Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.)

Global climate change is having a significant effect on agriculture by causing greater precipitation variability and an increased risk of drought. To mitigate these effects, it is important to identify specific traits, adaptations, and germplasm that improve tolerance to soil water deficit. Local varieties, known as landraces, have undergone generations of farmer-mediated selection and can serve as sources of variation, specifically for tolerance to abiotic stress. Landraces can possess local adaptations, where accessions adapted to a particular environment will outperform others grown under the same conditions. We explore adaptations to water deficit in chile pepper landraces from across an environmental gradient in Mexico, a center of crop domestication and diversity, as well in improved varieties bred for the US. In the present study, we evaluated 25 US and Mexico accessions in a greenhouse experiment under well-watered and water deficit conditions and measured morphological, physiological, and agronomic traits. Accession and irrigation regime influenced plant biomass and height, while branching, CO2 assimilation, and fruit weight were all influenced by an interaction between accession and irrigation. A priori group contrasts revealed possible adaptations to water deficit for branching, CO2 assimilation, and plant height associated with geographic origin, domestication level, and pepper species. Additionally, within the Mexican landraces, the number of primary branches had a strong relationship with precipitation from the environment of origin. This work provides insight into chile pepper response to water deficit and adaptation to drought and identifies possibly tolerant germplasm.

CRISPR/Cas9-mediated mutagenesis of sweet basil candidate susceptibility gene ObDMR6 enhances downy mildew resistance

Sweet basil (Ocimum basilicum) is an economically important allotetraploid (2n = 4x = 48) herb whose global production is threatened by downy mildew disease caused by the obligate biotrophic oomycete, Peronospora belbahrii. Generation of disease resistant cultivars by mutagenesis of susceptibility (S) genes via CRISPR/Cas9 is currently one of the most promising strategies to maintain favored traits while improving disease resistance. Previous studies have identified Arabidopsis DMR6 (Downy Mildew Resistance 6) as an S gene required for pathogenesis of the downy mildew-causing oomycete pathogen Hyaloperonospora arabidopsidis. In this study, a sweet basil homolog of DMR6, designated ObDMR6, was identified in the popular sweet basil cultivar Genoveser and found to exist with a high copy number in the genome with polymorphisms among the variants. Two CRISPR/Cas9 constructs expressing one or two single guide RNAs (sgRNAs) targeting the conserved regions of ObDMR6 variants were generated and used to transform Genoveser via Agrobacterium-mediated transformation. 56 T0 lines were generated, and mutations of ObDMR6 were detected by analyzing the Sanger sequencing chromatograms of an ObDMR6 fragment using the Interference of CRISPR Edits (ICE) software. Among 54 lines containing mutations in the targeted sites, 13 had an indel percentage greater than 96% suggesting a near-complete knockout (KO) of ObDMR6. Three representative transgene-free lines with near-complete KO of ObDMR6 determined by ICE were identified in the T1 segregating populations derived from three independent T0 lines. The mutations were further confirmed using amplicon deep sequencing. Disease assays conducted on T2 seedlings of the above T1 lines showed a reduction in production of sporangia by 61-68% compared to the wild-type plants and 69-93% reduction in relative pathogen biomass determined by quantitative PCR (qPCR). This study not only has generated transgene-free sweet basil varieties with improved downy mildew resistance, but also contributed to our understanding of the molecular interactions of sweet basil-P. belbahrii.

Who infects whom?-Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data

Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johne’s disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1–4 other cows and spread infection to 0–17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.

Phylogenetic and phenotypic characterization of Fusarium oxysporum f. sp. niveum isolates from Florida-grown watermelon

Fusarium wilt of watermelon (Citrullus lanatus) caused by Fusarium oxysporum f. sp. niveum (Fon), has become an increasing concern of farmers in the southeastern USA, especially in Florida. Management of this disease, most often through the use of resistant cultivars and crop rotation, requires an accurate understanding of an area’s pathogen population structure and phenotypic characteristics. This study improved the understanding of the state’s pathogen population by completing multilocus sequence analysis (MLSA) of two housekeeping genes (BT and TEF) and two loci (ITS and IGS), aggressiveness and race-determining bioassays on 72 isolates collected between 2011 and 2015 from major watermelon production areas in North, Central, and South Florida. Multilocus sequence analysis (MLSA) failed to group race 3 isolates into a single large clade; moreover, clade membership was not apparently correlated with aggressiveness (which varied both within and between clades), and only slightly with sampling location. The failure of multilocus sequence analysis using four highly conserved housekeeping genes and loci to clearly group and delineate known Fon races provides justification for future whole genome sequencing efforts whose more robust genomic comparisons will provide higher resolution of intra-species genetic distinctions. Consequently, these results suggest that identification of Fon isolates by race determination alone may fail to detect economically important phenotypic characteristics such as aggressiveness leading to inaccurate risk assessment.

Evaluation of curcumin and copper acetate against Salmonella Typhimurium infection, intestinal permeability, and cecal microbiota composition in broiler chickens

BACKGROUND

Interest in the use of natural feed additives as an alternative to antimicrobials in the poultry industry has increased in recent years because of the risk of bacterial resistance. One of the most studied groups are polyphenolic compounds, given their advantages over other types of additives and their easy potentiation of effects when complexes are formed with metal ions. Therefore, the objective of the present study was to evaluate the impact of dietary supplementation of copper acetate (CA), curcumin (CR), and their combination (CA-CR) against Salmonella Typhimurium colonization, intestinal permeability, and cecal microbiota composition in broiler chickens through a laboratory Salmonella infection model. S. Typhimurium recovery was determined on day 10 post-challenge by isolating Salmonella in homogenates of the right cecal tonsil (12 chickens per group) on Xylose Lysine Tergitol-4 (XLT-4) with novobiocin and nalidixic acid. Intestinal integrity was indirectly determined by the fluorometric measurement of fluorescein isothiocyanate dextran (FITC-d) in serum samples from blood obtained on d 10 post-S. Typhimurium challenge. Finally, microbiota analysis was performed using the content of the left caecal tonsil of 5 chickens per group by sequencing V4 region of 16S rRNA gene.

RESULTS

The results showed that in two independent studies, all experimental treatments were able to significantly reduce the S. Typhimurium colonization in cecal tonsils (CT, P < 0.0001) compared to the positive control (PC) group. However, only CA-CR was the most effective treatment in reducing S. Typhimurium counts in both independent studies. Furthermore, the serum fluorescein isothiocyanate dextran (FITC-d) concentration in chickens treated with CR was significantly lower when compared to PC (P = 0.0084), which is related to a decrease in intestinal permeability and therefore intestinal integrity. The effect of dietary treatments in reducing Salmonella was further supported by the analysis of 16S rRNA gene sequences using Linear discriminant analysis effect size (LEfSe) since Salmonella was significantly enriched in PC group (LDA score > 2.0 and P < 0.05) compared to other groups. In addition, Coprobacillus, Eubacterium, and Clostridium were significantly higher in the PC group compared to other treatment groups. On the contrary, Fecalibacterium and Enterococcus in CR, unknown genus of Erysipelotrichaceae at CA-CR, and unknown genus of Lachnospiraceae at CA were significantly more abundant respectively.

CONCLUSIONS

CR treatment was the most effective treatment to reduce S. Typhimurium intestinal colonization and maintain better intestinal homeostasis which might be achieved through modulation of cecal microbiota.

Novel ethanol production using biomass preprocessing to increase ethanol yield and reduce overall costs

BACKGROUND

Ethanol biorefineries need to lower their overall production costs to become economically feasible. Two strategies to achieve this are to reduce costs using cheaper feedstocks or to increase the ethanol production yield. Low-cost feedstocks usually have high non-structural components (NSC) content; therefore, a new process is necessary to accommodate these feedstocks and overcome the negative effects of NSC. This study developed a novel ethanol biorefinery process including a biomass preprocessing step that enabled the use of lower-cost feedstocks while improving ethanol production without detoxification (overliming). Two types of poplar feedstocks were used, low-quality whole-tree chips (WTC) and high-quality clean pulp chips (CPC), to determine if the proposed process is effective while using feedstocks with different NSC contents.

RESULTS

Technical assessment showed that acidic preprocessing increased the monomeric sugar recovery of WTC from 73.2% (untreated) to 87.5% due to reduced buffering capacity of poplar, improved sugar solubilization during pretreatment, and better enzymatic hydrolysis conversion. Preprocessing alone significantly improved the fermentability of the liquid fraction from 1-2% to 49-56% for both feedstocks while overliming improved it to 45%. Consequently, it was proposed that preprocessing can substitute for the detoxification step. The economic assessment revealed that using poplar WTC via the new process increased annual ethanol production of 10.5 million liters when compared to using CPC via overliming (base case scenario). Also, savings in total operating costs were about $10 million per year when using cheaper poplar WTC instead of CPC, and using recycled water for preprocessing lowered its total operating costs by 45-fold.

CONCLUSIONS

The novel process developed in this study was successful in increasing ethanol production while decreasing overall costs, thus facilitating the feasibility of lignocellulosic ethanol biorefineries. Key factors to achieving this outcome included substituting overliming by preprocessing, enabling the use of lower-quality feedstock, increasing monomeric sugar recovery and ethanol fermentation yield, and using recycled water for preprocessing. In addition, preprocessing enabled the implementation of an evaporator-combustor downstream design, resulting in a low-loading waste stream that can be treated in a wastewater treatment plant with a simple configuration.

Promoting adoption of two-stage agricultural drainage ditches: A change agent perspective

Adoption of innovations, including adoption of conservation practices, is a topic of extensive scholarly enterprise. The diffusion of innovations literature has often examined the characteristics of three sets of variables: the adopter, the change agent, and the innovation. This literature clearly establishes the crucial role of change agents in promoting an innovation. However, what we don’t know is what makes change agents want to promote a particular innovation. In this study, change agents’ perceptions of the attributes of two-stage drainage ditches, an innovative agricultural drainage ditch design, are examined in order to understand what affects their willingness to promote them. Diffusion of innovation theory provides the conceptual grounding as well as the theoretical motivation for this study. The data for this study come from semi-structured interviews with 17 change agents. Results suggest that change agents perceive the relative advantage associated with two-stage ditches to be low, and that two-stage ditches might be perceived by potential adopters to be incompatible with the prevalent sociocultural beliefs about drainage ditch management. Results also indicate that change agents’ perceptions of environmental benefits of adopting two-stage ditches affects their willingness to promote them. Results are more broadly informative about promoting conservation practices, and is relevant for both academicians and practitioners.

Dynamic evolution in the key honey bee pathogen deformed wing virus: Novel insights into virulence and competition using reverse genetics

The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health, which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States honey bee colonies. Phylogenetic analysis showed that divergent US DWV genotypes are of monophyletic origin and were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to coexisting DWV genotypes, thereby devising a reverse-genetics system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone–derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to coexist. Mutational and recombination events were observed across clone progeny, providing new insights into the forces that drive and constrain virus diversification. Accordingly, our results suggest that Varroa influences DWV dynamics by causing an initial selective sweep, which is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. We suggest that this selection might reflect the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this hypothesis, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population.

Deformed wing virus, a key pathogen of honey bees, shows rapid diversification after genetic bottlenecks; a novel reverse-genetic system provides insights into the forces that shape virus diversity, suggesting that virus quasi-species diversification may be driven by selection of genotypes capable of evading host RNAi defences.

Novel transcriptional responses to heat revealed by turning up the heat at night

KEY MESSAGE

The circadian clock controls many molecular activities, impacting experimental interpretation. We quantify the genome-wide effects of time-of-day on the heat-shock response and the effects of "diurnal bias" in stress experiments. Heat stress has significant adverse effects on plant productivity worldwide. Most experiments examining heat stress are performed during daytime hours, generating a 'diurnal bias' in the pathways and regulatory mechanisms identified. Such bias may confound downstream interpretations and limit our understanding of the full response to heat stress. Here we show that the transcriptional and physiological responses to a sudden heat shock in Arabidopsis are profoundly sensitive to the time of day. We observe that plant tolerance and acclimation to heat shock vary throughout the day and are maximal at dusk. Consistently, over 75% of heat-responsive transcripts show a time of day-dependent response, including many previously characterized heat-response genes. This temporal sensitivity implies a complex interaction between time and temperature where daily variations in basal transcription influence thermotolerance. When we examined these transcriptional responses, we uncovered novel night-response genes and cis-regulatory elements, underpinning new aspects of heat stress responses not previously appreciated. Exploiting this temporal variation can be applied to most environmental responses to understand the underlying network wiring. Therefore, we propose that using time as a perturbagen is an approach that will enhance our understanding of plant regulatory networks and responses to environmental stresses.

Spectral characterization of wheat functional trait responses to Hessian fly: Mechanisms for trait-based resistance

Insect herbivores can manipulate host plants to inhibit defenses. Insects that induce plant galls are excellent examples of these interactions. The Hessian fly (HF, Mayetiola destructor) is a destructive pest of wheat (Triticum spp.) that occurs in nearly all wheat producing globally. Under compatible interactions (i.e., successful HF establishment), HF larvae alter host tissue physiology and morphology for their benefit, manifesting as the development of plant nutritive tissue that feeds the larva and ceases plant cell division and elongation. Under incompatible interactions (i.e., unsuccessful HF establishment), plants respond to larval feeding by killing the larva, permitting normal plant development. We used reflectance spectroscopy to characterize whole-plant functional trait responses during both compatible and incompatible interactions and related these findings with morphological and gene expression observations from earlier studies. Spectral models successfully characterized wheat foliar traits, with mean goodness of fit statistics of 0.84, 0.85, 0.94, and 0.69 and percent root mean square errors of 22, 10, 6, and 20%, respectively, for nitrogen and carbon concentrations, leaf mass per area, and total phenolic content. We found that larvae capable of generating compatible interactions successfully manipulated host plant chemical and morphological composition to create a more hospitable environment. Incompatible interactions resulted in lower host plant nutritional quality, thicker leaves, and higher phenolic levels. Spectral measurements successfully characterized wheat responses to compatible and incompatible interactions, providing an excellent example of the utility of Spectral phenotyping in quantifying responses of specific plant functional traits associated with insect resistance.

Measuring network rewiring over time

Recent years have seen tremendous advances in the scientific study of networks, as more and larger data sets of relationships among nodes have become available in many different fields. This has led to pathbreaking discoveries of near-universal network behavior over time, including the principle of preferential attachment and the emergence of scaling in complex networks. Missing from the set of network analysis methods to date is a measure that describes for each node how its relationship (or links) with other nodes changes from one period to the next. Conventional measures of network change for the most part show how the degrees of a node change; these are scalar comparisons. Our contribution is to use, for the first time, the cosine similarity to capture not just the change in degrees of a node but its relationship to other nodes. These are vector (or matrix)-based comparisons, rather than scalar, and we refer to them as “rewiring” coefficients. We apply this measure to three different networks over time to show the differences in the two types of measures. In general, bigger increases in our rewiring measure are associated with larger increases in network density, but this is not always the case.

An integration framework for linking avifauna niche and forest landscape models

Avian cavity nesters (ACN) are viable indicators of forest structure, composition, and diversity. Utilizing these species responses in multi-disciplinary climate-avian-forest modeling can improve climate adaptive management. We propose a framework for integrating and evaluating climate-avian-forest models by linking two ACN niche models with a forest landscape model (FLM), LANDIS-II. The framework facilitates the selection of available ACN models for integration, evaluation of model transferability, and evaluation of successful integration of ACN models with a FLM. We found selecting a model for integration depended on its transferability to the study area (Northern Rockies Ecoregion of Idaho in the United States), which limited the species and model types available for transfer. However, transfer evaluation of the tested ACN models indicated a good fit for the study area. Several niche model variables (canopy cover, snag density, and forest cover type) were not directly informed by the LANDIS-II model, which required secondary modeling (Random Forest) to derive values from the FLM outputs. In instances where the Random Forest models performed with a moderate classification accuracy, the overall effect on niche predictions was negligible. Predictions based on LANDIS-II simulations performed similarly to predictions based on the niche model’s original training input types. This supported the conclusion that the proposed framework is viable for informing avian niche models with FLM simulations. Even models that poorly approximate habitat suitability, due to the inherent constraints of predicting spatial niche use of irruptive species produced informative results by identifying areas of management focus. This is primarily because LANDIS-II estimates spatially explicit variables that were unavailable over large spatial extents from alternative datasets. Thus, without integration, one of the ACN niche models was not applicable to the study area. The framework will be useful for integrating avifauna niche and forest ecosystem models, which can inform management of contemporary and future landscapes under differing management and climate scenarios.

Testing Empirical Support for Evolutionary Models that Root the Tree of Life

Trees of life (ToLs) can only be rooted with direct methods that seek optimization of character state information in ingroup taxa. This involves optimizing phylogenetic tree, model and data in an exercise of reciprocal illumination. Rooted ToLs have been built from a census of protein structural domains in proteomes using two kinds of models. Fully-reversible models use standard-ordered (additive) characters and Wagner parsimony to generate unrooted trees of proteomes that are then rooted with Weston's generality criterion. Non-reversible models directly build rooted trees with unordered characters and asymmetric stepmatrices of transformation costs that penalize gain over loss of domains. Here, we test the empirical support for the evolutionary models with character state reconstruction methods using two published proteomic datasets. We show that the reversible models match reconstructed frequencies of character change and are faithful to the distribution of serial homologies in trees. In contrast, the non-reversible models go counter to trends in the data they must explain, attracting organisms with large proteomes to the base of the rooted trees while violating the triangle inequality of distances. This can lead to serious reconstruction inconsistencies that show model inadequacy. Our study highlights the aprioristic perils of disposing of countering evidence in natural history reconstruction.

A highly expressed intestinal cysteine protease of Ancylostoma ceylanicum protects vaccinated hamsters from hookworm infection

BACKGROUND

Human hookworms (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) are intestinal blood-feeding parasites that infect ~500 million people worldwide and are among the leading causes of iron-deficiency anemia in the developing world. Drugs are useful against hookworm infections, but hookworms rapidly reinfect people, and the parasites can develop drug resistance. Therefore, having a hookworm vaccine would be of tremendous benefit.

METHODOLOGY/PRINCIPAL FINDINGS

We investigated the vaccine efficacy in outbred Syrian hamsters of three A. ceylanicum hookworm antigen candidates from two classes of proteins previously identified as promising vaccine candidates. These include two intestinally-enriched, putatively secreted cathepsin B cysteine proteases (AceyCP1, AceyCPL) and one small Kunitz-type protease inhibitor (AceySKPI3). Recombinant proteins were produced in Pichia pastoris, and adsorbed to Alhydrogel. Recombinant AceyCPL (rAceyCPL)/Alhydrogel and rAceySKPI3/Alhydrogel induced high serum immunoglobulin G (IgG) titers in 8/8 vaccinates, but were not protective. rAceyCP1/Alhydrogel induced intermediate serum IgG titers in ~60% of vaccinates in two different trials. rAceyCP1 serum IgG responders had highly significantly decreased hookworm burdens, fecal egg counts and clinical pathology compared to Alhydrogel controls and nonresponders. Protection was highly correlated with rAceyCP1 serum IgG titer. Antisera from rAceyCP1 serum IgG responders, but not nonresponders or rAceyCPL/Alhydrogel vaccinates, significantly reduced adult A. ceylanicum motility in vitro. Furthermore, rAceyCP1 serum IgG responders had canonical Th2-specific recall responses (IL4, IL5, IL13) in splenocytes stimulated ex vivo.

CONCLUSIONS/SIGNIFICANCE

These findings indicate that rAceyCP1 is a promising vaccine candidate and validates a genomic/transcriptomic approach to human hookworm vaccine discovery.

High-density multi-population consensus genetic linkage map for peach

Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.

Hyperspectral band selection using genetic algorithm and support vector machines for early identification of charcoal rot disease in soybean stems

BACKGROUND

Charcoal rot is a fungal disease that thrives in warm dry conditions and affects the yield of soybeans and other important agronomic crops worldwide. There is a need for robust, automatic and consistent early detection and quantification of disease symptoms which are important in breeding programs for the development of improved cultivars and in crop production for the implementation of disease control measures for yield protection. Current methods of plant disease phenotyping are predominantly visual and hence are slow and prone to human error and variation. There has been increasing interest in hyperspectral imaging applications for early detection of disease symptoms. However, the high dimensionality of hyperspectral data makes it very important to have an efficient analysis pipeline in place for the identification of disease so that effective crop management decisions can be made. The focus of this work is to determine the minimal number of most effective hyperspectral wavebands that can distinguish between healthy and diseased soybean stem specimens early on in the growing season for proper management of the disease. 111 hyperspectral data cubes representing healthy and infected stems were captured at 3, 6, 9, 12, and 15 days after inoculation. We utilized inoculated and control specimens from 4 different genotypes. Each hyperspectral image was captured at 240 different wavelengths in the range of 383-1032 nm. We formulated the identification of best waveband combination from 240 wavebands as an optimization problem. We used a combination of genetic algorithm as an optimizer and support vector machines as a classifier for the identification of maximally-effective waveband combination.

RESULTS

A binary classification between healthy and infected soybean stem samples using the selected six waveband combination (475.56, 548.91, 652.14, 516.31, 720.05, 915.64 nm) obtained a classification accuracy of 97% for the infected class. Furthermore, we achieved a classification accuracy of 90.91% for test samples from 3 days after inoculation using the selected six waveband combination.

CONCLUSIONS

The results demonstrated that these carefully-chosen wavebands are more informative than RGB images alone and enable early identification of charcoal rot infection in soybean. The selected wavebands could be used in a multispectral camera for remote identification of charcoal rot infection in soybean.

Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and landscape characteristics on invasions with a case study using a model parameterized for the potentially invasive biomass crop, Miscanthus × giganteus. Using that model we simulate invasions on 1000 real landscapes to evaluate how landscape characteristics, including both composition and spatial structure, affect invasion outcomes. We conducted replicate simulations with differing strengths of plant invasiveness traits (dispersal ability, establishment ability, population growth rate, and the ability to utilize dispersal corridors) to evaluate how the importance of landscape characteristics for predicting invasion patterns changes depending on the invader details. Analysis of simulations showed that the presence of highly suitable habitat (e.g., grasslands) is generally the strongest determinant of invasion dynamics but that there are also more subtle interactions between landscapes and invader traits. These effects can also vary between different aspects of invasion dynamics (short vs. long time scales and population size vs. spatial extent). These results illustrate that invasions are complex emergent processes with multiple drivers and effective management needs to reflect the ecology of the species of interest and the particular goals or risks for which efforts need to be optimized.

Estimating plant distance in maize using Unmanned Aerial Vehicle (UAV)

Distance between rows and plants are essential parameters that affect the final grain yield in row crops. This paper presents the results of research intended to develop a novel method to quantify the distance between maize plants at field scale using an Unmanned Aerial Vehicle (UAV). Using this method, we can recognize maize plants as objects and calculate the distance between plants. We initially developed our method by training an algorithm in an indoor facility with plastic corn plants. Then, the method was scaled up and tested in a farmer’s field with maize plant spacing that exhibited natural variation. The results of this study demonstrate that it is possible to precisely quantify the distance between maize plants. We found that accuracy of the measurement of the distance between maize plants depended on the height above ground level at which UAV imagery was taken. This study provides an innovative approach to quantify plant-to-plant variability and, thereby final crop yield estimates.

Structural characterization of a putative chitin synthase gene in Phytophthora spp. and analysis of its transcriptional activity during pathogenesis on potato and soybean plants

Although chitin is a major component of the fungal cell wall, in oomycetes (fungal-like organisms), this compound has only been found in very little amounts, mostly in the cell wall of members of the genera Achlya and Saprolegnia. In the oomycetes Phytophthora infestans and P. sojae the presence of chitin has not been demonstrated; however, the gene putatively encoding chitin synthase (CHS), the enzyme that synthesizes chitin, is present in their genomes. The evolutionary significance of the CHS gene in P. infestans and P. sojae genomes is not fully understood and, therefore, further studies are warranted. We have cloned and characterized the putative CHS genes from two Phytophthora spp. and multiple isolates of P. infestans and P. sojae and analyzed their phylogenetic relationships. We also conducted CHS inhibition assays and measured CHS transcriptional activity in Phytophthora spp. during infection of susceptible plants. Results of our investigations suggest that CHS contains all the motifs that are typical in CHS genes of fungal origin and is expressed, at least at the mRNA level, during in vitro and in planta growth. In infected tissues, the highest levels of expression occurred in the first 12 h post inoculation. In addition, results from our inhibition experiments appear to suggest that CHS activity is important for P. infestans normal vegetative growth. Because of the considerable variation in expression during infection when compared to basal expression observed in in vitro cultures of non-sporulating mycelium, we hypothesize that CHS may have a meaningful role in Phytophthora pathogenicity.

Evaluation of Assays to Quantify Infectious Human Norovirus for Heat and High-Pressure Inactivation Studies Using Tulane Virus

We compared the heat and high hydrostatic pressure (HHP) inactivation results of Tulane virus (TV), a human norovirus (HuNoV) surrogate, obtained by plaque assay, direct quantitative reverse transcription PCR (RT-qPCR), porcine gastric mucin magnetic beads (PGM-MBs) binding assay followed by RT-qPCR (PGM/PCR), and propidium monoazide (PMA) assay followed by RT-qPCR (PMA/PCR). Heat and HHP inactivation of a HuNoV genotype I.1 (GI.1) strain and a genotype II.4 (GII.4) strain was also evaluated using those molecular assays. Viruses were heat treated at 50-90 °C for 2 min and HHP treated at 100-550 MPa at initial temperatures of 4 or 21 °C for 2 min. For heat treatment, the three molecular methods significantly underestimated the inactivation of TV. It could be logically concluded that the PGM/PCR assay was better than the PMA/PCR and direct RT-qPCR assays in estimating the inactivation of HuNoV GI.1. The three molecular methods were comparable in estimating the heat inactivation of GII.4. For HHP treatment, both PGM/PCR and PMA/PCR assays were able to estimate inactivation of TV at ≤~2-log reduction levels, but significantly underestimated its inactivation at >~2-log reduction levels. The direct RT-qPCR assay was the worst method for estimating HHP inactivation of TV. It could be logically concluded that the PGM/PCR and PMA/PCR assays were comparable in estimating the HHP inactivation of GI.1 and both were significantly better than the direct RT-qPCR assay. Among the three molecular methods, the PGM/PCR assay was the best in estimating the HHP inactivation of GII.4. These results demonstrated that the PGM/PCR assay was probably the method of choice in estimating the inactivation of HuNoV GI.1 and GII.4 for heat and HHP treatments, but this method would likely result in underestimation of HuNoV inactivation.

The effector AvrRxo1 phosphorylates NAD in planta

Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity. Most characterized effectors work through modification of host proteins or transcriptional regulators, although a few are known to modify small molecule targets. The Xanthomonas type III secreted avirulence factor AvrRxo1 is a structural homolog of the zeta toxin family of sugar-nucleotide kinases that suppresses bacterial growth. AvrRxo1 was recently reported to phosphorylate the central metabolite and signaling molecule NAD in vitro, suggesting that the effector might enhance bacterial virulence on plants through manipulation of primary metabolic pathways. In this study, we determine that AvrRxo1 phosphorylates NAD in planta, and that its kinase catalytic sites are necessary for its toxic and resistance-triggering phenotypes. A global metabolomics approach was used to independently identify 3'-NADP as the sole detectable product of AvrRxo1 expression in yeast and bacteria, and NAD kinase activity was confirmed in vitro. 3'-NADP accumulated upon transient expression of AvrRxo1 in Nicotiana benthamiana and in rice leaves infected with avrRxo1-expressing strains of X. oryzae. Mutation of the catalytic aspartic acid residue D193 abolished AvrRxo1 kinase activity and several phenotypes of AvrRxo1, including toxicity in yeast, bacteria, and plants, suppression of the flg22-triggered ROS burst, and ability to trigger an R gene-mediated hypersensitive response. A mutation in the Walker A ATP-binding motif abolished the toxicity of AvrRxo1, but did not abolish the 3'-NADP production, virulence enhancement, ROS suppression, or HR-triggering phenotypes of AvrRxo1. These results demonstrate that a type III effector targets the central metabolite and redox carrier NAD in planta, and that this catalytic activity is required for toxicity and suppression of the ROS burst.

Priming Cross-Protective Bovine Viral Diarrhea Virus-Specific Immunity Using Live-Vectored Mosaic Antigens

Bovine viral diarrhea virus (BVDV) plays a key role in bovine respiratory disease complex, which can lead to pneumonia, diarrhea and death of calves. Current vaccines are not very effective due, in part, to immunosuppressive traits and failure to induce broad protection. There are diverse BVDV strains and thus, current vaccines contain representative genotype 1 and 2 viruses (BVDV-1 & 2) to broaden coverage. BVDV modified live virus (MLV) vaccines are superior to killed virus vaccines, but they are susceptible to neutralization and complement-mediated destruction triggered by passively acquired antibodies, thus limiting their efficacy. We generated three novel mosaic polypeptide chimeras, designated N^proE2¹²³; NS²³¹; and NS²³², which incorporate protective determinants that are highly conserved among BVDV-1a, 1b, and BVDV-2 genotypes. In addition, strain-specific protective antigens from disparate BVDV strains were included to broaden coverage. We confirmed that adenovirus constructs expressing these antigens were strongly recognized by monoclonal antibodies, polyclonal sera, and IFN-γ-secreting T cells generated against diverse BVDV strains. In a proof-of-concept efficacy study, the multi-antigen proto-type vaccine induced higher, but not significantly different, IFN-γ spot forming cells and T-cell proliferation compared to a commercial MLV vaccine. In regards to the humoral response, the prototype vaccine induced higher BVDV-1 specific neutralizing antibody titers, whereas the MLV vaccine induced higher BVDV-2 specific neutralizing antibody titers. Following BVDV type 2a (1373) challenge, calves immunized with the proto-type or the MLV vaccine had lower clinical scores compared to naïve controls. These results support the hypothesis that a broadly protective subunit vaccine can be generated using mosaic polypeptides that incorporate rationally selected and validated protective determinants from diverse BVDV strains. Furthermore, regarding biosafety of using a live vector in cattle, we showed that recombinant human adenovirus-5 was cleared within one week following intradermal inoculation.

Drosophila Spidey/Kar Regulates Oenocyte Growth via PI3-Kinase Signaling

Cell growth and proliferation depend upon many different aspects of lipid metabolism. One key signaling pathway that is utilized in many different anabolic contexts involves Phosphatidylinositide 3-kinase (PI3K) and its membrane lipid products, the Phosphatidylinositol (3,4,5)-trisphosphates. It remains unclear, however, which other branches of lipid metabolism interact with the PI3K signaling pathway. Here, we focus on specialized fat metabolizing cells in Drosophila called larval oenocytes. In the presence of dietary nutrients, oenocytes undergo PI3K-dependent cell growth and contain very few lipid droplets. In contrast, during starvation, oenocytes decrease PI3K signaling, shut down cell growth and accumulate abundant lipid droplets. We now show that PI3K in larval oenocytes, but not in fat body cells, functions to suppress lipid droplet accumulation. Several enzymes of fatty acid, triglyceride and hydrocarbon metabolism are required in oenocytes primarily for lipid droplet induction rather than for cell growth. In contrast, a very long chain fatty-acyl-CoA reductase (FarO) and a putative lipid dehydrogenase/reductase (Spidey, also known as Kar) not only promote lipid droplet induction but also inhibit oenocyte growth. In the case of Spidey/Kar, we show that the growth suppression mechanism involves inhibition of the PI3K signaling pathway upstream of Akt activity. Together, the findings in this study show how Spidey/Kar and FarO regulate the balance between the cell growth and lipid storage of larval oenocytes.

Lipids play diverse roles in health and disease. Some types of lipids function as metabolic fuels for energy homeostasis, whereas others act as components of cell membranes or serve as signals regulating cell behaviors. Much, however, remains to be discovered about the molecular connections between different categories of lipids. Phosphatidylinositide 3-kinase (PI3K) is an enzyme that synthesizes phosphatidylinositide lipids, which act as signals essential for growth during normal development and cancer. Using genetics in the fruit fly, Drosophila, we identify new regulatory links between phosphatidylinositides and lipid oxidoreductases in specialized fat-metabolizing cells called oenocytes. We find that an enzyme metabolizing very long chain fatty acids (VLCFAs) and also a putative lipid dehydrogenase/reductase both act to prevent the inappropriate overgrowth of oenocytes. In the case of the latter enzyme, it suppresses cell growth by inhibiting phosphatidylinositide signaling. Future studies will determine whether similar lipid enzymes regulate PI3K signaling in other cell and tissue types during normal development and tumorigenesis.

Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust

KEY MESSAGE

Barley resistance to wheat stripe rust has remained effective for a long time and, therefore, the genes underlying this resistance can be a valuable tool to engineer durable resistance in wheat. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major disease of wheat that is causing large economic losses in many wheat-growing regions of the world. Deployment of Pst resistance genes has been an effective strategy for controlling this pathogen, but many of these genes have been defeated by new Pst races. In contrast, genes providing resistance to this wheat pathogen in other grass species (nonhost resistance) have been more durable. Barley varieties (Hordeum vulgare ssp. vulgare) are predominately immune to wheat Pst, but we identified three accessions of wild barley (Hordeum vulgare ssp. spontaneum) that are susceptible to Pst. Using these accessions, we mapped a barley locus conferring resistance to Pst on the distal region of chromosome arm 7HL and designated it as Rps6. The detection of the same locus in the cultivated barley 'Tamalpais' and in the Chinese barley 'Y12' by an allelism test suggests that Rps6 may be a frequent component of barley intermediate host resistance to Pst. Using a high-density mapping population (>10,000 gametes) we precisely mapped Rps6 within a 0.14 cM region (~500 kb contig) that is colinear to regions in Brachypodium (<94 kb) and rice (<9 kb). Since no strong candidate gene was identified in these colinear regions, a dedicated positional cloning effort in barley will be required to identify Rps6. The identification of this and other barley genes conferring resistance to Pst can contribute to our understanding of the mechanisms for durable resistance against this devastating wheat pathogen.

Endophytic Epichloë species and their grass hosts: from evolution to applications

The closely linked fitness of the Epichloë symbiont and the host grass is presumed to align the coevolution of the species towards specialization and mutually beneficial cooperation. Ecological observations demonstrating that Epichloë-grass symbioses can modulate grassland ecosystems via both above- and belowground ecosystem processes support this. In many cases the detected ecological importance of Epichloë species is directly or indirectly linked to defensive mutualism attributable to alkaloids of fungal-origin. Now, modern genetic and molecular techniques enable the precise studies on evolutionary origin of endophytic Epichloë species, their coevolution with host grasses and identification the genetic variation that explains phenotypic diversity in ecologically relevant characteristics of Epichloë-grass associations. Here we briefly review the most recent findings in these areas of research using the present knowledge of the genetic variation that explains the biosynthetic pathways driving the diversity of alkaloids produced by the endophyte. These findings underscore the importance of genetic interplay between the fungus and the host in shaping their coevolution and ecological role in both natural grass ecosystems, and in the agricultural arena.

Impact of the shedding level on transmission of persistent infections in Mycobacterium avium subspecies paratuberculosis (MAP)

Super-shedders are infectious individuals that contribute a disproportionate amount of infectious pathogen load to the environment. A super-shedder host may produce up to 10,000 times more pathogens than other infectious hosts. Super-shedders have been reported for multiple human and animal diseases. If their contribution to infection dynamics was linear to the pathogen load, they would dominate infection dynamics. We here focus on quantifying the effect of super-shedders on the spread of infection in natural environments to test if such an effect actually occurs in Mycobacterium avium subspecies paratuberculosis (MAP). We study a case where the infection dynamics and the bacterial load shed by each host at every point in time are known. Using a maximum likelihood approach, we estimate the parameters of a model with multiple transmission routes, including direct contact, indirect contact and a background infection risk. We use longitudinal data from persistent infections (MAP), where infectious individuals have a wide distribution of infectious loads, ranging upward of three orders of magnitude. We show based on these parameters that the effect of super-shedders for MAP is limited and that the effect of the individual bacterial load is limited and the relationship between bacterial load and the infectiousness is highly concave. A 1000-fold increase in the bacterial contribution is equivalent to up to a 2-3 fold increase in infectiousness.

Environmental assessment of mild bisulfite pretreatment of forest residues into fermentable sugars for biofuel production

BACKGROUND

Sugar production via pretreatment and enzymatic hydrolysis of cellulosic feedstock, in this case softwood harvest residues, is a critical step in the biochemical conversion pathway towards drop-in biofuels. Mild bisulfite (MBS) pretreatment is an emerging option for the breakdown and subsequent processing of biomass towards fermentable sugars. An environmental assessment of this process is critical to discern its future sustainability in the ever-changing biofuels landscape.

RESULTS

The subsequent cradle-to-gate assessment of a proposed sugar production facility analyzes sugar made from woody biomass using MBS pretreatment across all seven impact categories (functional unit 1 kg dry mass sugar), with a specific focus on potential global warming and eutrophication impacts. The study found that the eutrophication impact (0.000201 kg N equivalent) is less than the impacts from conventional beet and cane sugars, while the global warming impact (0.353 kg CO2 equivalent) falls within the range of conventional processes.

CONCLUSIONS

This work discusses some of the environmental impacts of designing and operating a sugar production facility that uses MBS as a method of treating cellulosic forest residuals. The impacts of each unit process in the proposed facility are highlighted. A comparison to other sugar-making process is detailed and will inform the growing biofuels literature.

GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

BACKGROUND

With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference.

RESULTS

The GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) developed and presented here adopts a clustering strategy to build a population-tailored "Mock Reference" from the same GBS data used for downstream SNP calling and genotyping. Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed read-length uniformity requirements. Using 150 bp PE reads from a GBS library of 48 accessions of tetraploid kiwiberry (Actinidia arguta), GBS-SNP-CROP yielded on average three times as many SNPs as TASSEL-GBS analyses (32 and 64 bp tag lengths) and over 18 times as many as TASSEL-UNEAK, with fewer genotyping errors in all cases, as evidenced by comparing the genotypic characterizations of biological replicates. Using the published reference genome of a related diploid species (A. chinensis), the reference-based version of GBS-SNP-CROP behaved similarly to TASSEL-GBS in terms of the number of SNPs called but had an improved read depth distribution and fewer genotyping errors. Our results also indicate that the sets of SNPs detected by the different pipelines above are largely orthogonal to one another; thus GBS-SNP-CROP may be used to augment the results of alternative analyses, whether or not a reference is available.

CONCLUSIONS

By achieving high-density SNP genotyping in populations for which no reference genome is available, GBS-SNP-CROP is worth consideration by curators, researchers, and breeders of under-researched plant genetic resources. In cases where a reference is available, especially if from a related species or when the target population is particularly diverse, GBS-SNP-CROP may complement other reference-based pipelines by extracting more information per sequencing dollar spent. The current version of GBS-SNP-CROP is available at https://github.com/halelab/GBS-SNP-CROP.git.

WheatExp: an RNA-seq expression database for polyploid wheat

BACKGROUND

For functional genomics studies, it is important to understand the dynamic expression profiles of transcribed genes in different tissues, stages of development and in response to environmental stimuli. The proliferation in the use of next-generation sequencing technologies by the plant research community has led to the accumulation of large volumes of expression data. However, analysis of these datasets is complicated by the frequent occurrence of polyploidy among economically-important crop species. In addition, processing and analyzing such large volumes of sequence data is a technical and time-consuming task, limiting their application in functional genomics studies, particularly for smaller laboratories which lack access to high-powered computing infrastructure. Wheat is a good example of a young polyploid species with three similar genomes (97 % identical among homoeologous genes), rapidly accumulating RNA-seq datasets and a large research community.

DESCRIPTION

We present WheatExp, an expression database and visualization tool to analyze and compare homoeologue-specific transcript profiles across a broad range of tissues from different developmental stages in polyploid wheat. Beginning with publicly-available RNA-seq datasets, we developed a pipeline to distinguish between homoeologous transcripts from annotated genes in tetraploid and hexaploid wheat. Data from multiple studies is processed and compiled into a database which can be queried either by BLAST or by searching for a known gene of interest by name or functional domain. Expression data of multiple genes can be displayed side-by-side across all expression datasets providing immediate access to a comprehensive panel of expression data for specific subsets of wheat genes.

CONCLUSIONS

The development of a publicly accessible expression database hosted on the GrainGenes website - http://wheat.pw.usda.gov/WheatExp/ - coupled with a simple and readily-comparable visualization tool will empower the wheat research community to use RNA-seq data and to perform functional analyses of target genes. The presented expression data is homoeologue-specific allowing for the analysis of relative contributions from each genome to the overall expression of a gene, a critical consideration for breeding applications. Our approach can be expanded to other polyploid species by adjusting sequence mapping parameters according to the specific divergence of their genomes.

A dietary phytochemical alters caste-associated gene expression in honey bees

In the eusocial honey bee Apis mellifera, with reproductive queens and sterile workers, a female larva's developmental fate depends on its diet; nurse bees feed queen-destined larvae exclusively royal jelly, a glandular secretion, but worker-destined larvae receive royal jelly for 3 days and subsequently jelly to which honey and beebread are added. RNA-Seq analysis demonstrated that p-coumaric acid, which is ubiquitous in honey and beebread, differentially regulates genes involved in caste determination. Rearing larvae in vitro on a royal jelly diet to which p-coumaric acid has been added produces adults with reduced ovary development. Thus, consuming royal jelly exclusively not only enriches the diet of queen-destined larvae but also may protect them from inhibitory effects of phytochemicals present in the honey and beebread fed to worker-destined larvae.