Plants are exposed to combinations of various biotic and abiotic stresses, but stress responses are usually investigated for single stresses only.
Here, we investigated the genetic architecture underlying plant responses to 11 single stresses and several of their combinations by phenotyping 350 Arabidopsis thaliana accessions. A set of 214 000 single nucleotide polymorphisms (SNPs) was screened for marker-trait associations in genome-wide association (GWA) analyses using tailored multi-trait mixed models.
Stress responses that share phytohormonal signaling pathways also share genetic architecture underlying these responses. After removing the effects of general robustness, for the 30 most significant SNPs, average quantitative trait locus (QTL) effect sizes were larger for dual stresses than for single stresses.
Plants appear to deploy broad-spectrum defensive mechanisms influencing multiple traits in response to combined stresses. Association analyses identified QTLs with contrasting and with similar responses to biotic vs abiotic stresses, and below-ground vs above-ground stresses.
Our approach allowed for an unprecedented comprehensive genetic analysis of how plants deal with a wide spectrum of stress conditions.
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.
It looks like 2,000 citizens in Finland will welcome the new year with outstretched arms.
These Finns are the lucky recipients of a guaranteed income beginning this year, as the country’s government finally rolls out its universal basic income (UBI) trial run.
UBI is a potential source of income that could one day be available to all adult citizens, regardless of income, wealth, or employment status.
This pioneering UBI program was launched by the federal social security institution, Kela. It will give out €560 (US$587) a month, tax free, to 2,000 Finns that were randomly selected.
The only requirement was that they had to be already receiving unemployment benefits or an income subsidy.
The program allows unemployed Finns to not lose their benefits, even when they try out odd jobs.
"Incidental earnings do not reduce the basic income, so working and … self-employment are worthwhile no matter what," says Marjukka Turunen, legal unit head at Kela.
If successful, the program could be extended to include all adult Finns.
"Its purpose is to reduce the work involved in applying for subsidies, as well as free up time and resources for other activities, such as making or applying for work," according to a press release by Kela.
Furthermore, the Finnish government, as well as UBI advocates, may see how this program can end up saving more money for Finland in the long run - as it is less costly than maintaining social welfare services for the unemployed.
This special issue of Journal of Experimental Botany focuses on the developmental mechanisms required to generate plant vascular tissue. The focus is Arabidopsis, including the three models for initial patterning involving the interaction of auxin and cytokinin, and going on to look at expansion and differentiation into xylem and phloem. Bryophyte and tree models are also considered, as well as new techniques for analyzing the vasculature of mature plants.
ITHACA, NY–Researchers have sequenced the genome of the whitefly (Bemisia tabici), an invasive insect responsible for spreading plant viruses worldwide, causing billions of dollars in crop losses each year.
The genome study, led by Associate Professor Zhangjun Fei of the Boyce Thompson Institute (BTI), offers many clues to the insect's remarkable ability to resist pesticides, transmit more than 300 plant viruses, and to feed on at least 1,000 different plant species. Published today in the journal BMC Biology, the study will serve as a foundation for future work to combat this global pest.
"Whitefly is an economically important pest for agriculture crops. It causes direct damage and also is a major vector for viruses, like Tomato yellow leaf curl virus, Cassava mosaic virus and Cassava brown streak virus, so it creates huge crop losses and poses serious threats to food security, especially in Africa and other parts of the developing world," said Fei.
In collaboration with a group of international colleagues, BTI researchers created a high-quality draft genome sequence of the whitefly and identified genes that code for proteins. The genome sequence can be accessed at the whitefly genome database developed by the Fei lab.
An analysis showed that, compared to related species, the whitefly has expanded families of detoxification genes. It also has extra genes that code for proteins related to virus acquisition and transmission, as well as insecticide resistance.
In an impressive example of horizontal gene transfer, the whitefly has acquired 142 genes from bacteria or fungi, including some coding for enzymes that break down foreign chemicals. These genes likely allow the whitefly to feed on diverse types of plants and to rapidly evolve resistance to insecticides.
Because pesticides are ineffective at keeping whitefly populations in check, collaborators at USDA plan to use the genome sequence to develop a control strategy using RNA interference (RNAi). Once scientists pinpoint the genes necessary for virus transmission and survival in the whitefly genome, they can develop new varieties of crops that will produce RNA molecules that block the expression of those necessary genes, killing the whitefly or preventing it from spreading the virus .
Deprivation of mineral nutrients causes significant retardation of plant growth. This retardation is associated with nutrient-specific and general stress-induced transcriptional responses. In this study, we adjusted the external supply of iron, potassium and sulfur to cause the same retardation of shoot growth. Nevertheless, limitation by individual nutrients resulted in specific morphological adaptations and distinct shifts within the root metabolite fingerprint. The metabolic shifts affected key metabolites of primary metabolism and the stress-related phytohormones, jasmonic, salicylic and abscisic acid. These phytohormone signatures contributed to specific nutrient deficiency-induced transcriptional regulation. Limitation by the micronutrient iron caused the strongest regulation and affected 18% of the root transcriptome. Only 130 genes were regulated by all nutrients. Specific co-regulation between the iron and sulfur metabolic routes upon iron or sulfur deficiency was observed. Interestingly, iron deficiency caused regulation of a different set of genes of the sulfur assimilation pathway compared with sulfur deficiency itself, which demonstrates the presence of specific signal-transduction systems for the cross-regulation of the pathways. Combined iron and sulfur starvation experiments demonstrated that a requirement for a specific nutrient can overrule this cross-regulation. The comparative metabolomics and transcriptomics approach used dissected general stress from nutrient-specific regulation in roots of Arabidopsis.
Already a proven mechanism for drought resilience, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency by means of an inverse (compared to C3 and C4 photosynthesis) day/night pattern of stomatal closure/opening to shift CO2 uptake to the night, when evapotranspiration rates are low. A systems-level understanding of temporal molecular and metabolic controls is needed to define the cellular behaviour underpinning CAM. Here, we report high-resolution temporal behaviours of transcript, protein and metabolite abundances across a CAM diel cycle and, where applicable, compare the observations to the well-established C3 model plant Arabidopsis. A mechanistic finding that emerged is that CAM operates with a diel redox poise that is shifted relative to that in Arabidopsis. Moreover, we identify widespread rescheduled expression of genes associated with signal transduction mechanisms that regulate stomatal opening/closing. Controlled production and degradation of transcripts and proteins represents a timing mechanism by which to regulate cellular function, yet knowledge of how this molecular timekeeping regulates CAM is unknown. Here, we provide new insights into complex post-transcriptional and -translational hierarchies that govern CAM in Agave. These data sets provide a resource to inform efforts to engineer more efficient CAM traits into economically valuable C3 crops.
Root branching in plants relies on the de novo formation of lateral roots. These are initiated from founder cells, triggering new formative divisions that generate lateral root primordia (LRP). The LRP size and shape depends on the balance between positive and negative signals that control cell proliferation.
The mechanisms controlling proliferation potential of LRP cells remains poorly understood. We found that Arabidopsis thaliana MYB36, which have been previously shown to regulate genes required for Casparian strip formation and the transition from proliferation to differentiation in the primary root, plays a new role in controlling LRP development at later stages.
We found that MYB36 is a novel component of LR development at later stages. MYB36 was expressed in the cells surrounding LRP where it controls a set of peroxidase genes, which maintain reactive oxygen species (ROS) balance. This was required to define the transition between proliferating and arrested cells inside the LRP, coinciding with the change from flat to dome-shaped primordia. Reducing the levels of hydrogen peroxide (H2O2) in myb36-5 significantly rescues the mutant phenotype.
Our results uncover a role for MYB36 outside the endodermis during LRP development through a mechanism analogous to regulating the proliferation/differentiation transition in the root meristem.
Trade-offs between growth, reproduction, and defence have been documented. Oxidative stress is one of the physiological mechanisms that underlie trade-offs at the cellular and organ levels. The diversity of plant life forms and the complexity of scaling up limit our knowledge of oxidative stress as a universal mediator of life-history trade-offs at the organism level. Joint efforts by plant physiologists and ecologists will undoubtedly provide novel insights into this topic in the near future.
The challenge to produce more food for a rising global population on diminishing agricultural land is complicated by the effects of climate change on agricultural productivity. Although great progress has been made in crop improvement, so far most efforts have targeted above-ground traits. Roots are essential for plant adaptation and productivity, but are less studied due to the difficulty of observing them during the plant life cycle. Root system architecture, made up of structural features like root length, spread, number, and length of lateral roots, among others, exhibits great plasticity in response to environmental changes, and could be critical to developing crops with more efficient roots. Much of the research on root traits has thus far focused on the most common cereal crops and model plants. As cereal yields have reached their yield potential in some regions, understanding their root system may help overcome these plateaus. However, root and tuber crops such as potato, sweetpotato, cassava, and yam may hold more potential for providing food security in the future, and knowledge of their root system additionally focuses directly on the edible portion. Root-trait modeling for multiple stress scenarios, together with high-throughput phenotyping and genotyping techniques, robust databases, and data analytical pipelines, may provide a valuable base for a truly inclusive ‘green revolution’. In the current review, we discuss root system architecture with special reference to root and tuber crops, and how knowledge on genetics of root system architecture can be manipulated to improve their tolerance to abiotic stresses.
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
Soil salinity is becoming an increasingly large problem in agriculture. In this study, we have investigated whether a capacity to withstand salinity can be induced in the salinity sensitive plant species Arabidopsis thaliana, and whether it can be maintained in subsequent generations. To this end, we have used zinc finger artificial transcription factor (ZF-ATFs) mediated genome interrogation. Already within a relatively small collection Arabidopsis lines expressing ZF-ATFs, we found 41 lines that were tolerant to 100 mM NaCl. Furthermore, ZF-ATF encoding gene constructs rescued from the most strongly salinity tolerant lines were indeed found to act as dominant and heritable agents for salinity tolerance. Altogether, our data provide evidence that a silent capacity to withstand normally lethal levels of salinity exists in Arabidopsis and can be evoked relatively easily by in trans acting transcription factors like ZF-ATFs.
Throughout many regions of the world, climate change has limited the availability of water for irrigating crops. Indeed, current models of climate change predict that arid and semi-arid zones will be places where precipitation will drastically decrease. In this context, plant root-associated fungi appear as a new strategy to improve ecophysiological performance and yield of crops under abiotic stress. Thus, use of fungal endophytes from ecosystems currently subjected to severe drought conditions could improve the ecophysiological performance and quantum yield of crops exposed to drought. In this study, we evaluated how the inoculation of fungal endophytes isolated from Antarctic plants can improve the net photosynthesis, water use efficiency and production of fresh biomass in a lettuce cultivar, grown under different water availability regimes. In addition, we assessed if the presence of biochemical mechanisms and gene expression related with environmental tolerance are improved in presence of fungal endophytes. Overall, those individuals with presence of endophytes showed higher net photosynthesis and maintained higher water use efficiency in drought conditions, which was correlated with greater fresh and dry biomass production as well as greater root system development. In addition, presence of fungal endophytes was correlated with a higher proline concentration, lower peroxidation of lipids and up-/down-regulation of ion homeostasis. Our results suggest that presence of fungal endophytes could minimize the negative effect of drought by improving drought tolerance through biochemical mechanisms and improving nutritional status. Thus, root-endophytes might be a successful biotechnological tool to maintain high levels of ecophysiological performance and productivity in zones under drought.
Drought stress is a major problem for agriculture worldwide, causing significant yield losses. Plants have developed highly flexible mechanisms to deal with drought, including organ- and developmental stage-specific responses. In young leaves, growth is repressed as an active mechanism to save water and energy, increasing the chances of survival but decreasing yield. Despite its importance, the molecular basis for this growth inhibition is largely unknown. Here, we present a novel approach to explore early molecular mechanisms controlling Arabidopsis leaf growth inhibition following mild drought. We found that growth and transcriptome responses to drought are highly dynamic. Growth was only repressed by drought during the day, and our evidence suggests that this may be due to gating by the circadian clock. Similarly, time of day strongly affected the extent, specificity, and in certain cases even direction of drought-induced changes in gene expression. These findings underscore the importance of taking into account diurnal patterns to understand stress responses, as only a small core of drought-responsive genes are affected by drought at all times of the day. Finally, we leveraged our high-resolution data to demonstrate that phenotypic and transcriptome responses can be matched to identify putative novel regulators of growth under mild drought.
Because soil salinity is a major abiotic constraint affecting crop yield, much research has been conducted to develop plants with improved salinity tolerance. Salinity stress impacts many aspects of a plant’s physiology, making it difficult to study in toto. Instead, it is more tractable to dissect the plant’s response into traits that are hypothesized to be involved in the overall tolerance of the plant to salinity.
Scope and conclusions
We discuss how to quantify the impact of salinity on different traits, such as relative growth rate, water relations, transpiration, transpiration use efficiency, ionic relations, photosynthesis, senescence, yield and yield components. We also suggest some guidelines to assist with the selection of appropriate experimental systems, imposition of salinity stress, and obtaining and analysing relevant physiological data using appropriate indices. We illustrate how these indices can be used to identify relationships amongst the proposed traits to identify which traits are the most important contributors to salinity tolerance. Salinity tolerance is complex and involves many genes, but progress has been made in studying the mechanisms underlying a plant’s response to salinity. Nevertheless, several previous studies on salinity tolerance could have benefited from improved experimental design. We hope that this paper will provide pertinent information to researchers on performing proficient assays and interpreting results from salinity tolerance experiments.
The year 2014 marked the 25th International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
The combined availability of whole genome sequences and genome editing tools is set to revolutionize the field of fruit biotechnology by enabling the introduction of targeted genetic changes with unprecedented control and accuracy, both to explore emergent phenotypes and to introduce new functionalities. Although plasmid-mediated delivery of genome editing components to plant cells is very efficient, it also presents some drawbacks, such as possible random integration of plasmid sequences in the host genome. Additionally, it may well be intercepted by current process-based GMO regulations, complicating the path to commercialization of improved varieties. Here, we explore direct delivery of purified CRISPR/Cas9 ribonucleoproteins (RNPs) to the protoplast of grape cultivar Chardonnay and apple cultivar such as Golden delicious fruit crop plants for efficient targeted mutagenesis. We targeted MLO-7, a susceptible gene in order to increase resistance to powdery mildew in grape cultivar and DIPM-1, DIPM-2, and DIPM-4 in the apple to increase resistance to fire blight disease. Furthermore, efficient protoplast transformation, the molar ratio of Cas9 and sgRNAs were optimized for each grape and apple cultivar. The targeted mutagenesis insertion and deletion rate was analyzed using targeted deep sequencing. Our results demonstrate that direct delivery of CRISPR/Cas9 RNPs to the protoplast system enables targeted gene editing and paves the way to the generation of DNA-free genome edited grapevine and apple plants.
Protein phosphatase 2A (PP2A) is an enzyme consisting of three subunits: a scaffolding A subunit, a regulatory B subunit and a catalytic C subunit. PP2As were shown to play diverse roles in eukaryotes. In this study, the function of the Arabidopsis PP2A-C5 gene that encodes the catalytic subunit 5 of PP2A was studied using both loss-of-function and gain-of-function analyses. Loss-of-function mutant pp2a-c5-1 displayed more impaired growth during root and shoot development, whereas overexpression of PP2A-C5 conferred better root and shoot growth under different salt treatments, indicating that PP2A-C5 plays an important role in plant growth under salt conditions. Double knockout mutants of pp2a-c5-1 and salt overly sensitive (sos) mutants sos1-1, sos2-2 or sos3-1 showed additive sensitivity to NaCl, indicating that PP2A-C5 functions in a pathway different from the SOS signalling pathway. Using yeast two-hybrid analysis, four vacuolar membrane chloride channel (CLC) proteins, AtCLCa, AtCLCb, AtCLCc and AtCLCg, were found to interact with PP2A-C5. Moreover, overexpression of AtCLCc leads to increased salt tolerance and Cl− accumulation in transgenic Arabidopsis plants. These data indicate that PP2A-C5-mediated better growth under salt conditions might involve up-regulation of CLC activities on vacuolar membranes and that PP2A-C5 could be used for improving salt tolerance in crops.
• Plants produce highly conserved root structures from diverse tissue origins.
• Many early programs for induction of roots are specific to developmental contexts.
• Late stage patterning is regulated by homologous if not identical genes.
• Auxin–cytokinin interactions play a fundamental role in tissue patterning stages.
• It is not clear if universal signaling ‘rules’ organize a generic root body plan.
Plants often make the same organ in different development contexts. Roots are a quintessential example, with embryonic, primary, lateral, adventitious, and regenerative roots common to many plants. The cellular origins and early morphologies of different roots can vary greatly, but the adult structures can be remarkably similar. Recent studies have highlighted the diversity of mechanisms that can initiate roots while late patterning mechanisms are frequently shared. In the middle stages when patterning emerges, evidence shows that antagonistic auxin–cytokinin interactions regulate tissue patterns in root embryogenesis, vascular organization, and regeneration but it is not yet clear if a common ontogeny for the root body plan exists.
To discover mechanisms that controlled the growth of the rooting system in the earliest land plants, we identified genes that control the development of rhizoids in the liverwort Marchantia polymorpha. 336,000 T-DNA transformed lines were screened for mutants with defects in rhizoid growth, and a de novo genome assembly was generated to identify the mutant genes. We report the identification of 33 genes required for rhizoid growth, of which 6 had not previously been functionally characterized in green plants. We demonstrate that members of the same orthogroup are active in cell wall synthesis, cell wall integrity sensing, and vesicle trafficking during M. polymorpha rhizoid and Arabidopsis thaliana root hair growth. This indicates that the mechanism for constructing the cell surface of tip-growing rooting cells is conserved among land plants and was active in the earliest land plants that existed sometime more than 470 million years ago [ 1 and 2].
B vitamins are the precursors of essential metabolic cofactors but are prone to destruction under stress conditions. It is therefore a priori reasonable that stressed plants suffer B vitamin deficiencies and that certain stress symptoms are metabolic knock-on effects of these deficiencies. Given the logic of these arguments, and the existence of data to support them, it is a shock to realize that the roles of B vitamins in plant abiotic stress have had minimal attention in the literature (100-fold less than hormones) and continue to be overlooked. In this article, we therefore aim to explain the connections among B vitamins, enzyme cofactors, and stress conditions in plants. We first outline the chemistry and biochemistry of B vitamins and explore the concept of vitamin deficiency with the help of information from mammals. We then summarize classical and recent evidence for stress-induced vitamin deficiencies and for plant responses that counter these deficiencies. Lastly, we consider potential implications for agriculture.
Sugars are the most important regulators that facilitate many physiological processes, such as photosynthesis, seed germination, flowering, senescence, and many more under various abiotic stresses. Exogenous application of sugars in low concentration promote seed germination, up regulates photosynthesis, promotes flowering, delayed senescence under various unfavorable environmental conditions. However, high concentration of sugars reverses all these physiological process in a concentration dependent manner. Thus, this review focuses the correlation between sugars and their protective functions in several physiological processes against various abiotic stresses. Keeping in mind the multifaceted role of sugars, an attempt has been made to cover the role of sugar-regulated genes associated with photosynthesis, seed germination and senescence. The concentration of sugars determines the expression of these sugar-regulated genes. This review also enlightens the interaction of sugars with several phytohormones, such as abscisic acid, ethylene, cytokinins and gibberellins and its effect on their biosynthesis under abiotic stress conditions.
Amino acids are the main form of nitrogen transported between the plant organs. Transport of amino acids across membranes is mediated by specialized proteins: importers, exporters, and facilitators. Unlike amino acid importers, amino acid exporters have not been thoroughly studied, partly due to a lack of high-throughput techniques enabling their isolation. Usually Multiple Acids Move In and out Transporters 14 (UMAMIT14) from Arabidopsis shares sequence similarity to the amino acid facilitator Silique Are Red1 (UMAMIT18), and has been shown to be involved in amino acid transfer to the seeds. We show here that UMAMIT14 is also expressed in root pericycle and phloem cells and mediates export of a broad range of amino acids in yeast. Loss-of-function of UMAMIT14 leads to a reduced shoot-to-root and root-to-medium transfer of amino acids originating from the leaves. These fluxes were further reduced in an umamti14 umamit18 double loss-of-function mutant. This study suggests that UMAMIT14 is involved in phloem unloading of amino acids in roots, and that UMAMIT14 and UMAMIT18 are involved in the radial transport of amino acids in roots, which is essential for maintaining amino acid secretion to the soil.
Climate change ecology has focused on climate effects on trophic interactions through the lenses of temperature effects on organismal physiology and phenological asynchronies. Trophic interactions are also affected by the nutrient content of resources, but this topic has received less attention. Using concepts from nutritional ecology, we propose a conceptual framework for understanding how climate affects food webs through top-down and bottom-up processes impacted by co-occurring environmental drivers.
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