, functional traits, neonative species, human-assisted transport,-and view those concepts through the lens of metacommunity theory. In doing so, we accomplish several goals. First, we show that work on metacommunities has generated multiple predictions, models, and the tools that

The development of gene-editing technology holds tremendous potential for accelerating crop trait improvement to help us address the need to feed a growing global population. However, the delivery and access of gene-editing tools to the host genome and subsequent recovery of successfully edited plants form significant bottlenecks in the application of new plant breeding technologies. Moreover, the methods most suited to achieve a desired outcome vary substantially, depending on species' genotype and the targeted genetic changes. Hence, it is of importance to develop and improve multiple strategies for delivery and regeneration in order to be able to approach each application from various angles. The use of transient transformation and regeneration of plant protoplasts is one such strategy that carries unique advantages and challenges. Here, we will discuss the use of protoplast regeneration in the application of new plant breeding technologies and review pertinent literature on successful protoplast regeneration.

Current trends in agriculture have moved toward more sustainable cultivation systems with higher efficiency of input use. A variety of materials, derived from different resources, can serve as a crop nutrient sources. An Integrated Plant Nutrition System (IPNS) uses the combined and harmonious use of inorganic, organic and biological nutrient resources to maximize efficiency of inputs. We evaluated the effects of commercial nitrogen (N) fertilizer, humic acid compounds (HA), compost/manure teas and bioinoculants as inorganic, organic and biological resources, respectively and their synergy over three years on corn (Zea mays L.) in the Mid-Atlantic USA. The individual and combined application of HA and biofertilizer following the IPNS influenced corn height and leaf greenness to varying degrees, most likely due to biostimulant effects. In 2017, corn height, NDVI, greenness and vigor responded positively to biostimulant application to varying magnitudes and growth stages, however grain yield and nutrient content were not affected. In combined studies from 2018 and 2019 corn height was not impacted by biostimulant application but NDVI, photosynthetic efficiency, greenness and vigor were increased at different doses and corn growth stages. The combined use of HA + biofertilizer (Microlife Humic + Microgeo) was the only treatment leading to increased grain yield. This study demonstrates that the individual and combined application of HA and biofertilizer can influence corn growth and vigor at various points during the growing season. However, the current study cannot conclusively confirm that the integrated use of HA and biofertilizers (IPNS) is a better practice than the application of each compound individually.

In the eastern USA and several other apple-growing regions, apple blossom thinning using lime sulfur is a relatively new crop load management strategy. This study sought to evaluate how application timing of lime sulfur + stylet oil blossom thinning sprays would influence thinning efficacy and crop safety of ‘Gala’ apples. This project occurred at two locations in the USA, Winchester, Virginia, and Mills River, North Carolina, during the 2019 growing season. Two main timing strategies were assessed: (1) model-guided sprays with the pollen tube growth model (PTGM), (2) fixed spray intervals with the first spray applied at a specified percentage of open bloom (20% vs. 80%), and the second spray applied at a reapplication interval (48 h vs. 72 h). Model-guided and 20% open bloom + 48-h treatments reduced fruit set and increased fruit weight, diameter, and length at both sites. Treatments with a delayed first spray at 80% open bloom or a more extended second reapplication of 72 h were generally ineffective. There was no conclusive evidence that lime sulfur + stylet oil blossom thinning spray timing influenced russet incidence/severity or leaf phytotoxicity. This study demonstrated that effective and safe blossom thinning can be obtained from applying two sprays at 20% open bloom and 48 h thereafter or using the PTGM.

In alpine environments, many plants, bacteria, and fungi contain ice nuclei (IN) that control freezing events, providing survival benefits. Once airborne, IN could trigger ice nucleation in cloud droplets, influencing the radiation budget and the hydrological cycle. To estimate the atmospheric relevance of alpine IN, investigations near emission sources are inevitable. In this study, we collected 14 aerosol samples over three days in August 2019 at a single site in the Austrian Alps, close to a forest of silver birches, which are known to release IN from their surface. Samples were taken during and after rainfall, as possible trigger of aerosol emission by an impactor and impinger at the ground level. In addition, we collected aerosol samples above the canopy using a rotary wing drone. Samples were analyzed for ice nucleation activity, and bioaerosols were characterized based on morphology and auto-fluorescence using microscopic techniques. We found high concentrations of IN below the canopy, with a freezing behavior similar to birch extracts. Sampled particles showed auto-fluorescent characteristics and the morphology strongly suggested the presence of cellular material. Moreover, some particles appeared to be coated with an organic film. To our knowledge, this is the first investigation of aerosol emission sources in alpine vegetation with a focus on birches.

Background Intercropping is often used in the tea producing areas where land resources are not so abundant, and the produced green tea is tasted more delicious through a tea-Chinese chestnut intercropping system according to the experience of indigenous farmers. The length and weight of tea leaf increase under this intercropping system and their root systems are stratified vertically and coordinate symbiosis. However, the delicacy mechanism under the intercropping is not fully understood. Results Green tea from the Chinese chestnut–tea intercropping system established in the 1980s ranked highest compared with a pure tea plantation from the same region. Based on the non-targeted metabolomics, 100 differential metabolites were upregulated in the tea leaves from intercropping system relative to monoculture system. Twenty-one amino acids were upregulated and three downregulated in response to the intercropping based on the targeted metabolomics; half of the upregulated amino acids had positive effects on the tea taste. Levels of allantoic acid, sugars, sugar alcohols, and oleic acid were higher and less bitter flavonoids in the intercropping system than those in monoculture system. The upregulated metabolites could promote the quality of tea and its health-beneficial health effects. Flavone and flavonol biosynthesis and phenylalanine metabolism showed the greatest difference. Numerous pathways associated with amino acid metabolism altered, suggesting that the intercropping of Chinese chestnut–tea could greatly influence amino acid metabolism in tea plants. Conclusions These results enhance our understanding of the metabolic mechanisms by which tea quality is improved in the Chinese chestnut–tea intercropping system and demonstrate that there is great potential to improve tea quality at the metabolomic level by adopting such an intercropping system.

Subclinical doses of LPS (SD-LPS) are known to cause low-grade inflammatory activation of monocytes, which could lead to inflammatory diseases including atherosclerosis and metabolic syndrome. Sodium 4-phenylbutyrate is a potential therapeutic compound which can reduce the inflammation caused by SD-LPS. To understand the gene regulatory networks of these processes, we have generated scRNA-seq data from mouse monocytes treated with these compounds and identified 11 novel cell clusters. We have developed a machine learning method to integrate scRNA-seq, ATAC-seq, and binding motifs to characterize gene regulatory networks underlying these cell clusters. Using guided regularized random forest and feature selection, our method achieved high performance and outperformed a traditional enrichment-based method in selecting candidate regulatory genes. Our method is particularly efficient in selecting a few candidate genes to explain observed expression pattern. In particular, among 531 candidate TFs, our method achieves an auROC of 0.961 with only 10 motifs. Finally, we found two novel subpopulations of monocyte cells in response to SD-LPS and we confirmed our analysis using independent flow cytometry experiments. Our results suggest that our new machine learning method can select candidate regulatory genes as potential targets for developing new therapeutics against low grade inflammation.

In this study, four recombinant inbred line (RIL) soybean populations were screened for their response to infection by Pythium sylvaticum, Pythium irregulare, Pythium oopapillum, and Pythium torulosum. The parents, PI 424237A, PI 424237B, PI 408097, and PI 408029, had higher levels of resistance to these species in a preliminary screening and were crossed with “Williams,” a susceptible cultivar. A modified seed rot assay was used to evaluate RIL populations for their response to specific Pythium species selected for a particular population based on preliminary screenings. Over 2500 single-nucleotide polymorphism (SNP) markers were used to construct chromosomal maps to identify regions associated with resistance to Pythium species. Several minor and large effect quantitative disease resistance loci (QDRL) were identified including one large effect QDRL on chromosome 8 in the population of PI 408097 × Williams. It was identified by two different disease reaction traits in P. sylvaticum, P. irregulare, and P. torulosum. Another large effect QDRL was identified on chromosome 6 in the population of PI 408029 × Williams, and conferred resistance to P. sylvaticum and P. irregulare. These large effect QDRL will contribute toward the development of improved soybean cultivars with higher levels of resistance to these common soil-borne pathogens.

Three muscadine grape genotypes (Muscadinia rotundifolia (Michx.) Small) were evaluated for their metabolite profiling and antioxidant activities at different berry developmental stages. A total of 329 metabolites were identified using UPLC-TOF-MS analysis (Ultimate 3000LC combined with Q Exactive MS and screened with ESI-MS) in muscadine genotypes throughout different developmental stages. Untargeted metabolomics study revealed the dominant chemical groups as amino acids, organic acids, sugars, and phenolics. Principal component analysis indicated that developmental stages rather than genotypes could explain the variations among the metabolic profiles of muscadine berries. For instance, catechin, epicatechin-3-gallate, and gallic acid were more accumulated in ripening seeds (RIP-S). However, tartaric acid and malonic acid were more abundant during the fruit-set (FS) stage, and malic acid was more abundant in the veraison (V) stage. The variable importance in the projection (VIP > 0.5) in partial least-squares–discriminant analysis described 27 biomarker compounds, representing the muscadine berry metabolome profiles. A heatmap of Pearson’s correlation analysis between the 27 biomarker compounds and antioxidant activities was able to identify nine antioxidant determinants; among them, gallic acid, 4-acetamidobutanoic acid, trehalose, catechine, and epicatechin-3-gallate displayed the highest correlations with different types of antioxidant activities. For instance, DPPH and FRAP conferred a similar antioxidant activity pattern and were highly correlated with gallic acid and 4-acetamidobutanoic acid. This comprehensive study of the metabolomics and antioxidant activities of muscadine berries at different developmental stages is of great reference value for the plant, food, pharmaceutical, and nutraceutical sectors.

Maple trees (genus Acer) accomplish the task of distributing objects to a wide area by producing seeds, known as samaras, which are carried by the wind as they autorotate and slowly descend to the ground. With the goal of supporting engineering applications, such as gathering environmental data over a broad area, we developed 3D-printed artificial samaras. Here, we compare the behavior of both natural and artificial samaras in both still-air laboratory experiments and wind dispersal experiments in the field. We show that the artificial samaras are able to replicate (within one standard deviation) the behavior of natural samaras in a lab setting. We further use the notion of windage to compare dispersal behavior, and show that the natural samara has the highest mean windage, corresponding to the longest flights during both high wind and low wind experimental trials. This study demonstrated a bioinspired design for the dispersed deployment of sensors and provides a better understanding of wind-dispersal of both natural and artificial samaras.

Topdressing accounts for approximately 40% of the total nitrogen (N) application of winter wheat on the Huang-Huai-Hai Plain in China. However, N use efficiency of topdressing is low due to the inadaptable topdressing method used by local farmers. To improve the N use efficiency of winter wheat, an optimization method for topdressing (THP) is proposed that uses unmanned aerial vehicle (UAV)-based remote sensing to accurately acquire the growth status and an improved model for growth potential estimation and optimization of N fertilizer amount for topdressing (NFT). The method was validated and compared with three other methods by a field experiment: the conventional local farmer’s method (TLF), a nitrogen fertilization optimization algorithm (NFOA) proposed by Raun and Lukina (TRL) and a simplification introduced by Li and Zhang (TLZ). It shows that when insufficient basal fertilizer was provided, the proposed method provided as much NFT as the TLF method, i.e., 25.05% or 11.88% more than the TRL and TLZ methods and increased the yields by 4.62% or 2.27%, respectively; and when sufficient basal fertilizer was provided, the THP method followed the TRL and TLZ methods to reduce NFT but maintained as much yield as the TLF method with a decrease of NFT by 4.20%. The results prove that THP could enhance crop production under insufficient N preceding conditions by prescribing more fertilizer and increase nitrogen use efficiency (NUE) by lowering the fertilizer amount when enough basal fertilizer is provided.

The US native liana, poison ivy (Toxicodendron radicans), responsible for contact dermatitis in humans, is a competitive weed with great potential for expansion in disturbed habitats. To facilitate a better understanding of this threat, we sought to evaluate habitat suitability, population demography, and biotic interactions of poison ivy, using a series of complementary field studies in the two habitats where it most commonly occurs—forest interiors and edges. Of the 2500 seeds planted across both habitats, poison ivy initially colonized forest interiors (32% emergence) at a higher rate than edge habitats (16.5% emergence). However, forest interior seedlings were less likely to survive (interior n = 3; edge n = 15), which might be attributed to herbivore pressure when the seedlings were smaller in the less competitive forest interior. Once established, the poison ivy seedlings appeared to be more tolerant of herbivory, except that of large grazers such as deer. The early life stage of seedling emergence, survival, and establishment are critical in poison ivy success, with biotic pressure, especially from plant competition and deer, limiting recruitment. A suitable habitat of this expanding native liana would increase with increasing forest fragmentation, but might be buffered by the expanding deer population.

Edamame is a type of green, vegetable soybean and improving shoot architecture traits for edamame is important for breeding of high-yield varieties by decreasing potential loss due to harvesting. In this study, we use digital imaging technology and computer vision algorithms to characterize major traits of shoot architecture for edamame. Using a population of edamame PIs, we seek to identify underlying genetic control of different shoot architecture traits. We found significant variations in the shoot architecture of the edamame lines including long-skinny and candle stick-like structures. To quantify the similarity and differences of branching patterns between these edamame varieties, we applied a topological measurement called persistent homology. Persistent homology uses algebraic geometry algorithms to measure the structural similarities between complex shapes. We found intriguing relationships between the topological features of branching networks and pod numbers in our plant population, suggesting combination of multiple topological features contribute to the overall pod numbers on a plant. We also identified potential candidate genes including a lateral organ boundary gene family protein and a MADS-box gene that are associated with the pod numbers. This research provides insight into the genetic regulation of shoot architecture traits and can be used to further develop edamame varieties that are better adapted to mechanical harvesting.

Seed shatter is an important weediness trait on which the efficacy of harvest weed seed control (HWSC) depends. The level of seed shatter in a species is likely influenced by agroecological and environmental factors. In 2016 and 2017, we assessed seed shatter of eight economically important grass weed species in soybean [Glycine max (L.) Merr.] from crop physiological maturity to 4 wk after maturity at multiple sites spread across 11 states in the southern, northern, and mid-Atlantic United States. From soybean maturity to 4 wk after maturity, cumulative percent seed shatter was lowest in the southern U.S. regions and increased moving north through the states. At soybean maturity, the percent of seed shatter ranged from 1% to 70%. That range had shifted to 5% to 100% (mean: 42%) by 25 d after soybean maturity. There were considerable differences in seed-shatter onset and rate of progression between sites and years in some species that could impact their susceptibility to HWSC. Our results suggest that many summer annual grass species are likely not ideal candidates for HWSC, although HWSC could substantially reduce their seed output during certain years.

Despite the huge potential of using woodlands for small ruminant grazing in the southeast US, unmanaged understory shrubs grown beyond animals' access minimize the utilization of such vegetation. This study aimed to determine the effect of vegetation height and diurnal period on the behavior and distribution patterns of goats and sheep in woodlands around summer. The study was conducted in six woodland plots (0.4 ha each) comprising southern pines and non-pine (non-target) plant species. Non-pine plants in each study plot were assigned to four treatments: cut to 0 m, 0.9 m, or 1.5 m from the ground level or left uncut (control). Cut plant stubs were allowed to regrow to full canopy before stocking animals. Eight Kiko wethers and five Katahdin rams were rotationally stocked in separate plots, and their diurnal (dawn-dusk) behaviors and distribution patterns were monitored when they were in each plot (three plots per animal species) around the summer of 2018. Animal behavior data were analyzed using the general linear model (GLM) procedure with multivariate analysis of variance (MANOVA) in SAS, while animal distribution pattern and weather data were analyzed in SAS using a GLM procedure and the distribution evenness index (DEI) using the Kruskal-Wallis rank-sum test in R. Level of significance was set at 5%. Both animal species visited the control area the least. Wethers browsed predominantly in areas where non-pine plants were cut to 0.9 m from the ground level, and rams grazed mostly in areas where non-pine plants were cut to the ground level, mostly during the post-midday period. Browsing was the dominant feeding behavior of wethers (39% browsing vs. 4% grazing), while rams' feeding behavior was dominated with grazing (24% grazing vs. 12% browsing). Lying was a predominant diurnal behavior in both wethers (46%) and rams (35%), mostly during the midday period. Wethers had a higher value for DEI than rams during the morning and post-midday periods. This study establi

A field study was conducted in 2017 and 2018 to determine foliar efficacy of halauxifen-methyl, 2,4-D, or dicamba applied alone and in combination with glyphosate at preplant burndown timing. Experiments were conducted near Painter, VA; Rocky Mount, NC; Jackson, NC; and Gates, NC. Control of horseweed, henbit, purple deadnettle, cutleaf evening primrose, curly dock, purple cudweed, and common chickweed were evaluated. Halauxifen-methyl applied at 5 g ae ha(-1) controlled small and large horseweed 89% and 79%, respectively, and was similar to control by dicamba applied at 280 g ae ha(-1). Both rates of 2,4-D-533 g ae ha(-1)(low rate [LR]) or 1,066 g ae ha(-1) (high rate [HR])-were less effective than halauxifen-methyl and dicamba for controlling horseweed. Halauxifen-methyl was the only auxin herbicide to control henbit (90%) and purple deadnettle (99%). Cutleaf evening primrose was controlled 74% to 85%, 51%, and 4% by 2,4-D, dicamba, and halauxifen-methyl, respectively. Dicamba and 2,4-D controlled curly dock 59% to 70% and were more effective than halauxifen-methyl (5%). Auxin herbicides applied alone controlled purple cudweed and common chickweed 21% or less. With the exception of cutleaf evening primrose (35%) and curly dock (37%), glyphosate alone provided 95% or greater control of all weeds evaluated. These experiments demonstrate halauxifen-methyl effectively (>= 79%) controls horseweed, henbit, and purple deadnettle, whereas common chickweed, curly dock, cutleaf evening primrose, and purple cudweed control by the herbicide is inadequate (<= 7%).

The consumption of edamame [Glycine max (L.) Merr.] in the US has rapidly increased due to its nutritional value and potential health benefits. In this study, 10 edamame genotypes were planted in duplicates in three different locations in the US-Whitethorne, Virginia (VA), Little Rock, Arkansas (AR), and Painter, VA. Edamame samples were harvested at the R6 stage of the bean development when beans filled 80-90% of the pod cavity. Afterward, comprehensive chemical composition analysis, including sugars, alanine, protein, oil, neutral detergent fiber (NDF), starch, ash, and moisture contents, were conducted on powdered samples using standard methods and the total sweetness was calculated based on the measured sugars and alanine contents. Significant effects of the location were observed on all chemical constituents of edamame (p < 0.05). The average performance of the genotypes was higher in Whitethorne for the contents of free sucrose (59.29 mg/g), fructose (11.42 mg/g), glucose (5.38 mg/g), raffinose (5.32 mg/g), stachyose (2.34 mg/g), total sweetness (78.63 mg/g), and starch (15.14%) when compared to Little Rock and Painter. The highest soluble alanine (2.67 mg/g), NDF (9.00%), ash (5.60%), and moisture (70.36%) contents were found on edamame planted in Little Rock while edamame planted in Painter had the highest crude protein (43.11%) and oil (20.33%) contents. Significant effects of genotype were observed on most of the chemical constituents (p < 0.05) except NDF and raffinose. Among the 10 genotypes, R13-5029 consistently had high sucrose content and total sweetness across the three locations, meanwhile it had relatively high protein and fiber contents. Overall, the results indicate that to breed better edamame genotypes in the US, both genotype and planting location should be taken into considerations.

The use of untreated biological soil amendments of animal origin (BSAAO) have been identified as one potential mechanism for the dissemination and persistence of Salmonella in the produce growing environment. Data on factors influencing Salmonella concentration in amended soils are therefore needed. The objectives here were to (i) compare die-off between 12 Salmonella strains following inoculation in amended soil and (ii) characterize any significant effects associated with soil-type, irrigation regimen, and amendment on Salmonella survival and die-off. Three greenhouse trials were performed using a randomized complete block design. Each strain (similar to 4 log CFU/g) was homogenized with amended or non-amended sandy-loam or clay-loam soil. Salmonella levels were enumerated In 25 g samples 0, 0.167 (4 h), 1,2, 4, 7, 10, 14, 21,28, 56, 84, 112, 168, 210, 252, and 336 days post-inoculation (dpi), or until two consecutive samples were enrichment negative. Regression analysis was performed between strain, soil-type, Irrigation, and (i) time to last detect (survival) and (li) concentration at each time-point (die-off rate). Similar effects of strain, irrigation, soil-type, and amendment were identified using the survival and die-off models. Strain explained up to 18% of the variance in survival, and up to 19% of variance In die-off rate. On average Salmonella survived for 129 days in amended soils, however, Salmonella survived, on average, 30 days longer In clay-loam soils than sandy-loam soils [95% Confidence interval (Cl) = 45, 15], with survival time ranging from 84 to 210 days for the individual strains during dally irrigation. When strain- specific associations were investigated using regression trees, S. Javiana and S. Saintpaul were found to survive longer In sandy-loam soil, whereas most of the other strains survived longer In clay-loam soil. Salmonella also survived, on average, 128 days longer when irrigated weekly, compared to daily (Cl = 101, 154), and 89 da

Reliable measures of biomass, species composition, nitrogen status, and nutritive value provide important indicators of the status of pastures and rangelands, allowing managers to make informed decisions. Traditional methods of sample collection necessitate significant investments in time and labor. Proximal sensing technologies have the potential to collect more data with a smaller investment in time and labor. However, methods and protocols for conducting pasture assessments with proximal sensors are still in development, equipment and software vary considerably, and the accuracy and utility of these assessments differ between methods and sites. This review summarizes the methods currently being developed to assess pastures and rangelands worldwide and discusses these emerging technologies in the context of diffusion of innovation theory.

Nonphotosynthetic holoparasites exploit flexible targeting of phylloquinone biosynthesis to facilitate plasma membrane redox signaling. Phylloquinone is a lipophilic naphthoquinone found predominantly in chloroplasts and best known for its function in photosystem I electron transport and disulfide bridge formation of photosystem II subunits. Phylloquinone has also been detected in plasma membrane (PM) preparations of heterotrophic tissues with potential transmembrane redox function, but the molecular basis for this noncanonical pathway is unknown. Here, we provide evidence of PM phylloquinone biosynthesis in a nonphotosynthetic holoparasite Phelipanche aegyptiaca. A nonphotosynthetic and nonplastidial role for phylloquinone is supported by transcription of phylloquinone biosynthetic genes during seed germination and haustorium development, by PM-localization of alternative terminal enzymes, and by detection of phylloquinone in germinated seeds. Comparative gene network analysis with photosynthetically competent parasites revealed a bias of P. aegyptiaca phylloquinone genes toward coexpression with oxidoreductases involved in PM electron transport. Genes encoding the PM phylloquinone pathway are also present in several photoautotrophic taxa of Asterids, suggesting an ancient origin of multifunctionality. Our findings suggest that nonphotosynthetic holoparasites exploit alternative targeting of phylloquinone for transmembrane redox signaling associated with parasitism.

Dissecting the genetic mechanisms underlying dioecy (i.e., separate female and male individuals) is critical for understanding the evolution of this pervasive reproductive strategy. Nonetheless, the genetic basis of sex determination remains unclear in many cases, especially in systems where dioecy has arisen recently. Within the economically important plant genus Solanum (similar to 2,000 species), dioecy is thought to have evolved independently at least 4 times across roughly 20 species. Here, we generate the first genome sequence of a dioecious Solanum and use it to ascertain the genetic basis of sex determination in this species. We de novo assembled and annotated the genome of Solanum appendiculatum (assembly size: similar to 750 Mb scaffold N50: 0.92 Mb; similar to 35,000 genes), identified sex-specific sequences and their locations in the genome, and inferred that males in this species are the heterogametic sex. We also analyzed gene expression patterns in floral tissues of males and females, finding approximately 100 genes that are differentially expressed between the sexes. These analyses, together with observed patterns of gene-family evolution specific to S. appendiculatum, consistently implicate a suite of genes from the regulatory network controlling pectin degradation and modification in the expression of sex. Furthermore, the genome of a species with a relatively young sex-determination system provides the foundational resources for future studies on the independent evolution of dioecy in this Glade.

The growth and productivity of several apple rootstocks have been evaluated in various previous studies. However, limited information is available on their tolerance to osmotic stress. In the present study, the physiological and molecular responses as well as abscisic acid (ABA) levels were assessed in six apple rootstocks (M26, V3, G41, G935, B9 and B118) osmotically stressed with polyethylene glycol (PEG, 30%) application under greenhouse conditions. Our results showed that V3, G41, G935 and B9 had higher relative water content (RWC), and lower electrolyte leakage (EL) under stress conditions compared to M26 and B118. Additionally, water use efficiency (WUE) was higher in V3, G41 and B9 than M26, which might be partially due to the lower transpiration rate in these tolerant rootstocks. V3, G41 and B9 rootstocks also displayed high endogenous ABA levels which was combined with a reduction in stomatal conductance and decreased water loss. At the transcriptional level, genes involved in ABA-dependent and ABA-independent pathways, e.g., SnRK, DREB, ERD and MYC2, showed higher expression in V3, G41, G935 and B9 rootstocks compared to M26 in response to stress. In contrast, WRKY29 was down-regulated in response to stress in the tolerant rootstocks, and its expression was negatively correlated with ABA content and stomatal closure. Overall, the findings of this study showed that B9, V3 and G41 displayed better osmotic stress tolerance followed by G935 then M26 and B118 rootstocks.

Hyperspectral sensors combined with machine learning are increasingly utilized in agricultural crop systems for diverse applications, including plant disease detection. This study was designed to identify the most important wavelengths to discriminate between healthy and diseased peanut (Arachis hypogaea L.) plants infected with Athelia rolfsii, the causal agent of peanut stem rot, using in-situ spectroscopy and machine learning. In greenhouse experiments, daily measurements were conducted to inspect disease symptoms visually and to collect spectral reflectance of peanut leaves on lateral stems of plants mock-inoculated and inoculated with A. rolfsii. Spectrum files were categorized into five classes based on foliar wilting symptoms. Five feature selection methods were compared to select the top 10 ranked wavelengths with and without a custom minimum distance of 20 nm. Recursive feature elimination methods outperformed the chi-square and SelectFromModel methods. Adding the minimum distance of 20 nm into the top selected wavelengths improved classification performance. Wavelengths of 501–505, 690–694, 763 and 884 nm were repeatedly selected by two or more feature selection methods. These selected wavelengths can be applied in designing optical sensors for automated stem rot detection in peanut fields. The machine-learning-based methodology can be adapted to identify spectral signatures of disease in other plant-pathogen systems.

Sustainable practices are key to the improvement of soil fertility and quality in apple (Malus x domestica Borkh.) orchards. Rootstock genotype and fertilizer inputs can alter soil biology, as well as aboveground traits including nutrient acquisition. In this study, a factorial design was used to assess the interaction between two apple rootstocks, 'Geneva 41' ('G.41') and 'Malling 9' ('M.9') with four fertilizer treatments [chicken-litter compost, yardwaste compost, fertigation using Ca(NO3)(2), and an unamended control]. The bacterial community in the rhizosphere was assessed for its impact on both plant and soil properties for each rootstock x fertilizer treatment combination. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Planctomycetes, but Verrucomicrobia and Chloroflexi were the most responsive to the fertilizer treatments. The chicken litter and yardwaste treatments had a greater effect on bacterial community structure than the control. Yardwaste, in particular, was associated with increased relative abundance of Chloroflexi, which was correlated with soil nutrient concentrations. Malling 9 had a greater bacterial diversity than G.41, but the rootstock treatment had no independent effect on the rhizosphere community structure. There was, however, a strong interaction between the rootstock and fertilizer treatments. Carbon cycling was the most prominent functional change associated with the soil bacterial community. These results suggest that compost amendments have a more positive effect on soil bacterial activity and nutrient availability than Ca(NO3)(2). Our work shows that waste-stream amendments can lead to multiple positive responses, such as increasing aboveground tree biomass, thus potentially improving orchard productivity.

Sepsis remains a common cause of death in intensive care units, accounting for approximately 20% of total deaths worldwide. Its pathogenesis is partly attributable to dysregulated inflammatory responses to bacterial endotoxins (such as lipopolysaccharide, LPS), which stimulate innate immune cells to sequentially release early cytokines (such as tumor necrosis factor (TNF) and interferons (IFNs)) and late mediators (such as high-mobility group box 1, HMGB1). Despite difficulties in translating mechanistic insights into effective therapies, an improved understanding of the complex mechanisms underlying the pathogenesis of sepsis is still urgently needed. Here, we review recent progress in elucidating the intricate mechanisms underlying the regulation of HMGB1 release and action, and propose a few potential therapeutic candidates for future clinical investigations.

In addition to their role in the biosynthesis of important molecules such as proteins and specialized metabolites, amino acids are known to function as signaling molecules through various pathways to report nitrogen status and trigger appropriate metabolic and cellular responses. Moreover, changes in amino acid levels through altered amino acid transporter activities trigger plant immune responses. Specifically, loss of function of major amino acid transporter, over-expression of cationic amino acid transporter, or over-expression of the positive regulators of membrane amino acid export all lead to dwarfed phenotypes and upregulated salicylic acid (SA)-induced stress marker genes. However, whether increasing amino acid exporter protein levels lead to similar stress phenotypes has not been investigated so far. Recently, a family of transporters, namely USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTERS (UMAMITs), were identified as amino acid exporters. The goal of this study was to investigate the effects of increased amino acid export on plant development, growth, and reproduction to further examine the link between amino acid transport and stress responses. The results presented here show strong evidence that an increased expression of UMAMIT transporters induces stress phenotypes and pathogen resistance, likely due to the establishment of a constitutive stress response via a SA-dependent pathway.

Widespread observations of ecohydrological separation are interpreted by suggesting that water flowing through highly conductive soil pores resists mixing with matrix storage over periods of days to months (i.e., two 'water worlds' exist). These interpretations imply that heterogeneous flow can produce ecohydrological separation in soils, yet little mechanistic evidence exists to explain this phenomenon. We quantified the separation between mobile water moving through preferential flow paths versus less mobile water remaining in the soil matrix after free-drainage to identify the amount of preferential flow necessary to maintain a two water world's scenario. Soil columns of varying macropore structure were subjected to simulated rainfall of increasing rainfall intensity (26 mm h(-1), 60 mm h(-1), and 110 mm h(-1)) whose stable isotope signatures oscillated around known baseline values. Prior to rainfall, soil matrix water delta H-2 nearly matched the known value used to initially wet the pore space whereas soil delta O-18 deviated from this value by up to 3.4 parts per thousand, suggesting that soils may strongly fractionate O-18. All treatments had up to 100% mixing between rain and matrix water under the lowest (26 mm h(-1)) and medium (60 mm h(-1)) rainfall intensities. The highest rainfall intensity (110 mm h(-1)), however, reduced mixing of rain and matrix water for all treatments and produced significantly different preferential flow estimates between columns with intact soil structure compared to columns with reduced soil structure. Further, artificially limiting exchange between preferential flow paths and matrix water reduced bypass flow under the most intense rainfall. We show that (1) precipitation offset metrics such as lc-excess and d-excess may yield questionable interpretations when used to identify ecohydrological separation, (2) distinct domain separation may require extreme rainfall intensities and (3) domain exchange is an important component of m

Sustainable nutrient management in high tunnel production is critical for optimizing crop yield and quality and improving soil health. In this study, we investigated the influence of different pre-plant composts (composted broiler litter, vemicompost, and cotton gin compost) in combination with different rates of organic or conventional fertilizer on zinnia plant growth, marketable yield of cut flower stems (>30 cm), and soil nutrients in a high tunnel over two years. Results showed that in general, pre-plant compost influenced plant growth, and plants that received composted broiler litter had the highest plant growth index. However, pre-plant compost did not affect the number of marketable cut stems. Fertigation during the growing season influenced the number of marketable cut stems. Comparable rates of nitrogen, from either organic or conventional fertilizer, produced similar numbers of marketable stems, suggesting that the organic fertilizer used in this study can be used as a fertilizer source for the production of zinnia cut flowers. After two years of production under the high tunnel, soil-extractable phosphorus, sodium, zinc, and pH significantly increased, suggesting that salt accumulation should be closely monitored in response to different compost or fertilizer sources with long-term production under high tunnels.

Consumption of edamame (vegetable soybeans) has increased significantly in the U.S. over the last 20 years. Although market demand has been increasing, most edamame is still imported from Asian countries. A team of multistate plant-breeding programs in the mid-Atlantic and Southeast U.S. has focused on developing new breeding lines that grow well in the U.S. and deliver what domestic growers, processors and consumers need and expect from their edamame. In our study, sensory evaluation was used to identify edamame genotypes and sensory attributes preferred by consumers to support breeding selection criteria. In the first year (reported as our "screening study"), 20 edamame genotypes were grown in three locations: Newport, AR, and Blacksburg and Painter, VA. In the second year (reported as our "validation study"), 10 edamame genotypes selected after our screening study were grown in Blacksburg and Painter, VA, Portageville, MO, and Stoneville, MS. In both years of research, untrained participants (adults; vegetable consumers not allergic to soy; N >= 50) used a traditional 9-point acceptability (hedonic) scale (1 = "dislike extremely"; 9 = "like extremely") to evaluate overall-liking, aroma, appearance, taste, and texture, and a 5-point scale (1 = "not sweet," 5 = "extremely sweet") to evaluate sweetness intensity. Next, participants used a check-all-that-apply (CATA) list of selected sensory terms to describe the sensory characteristics of each edamame sample. Overall acceptability of edamame genotypes was significantly different among all genotypes (p < 0.05). Samples described as "bitter," "sour" (flavor) or "starchy" (texture) were associated with lower acceptability scores while "salty" and "sweet" (flavor) were correlated with higher acceptability. Sensory data from the screening study were used to select the best genotypes by use of a defined decision process based on the consumer data. The validation study tested the selection decisions and further supported t

In order to screen the aroma characteristics of soybean, a new method was established which can quickly quantify the content of 2-acetyl-1pyrroline (2-AP), an important compound related to soybean aroma, using gas chromatography-mass spectrometry (GC-MS). Based on peak profile, total peak area and retention time as test indexes, an accurate identification method for fragrant soybeans was established. The optimum parameters of the protocol consisted of column temperature 70 degrees C, sample injector temperature 180 degrees C, optimum extraction alcohol content 1 mL, NaCl content 0.1 g, ultrasonication time 10 min, and extraction time 1 h, which were established by using the orthogonal test of single factors and three factors with four levels (L-9(3)(4)). 2-AP content of leaves had significant correlations with seeds, which were easier to measure. The protocol was simple and easy to carry out, consumed only small amounts of reagents, and provided accurate and reliable results with good reproducibility. A total of 101 soybean genotypes from different geographical sources were analyzed using this protocol. The results showed that the average content of 2-AP was 0.29 mg L-1, ranging from 0.094 to 1.816 mg L-1, and the genetic diversity index was 0.54. Among all genotypes-tested, they were classified into three grades, including seven elite genotypes identified as "grade one fragrant soybeans", which were Zhonglong 608, Heinong 88, Ha13-2958, Hongmiandou, Heinong 82, Huangmaodou, and Jiyu 21. These results provide both an identification technique and several elite aroma genotypes for gene discovery and good quality breeding in soybean.

Background Human wastewater biosolids, hereafter referred to as biosolids, are produced in significant quantities around the world and often applied to an extensive land mass including agricultural fields, forests, mine lands, and urban areas. Land-application of biosolids has been reported in peer-reviewed and non-peer-reviewed work to change soil organic carbon stocks in varying amounts. Determining the potential of soil organic carbon (SOC) stock change and sequestration from biosolids land application is critical for biosolids producers and users to gain access to carbon credit markets. Our review question is, "what is the impact of biosolids application on long-term soil carbon sequestration rates?” We look to explore this main question with the follow-up, "does biosolids processing methods and characteristics, application method, soil properties, land management and other modifiers affect rates of carbon accumulation from land-applied biosolids?" Methods Searches will be conducted using online databases (i.e., Web of Science Core Collection, CAB Abstracts, Scopus, ProQuest Dissertations & Theses Global), search engines (Google Scholar and Microsoft Academic), and specialist websites to find primary field studies and grey literature of biosolids land-application effects on soil organic carbon stocks. We will use English search terms and predefined inclusion criteria of: (1) a field study of at least 24 months that reports soil organic carbon/matter (SOC/SOM) concentrations/stocks; (2) has two types of treatments: (i) a control (non-intervention AND/OR synthetic fertilizer) AND (ii) a biosolids-based amendment; and (3) information of amendment properties and application dates and rates to estimate the relative contribution of the applied materials to SOC changes. We will screen results in two stages: (1) title and abstract and (2) full text. A 10% subset will be screened by two reviewers for inclusion at the title and abstract level and use a kappa analysis to e

Introduced cool-season grasses are dominant in Virginia's grasslands, but their high digestible energy and nonstructural carbohydrate (NSC) levels pose a risk for horses prone to obesity and laminitis. Native warm-season grasses (NWSGs) have lower digestible energy and NSC levels that may be more suitable for horses susceptible to laminitis. Although NWSGs have desirable characteristics, they are novel forages for horses. Little is known about NWSG intake or potential toxicity to horses or how grazing by horses may affect NWSG swards. The overall objectives of this research were to 1) assess voluntary intake, toxicological response, and apparent digestibility of NWSG hays fed to horses; and 2) evaluate the characteristics of three NWSG species under equine grazing. For the first objective, a hay feeding trial using indiangrass (IG) (Sorghastrum nutans) and big bluestem (BB) (Andropogon gerardii) was conducted with nine Thoroughbred geldings in a replicated 3 x 3 Latin square design. Voluntary dry matter intake of IG and BB hays by horses were 1.3% and 1.1% of BW/d, lower than orchardgrass (Dactylis glomerata), an introduced cool-season grass, at 1.7% of BW/d (P = 0.0020). Biomarkers for hepatotoxicity remained within acceptable ranges for all treatments. Apparent dry matter digestibility (DMD) did not differ among hays, ranging from 39% to 43%. NSC levels ranged from 4.4% to 5.4%, below maximum recommended concentrations for horses susceptible to laminitis. For the second objective, a grazing trial was conducted comparing IG, BB, and eastern gamagrass (EG) (Tripsacum dactyloides) yields, forage losses, changes in vegetative composition, and effects on equine bodyweight. Nine, 0.1-ha plots were seeded with one of the three native grass treatments, and each plot was grazed by one Thoroughbred gelding in two grazing bouts, one in July and another in September 2019. IG had the greatest available forage, at 4,340 kg/ha, compared with 3,590 kg/ha from BB (P < 0.0001). EG

Background K-seq, a new genotyping methodology based on the amplification of genomic regions using two steps of Klenow amplification with short oligonucleotides, followed by standard PCR and Illumina sequencing, is presented. The protocol was accompanied by software developed to aid with primer set design. Results As the first examples, K-seq in species as diverse as tomato, dog and wheat was developed. K-seq provided genetic distances similar to those based on WGS in dogs. Experiments comparing K-seq and GBS in tomato showed similar genetic results, although K-seq had the advantage of finding more SNPs for the same number of Illumina reads. The technology reproducibility was tested with two independent runs of the tomato samples, and the correlation coefficient of the SNP coverages between samples was 0.8 and the genotype match was above 94%. K-seq also proved to be useful in polyploid species. The wheat samples generated specific markers for all subgenomes, and the SNPs generated from the diploid ancestors were located in the expected subgenome with accuracies greater than 80%. Conclusion K-seq is an open, patent-unencumbered, easy-to-set-up, cost-effective and reliable technology ready to be used by any molecular biology laboratory without special equipment in many genetic studies.

Potential effectiveness of harvest weed seed control (HWSC) systems depends upon seed shatter of the target weed species at crop maturity, enabling its collection and processing at crop harvest. However, seed retention likely is influenced by agroecological and environmental factors. In 2016 and 2017, we assessed seed-shatter phenology in 13 economically important broadleaf weed species in soybean [Glycine max (L.) Merr.] from crop physiological maturity to 4 wk after physiological maturity at multiple sites spread across 14 states in the southern, northern, and mid-Atlantic United States. Greater proportions of seeds were retained by weeds in southern latitudes and shatter rate increased at northern latitudes. Amaranthus spp. seed shatter was low (0% to 2%), whereas shatter varied widely in common ragweed (Ambrosia artemisiifolia L.) (2% to 90%) over the weeks following soybean physiological maturity. Overall, the broadleaf species studied shattered less than 10% of their seeds by soybean harvest. Our results suggest that some of the broadleaf species with greater seed retention rates in the weeks following soybean physiological maturity may be good candidates for HWSC.

Sexually transmitted microbes are hypothesized to influence the evolution of reproductive strategies. Though frequently discussed in this context, our understanding of the reproductive microbiome is quite nascent. Indeed, testing this hypothesis first re-quires establishing a baseline understanding of the temporal dynamics of the reproductive microbiome and of how individual variation in reproductive behavior and age influence the assembly and maintenance of the reproductive microbiome as a whole. Here, we ask how mating activity, breeding stage, and age influence the reproductive microbiome. We use observational and experimental approaches to explain variation in the cloacal microbiome of free- living, female tree swallows (Tachycineta bicolor). Using microsatellite- based parentage analyses, we determined the number of sires per brood (a proxy for female mating activity). We experimentally increased female sexual activity by administering exogenous 17ß-estradiol. Lastly, we used bacterial 16S rRNA amplicon sequencing to characterize the cloacal microbiome. Neither the number of sires per brood nor the increased sexual activity of females significantly influenced female cloacal microbiome richness or community structure. Female age, however, was positively correlated with cloacal microbiome richness and influenced overall community structure. A hypothesis to explain these patterns is that the effect of sexual activity and the number of mates on variation in the cloacal microbiome manifests over an individual's lifetime. Additionally, we found that cloacal microbiome alpha diversity (Shannon Index, Faith's phylogenetic distance) decreased and community structure shifted between breeding stages. This is one of few studies to document within-individual changes and age- related differences in the cloacal microbiome across successive breeding stages. More broadly, our results contribute to our understanding of the role that host life history and behavior play in shaping

Background Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions Alkaline salt tolerance of switchgrass may be achieved by t

Thirteen states associated with the Southern Extension and Research Activities Information Exchange Group-6 (SERA-IEG-6) agreed to share their soil test based P and K rate recommendations for nine major crops. The objectives were to compare fertilizer P and K rate recommendations, to look for opportunities to rationalize similar recommendations across state lines, and to examine challenges to the development of a cooperative regional approach to P and K recommendations. Mehlich-3 (eight states), Mehlich-1 (five states), or Lancaster (one state) extractions were the basis of plant available soil P (STP) and K (STK) assessment. Fertilizer recommendation philosophies (sufficiency, build and maintain, and/or hybrid) variation among the states might be the main reason behind such discrepancies. Although a few similarities in P and K rate recommendations were found, the different philosophies, numerical presentations, and extraction procedures drove important recommendation differences. Widespread adoption of the Mehlich-3 extraction procedure has not reduced variation in fertilizer P and K rate recommendations among the states. Instead, for states using Mehlich 3, soil test critical concentrations ranged from 30 to 75 mg P kg(-1) and 60 to 175 mg K kg(-1) for corn (Zea mays L.) grain and warm-season grass hay production. The adoption of uniform soil testing terminology, sample collection guidelines, extraction methods, and interpretations across common physiographic regions, soils, and state lines remains a challenge. Differences arise because of the different soil orders and properties, climate conditions, and resulting crop responses to added P and K fertilizers. Such differences in soil-test-based fertilizer P and K recommendations are state specific and highlight needs to examine the soil testing and recommendation process, make soil test results end-user friendly, and, when appropriate, standardize fundamental information used in the soil testing guidelines.

Weeds are among the major constraints to any crop production system, reducing productivity and profitability. Herbicides are among the most effective methods to control weeds, and reliance on herbicides for weed control has increased significantly with the advent of herbicide-resistant crops. Unfortunately, over-reliance on herbicides leads to environmental-health issues and herbicide-resistant weeds, causing human health and ecological concerns. Crop diversification can help manage weeds sustainably in major crop production systems. It acts as an organizing principle under which technological innovations and ecological insights can be combined to manage weeds sustainably. Diversified cropping can be defined as the conscious inclusion of functional biodiversity at temporal and/or spatial levels to improve the productivity and stability of ecosystem services. Crop diversification helps to reduce weed density by negatively impacting weed seed germination and weed growth. Additionally, diversified farming systems are more resilient to climate change than monoculture systems and provide better crop yield. However, there are a few challenges to adopting a diversified cropping system, ranging from technology innovations, government policies, farm-level decisions, climate change, and market conditions. In this review, we discuss how crop diversification supports sustainable weed management, the challenges associated with it, and the future of weed management with respect to the diversification concept.

Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to

Spray-induced gene silencing (SIGS) using topical dsRNA applications has risen as a promising, target-specific, and environmentally friendly disease management strategy against phytopathogenic fungi. However, dsRNA stability, efficacy, and scalability are still the main constraints facing SIGS broader application. Here we show that Escherichia coli-derived anucleated minicells can be utilized as a cost-effective, scalable platform for dsRNA production and encapsulation. We demonstrated that minicell-encapsulated dsRNA (ME-dsRNA) was shielded from RNase degradation and stabilized on strawberry surfaces, allowing dsRNA persistence in field-like conditions. ME-dsRNAs targeting chitin synthase class III (Chs3a, Chs3b) and DICER-like proteins (DCL1 and DCL2) genes of Botryotinia fuckeliana selectively knocked-down the target genes and led to significant fungal growth inhibition in vitro. We also observed a compensatory relationship between DCL1 and DCL2 gene transcripts, where the silencing of one gene upregulated the expression of the other. Contrary to naked-dsRNAs, ME-dsRNAs halted disease progression in strawberries for 12 days under greenhouse conditions. These results elucidate the potential of ME-dsRNAs to enable the commercial application of RNAi-based, species-specific biocontrols comparable in efficacy to conventional synthetics. ME-dsRNAs offer a platform that can readily be translated to large-scale production and deployed in open-field applications to control grey mould in strawberries.

Wheat (Triticum aestivum L.) production requires a large amount of nitrogen (N) supply because growers aim to achieve high grain yield and appropriate grain protein content simultaneously. A comprehensive understanding of the mechanisms that underpin efficient N usage at limited N in wheat can facilitate the development of new N-saving varieties in this major crop. Here, we performed comparative analysis of flag leaf responses to N availability in soft red winter wheat with contrasting N use efficiency (NUE); VA08MAS-369 (high NUE) and VA07W-415 (low NUE). This study demonstrated that accelerated senescence along with enhanced breakdown of protein and starch in flag leaves was correlated with higher grain yield, NUE for grain yield, and NUE for grain protein under N limitation. The more dramatic reductions in flag leaf N compounds and carbohydrate reserves in VA08MAS-369 were linked with significantly elevated expression of genes and enzymes associated with these metabolic pathways in this high NUE genotype. Consistent with the gene expression data, nitrate reductase, glutamine synthetase, and NAD-dependent glutamate dehydrogenase activities were highly induced under limited N in VA08MAS-369. It was previously reported that accelerated senescence contributes to increased grain protein content in wheat under regular N supply. This study provides molecular and physiological evidence that vigorous senescence and N remobilization also benefit grain yield under N deprivation.

Background Apple blotch (AB) caused by Diplocarpon coronariae (Dc) has been established in Europe since 2010. AB is a serious apple disease, mostly in low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. However, the epidemiology and population genetic structure of this pathogen is unknown. Methods We developed twelve Dc-specific microsatellite markers and screened DNA of both pure fungal isolates and infected apple leaves. The marker data of 313 European samples of Dc were compared to Dc isolates from Asia (n = 7) and the USA (n = 3). Results We found 31 distinct multilocus genotypes (MLGs) in European samples, and seven additional MLGs in the Asian and USA samples. The European samples had the typical genetic signature of a recently introduced species including high clonality, a low number of private alleles and one dominant MLG across all the sampling sites. All European MLGs were genetically distant from those MLGs of Asian and USA origin. Based on the lack of linkage disequilibrium observed, there is evidence that Dc undergoes regular cycles of sexual recombination in the European population, although the sexual stage (apothecia) has not been observed in Europe. Conclusions The twelve newly developed SSR markers reported here provide a useful tool to characterize the population genetic diversity and structure of Dc in Europe. Our study supports the hypothesis that Dc is a recently introduced pathogen in Europe, but of currently unknown origin. Dc has a large effective population size during field epidemics, so we believe that the pathogen has substantial evolutionary potential. Application of the SSR markers to large-scale and diverse Dc samples will help to better understand the epidemiology of AB, which has become a global apple disease, and will help guide effective mitigation strategies based on disease management and resistance breeding.

Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals’ protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds.

Pollinator refuges such as wildflower strips are planted on farms with the goals of mitigating wild pollinator declines and promoting crop pollination services. It is unclear, however, whether or how these goals are impacted by managed honey bee (Apis mellifera L.) hives on farms. We examined how wildflower strips and honey bee hives and/or their interaction influence wild bee communities and the fruit count of two pollinator-dependent crops across 21 farms in the Mid-Atlantic U.S. Although wild bee species richness increased with bloom density within wildflower strips, populations did not differ significantly between farms with and without them whereas fruit counts in both crops increased on farms with wildflower strips during one of 2 years. By contrast, wild bee abundance decreased by 48%, species richness by 20%, and strawberry fruit count by 18% across all farm with honey bee hives regardless of wildflower strip presence, and winter squash fruit count was consistently lower on farms with wildflower strips with hives as well. This work demonstrates that honey bee hives could detrimentally affect fruit count and wild bee populations on farms, and that benefits conferred by wildflower strips might not offset these negative impacts. Keeping honey bee hives on farms with wildflower strips could reduce conservation and pollination services.

A sufficient nitrogen (N) supply is pivotal for high grain yield and desired grain protein content in wheat (Triticum aestivum L.). Elucidation of physiological and molecular mechanisms underlying nitrogen use efficiency (NUE) will enhance our ability to develop new N-saving varieties in wheat. In this study, we analyzed two soft red winter wheat genotypes, VA08MAS-369 and VA07W-415, with contrasting NUE under limited N. Our previous study demonstrated that higher NUE in VA08MAS-369 resulted from accelerated senescence and N remobilization in flag leaves at low N. The present study revealed that VA08MAS-369 also exhibited higher nitrogen uptake efficiency (NUpE) than VA07W-415 under limited N. VA08MAS-369 consistently maintained root growth parameters such as maximum root depth, total root diameter, total root surface area, and total root volume under N limitation, relative to VA07W-415. Our time-course N content analysis indicated that VA08MAS-369 absorbed N more abundantly than VA07W-415 after the anthesis stage at low N. More efficient N uptake in VA08MAS-369 was associated with the increased expression of genes encoding a two-component high-affinity nitrate transport system, including four NRT2s and three NAR2s, in roots at low N. Altogether, these results demonstrate that VA08MAS-369 can absorb N efficiently even under limited N due to maintained root development and increased function of N uptake. The ability of VA08MAS-369 in N remobilization and uptake suggests that this genotype could be a valuable genetic material for the improvement of NUE in soft red winter wheat.

In grafted plants, the movement of long-distance signals from rootstocks can modulate the development and function of the scion. To understand the mechanisms by which tolerant rootstocks improve scion responses to osmotic stress (OS) conditions, mRNA transport of osmotic responsive genes (ORGs) was evaluated in a tomato/potato heterograft system. In this system, Solanum tuberosum was used as a rootstock and Solanum lycopersicum as a scion. We detected changes in the gene expression levels of 13 out of the 21 ORGs tested in the osmotically stressed plants; of these, only NPR1 transcripts were transported across the graft union under both normal and OS conditions. Importantly, OS increased the abundance of StNPR1 transcripts in the tomato scion. To examine mRNA mobility in transgrafted plants, StNPR1 and StDREB1 genes representing the mobile and non-mobile transcripts, respectively, were overexpressed in tobacco (Nicotiana tabacum). The evaluation of transgenic tobacco plants indicated that overexpression of these genes enhanced the growth and improved the physiological status of transgenic plants growing under OS conditions induced by NaCl, mannitol and polyethylene glycol (PEG). We also found that transgenic tobacco rootstocks increased the OS tolerance of the WT-scion. Indeed, WT scions on transgenic rootstocks had higher ORGs transcript levels than their counterparts on non-transgenic rootstocks. However, neither StNPR1 nor StDREB1 transcripts were transported from the transgenic rootstock to the wild-type (WT) tobacco scion, suggesting that other long-distance signals downstream these transgenes could have moved across the graft union leading to OS tolerance. Overall, our results signify the importance of StNPR1 and StDREB1 as two anticipated candidates for the development of stress-resilient crops through transgrafting technology.

The objective of this study was to examine peanut (Arachis hypogaea L.) kernel percent sound splits as a function of sound mature kernel seed size when shelled on a reciprocating sheller. Data were compiled from a total of 139 field experiments conducted in the Virginia-Carolina region and Georgia from 2005 to 2020. Runner and Virginia peanut market types were graded according to United States Department of Agriculture (USDA) standards using standard sheller screens with upper grid sizes corresponding to the red pan from the pre-sizer of 10.3 × 19.1 mm (26/64 × 3/4 ″) and 13.5 × 25.4 mm (34/64 × 1 ″) with minimum bar grid clearances of 8.7 (11/32 ″) and 12.7 mm (1/2 ″), respectively. A subset of runner market type samples was graded using the Virginia sheller screen. Grade data per market type and sheller screen was analyzed separately. Among runner market types shelled with the standard runner-type screen, percent sound splits increased linearly with increasing seed size at the logit rate of 1.16 per sound mature kernel g (p < 0.001). Sound splits for Virginia and runner market types shelled on the standard Virginia-type screen did not significantly vary by kernel size (p = 0.939 and 0.687, respectively). Extra-large kernels (proportion) for Virginia types linearly increased with seed size at 1.91 per sound mature kernel g (logit scale) (p < 0.001). Runner market types sized 75 to 91 g/100 sound mature kernels (605 to 500 seed/lb) were estimated to have a 50% probability of a 2.3 to 4.5% or greater increase in sound splits when shelled with the standard runner-type screen compared to runner-type seed sized 55 g/100 sound mature kernels (820 seed/lb), respectively, equivalent to a potential deduction increase of 1.8 to 4.4 USD /1000 kg. For both Virginia and runner market types, seed weight linearly increased with pod weight at 0.169 and 0.195 g/g (p < 0.001), respectively. Results from this study may be used as a referenc

Background: Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. Methods: Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. Results: LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset.

Plant stress is a real dilemma; it puzzles plant biologists and is a global problem that negatively affects people’s daily lives. Of particular interest is salinity, because it represents one of the major water-related stress types. We aimed to determine the signals that guide the cellular-related events where various adaptation mechanisms cross-talk to cope with salinity-related water stress in plants. In an attempt to unravel these mechanisms and introduce cellular events in the right context, we expansively discussed how salt-related signals are sensed, with particular emphasis on aquaporins, nonselective cation channels (NSCCs), and glycosyl inositol phosphorylceramide (GIPC). We also elaborated on the critical role Ca2+, H+, and ROS in mediating signal transduction pathways associated with the response and tolerance to salt stress. In addition, the fragmentary results from the literature were compiled to develop a harmonized, informational, and contemplative model that is intended to improve our perception of these adaptative mechanisms and set a common platform for plant biologists to identify intriguing research questions in this area.