Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana

Integrated Metabolomic and Transcriptomic Profiling Reveals the Defense Response of Tea Plants (Camellia sinensis) to Toxoptera aurantii

The tea plant (Camellia sinensis) is a unique beverage crop worldwide, but its yield and quality are adversely affected by Toxoptera aurantii. However, the response mechanisms of tea plants to T. aurantii stress remain poorly known. Herein, we present the life table of T. aurantii on resistant (W016) and susceptible (HJY) tea cultivars, demonstrating that the fitness of T. aurantii on W016 was lower than that on HJY. Integrated metabolic and transcriptomic analyses revealed that T. aurantii feeding activated pathways associated with phenylpropanoid biosynthesis, plant hormone signal transduction, and ATP-binding cassette (ABC) transporters. Notably, T. aurantii feeding significantly upregulated the levels of brassinolide and p-coumaryl alcohol in W016 but not in HJY. Furthermore, in vitro enzymatic assays indicated that C. sinensis cinnamyl alcohol dehydrogenase (CsCAD1) catalyzes the formation of p-coumaryl alcohol participation in lignin synthesis. Our findings highlight the role of brassinolide-mediated lignin biosynthesis of the tea plant in response to T. aurantii feeding.

Natural variation in Brachypodium distachyon responses to combined abiotic stresses

The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions of Brachypodium distachyon under drought, heat, and the combination of stresses. Heat alone causes the largest amounts of tissue damage while the combination of stresses causes the largest decrease in biomass compared to other treatments. Notably, Bd21-0, the reference line for B. distachyon, did not have robust growth under stress conditions, especially the heat and combined drought and heat treatments. The climate of origin was significantly associated with B. distachyon responses to the assessed stress conditions. Additionally, a GWAS found loci associated with changes in plant height and the amount of damaged tissue under stress. Some of these SNPs were closely located to genes known to be involved in responses to abiotic stresses and point to potential causative loci in plant stress response. However, SNPs found to be significantly associated with a response to heat or drought individually are not also significantly associated with the combination of stresses. This, with the phenotypic data, suggests that the effects of these abiotic stresses are not simply additive, and the responses to the combined stresses differ from drought and heat alone.

Genome-wide association analysis reveals genes controlling an antagonistic effect of biotic and osmotic stress on Arabidopsis thaliana growth

While the response of Arabidopsis thaliana to drought, herbivory or fungal infection has been well-examined, the consequences of exposure to a series of such (a)biotic stresses are not well studied. This work reports on the genetic mechanisms underlying the Arabidopsis response to single osmotic stress, and to combinatorial stress, either fungal infection using Botrytis cinerea or herbivory using Pieris rapae caterpillars followed by an osmotic stress treatment. Several small-effect genetic loci associated with rosette dry weight (DW), rosette water content (WC), and the projected rosette leaf area in response to combinatorial stress were mapped using univariate and multi-environment genome-wide association approaches. A single-nucleotide polymorphism (SNP) associated with DROUGHT-INDUCED 19 (DI19) was identified by both approaches, supporting its potential involvement in the response to combinatorial stress. Several SNPs were found to be in linkage disequilibrium with known stress-responsive genes such as PEROXIDASE 34 (PRX34), BASIC LEUCINE ZIPPER 25 (bZIP25), RESISTANCE METHYLATED GENE 1 (RMG1) and WHITE RUST RESISTANCE 4 (WRR4). An antagonistic effect between biotic and osmotic stress was found for prx34 and arf4 mutants, which suggests PRX34 and ARF4 play an important role in the response to the combinatorial stress.

Comprehensive transcriptome analyses of Fusarium-infected root xylem tissues to decipher genes involved in chickpea wilt resistance

Fusarium wilt is the most destructive soil-borne disease that poses a major threat to chickpea production. To comprehensively understand the interaction between chickpea and Fusarium oxysporum, the xylem-specific transcriptome analysis of wilt-resistant (WR315) and wilt-susceptible (JG62) genotypes at an early timepoint (4DPI) was investigated. Differential expression analysis showed that 1368 and 348 DEGs responded to pathogen infection in resistant and susceptible genotypes, respectively. Both genotypes showed transcriptional reprogramming in response to Foc2, but the responses in WR315 were more severe than in JG62. Results of the KEGG pathway analysis revealed that most of the DEGS in both genotypes with enrichment in metabolic pathways, secondary metabolite biosynthesis, plant hormone signal transduction, and carbon metabolism. Genes associated with defense-related metabolites synthesis such as thaumatin-like protein 1b, cysteine-rich receptor-like protein kinases, MLP-like proteins, polygalacturonase inhibitor 2-like, ethylene-responsive transcription factors, glycine-rich cell wall structural protein-like, beta-galactosidase-like, subtilisin-like protease, thioredoxin-like protein, chitin elicitor receptor kinase-like, proline transporter-like, non-specific lipid transfer protein and sugar transporter were mostly up-regulated in resistant as compared to susceptible genotypes. The results of this study provide disease resistance genes, which would be helpful in understanding the Foc resistance mechanism in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03803-9.

Microbial degradation of plant toxins

Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.

A review of plants strategies to resist biotic and abiotic environmental stressors

Plants exposed to a variety of abiotic and biotic stressors including environmental pollution and global warming pose significant threats to biodiversity and ecosystem services. Despite substantial literature documenting how plants adapt to distinct stressors, there still is a lack of knowledge regarding responses to multiple stressors and how these affects growth and development. Exposure of plants to concurrent biotic and abiotic stressors such as cadmium and drought, leads to pronounced inhibition in above ground biomass, imbalance in oxidative homeostasis, nutrient assimilation and stunted root growth, elucidating the synergistic interactions of multiple stressors culminating in adverse physiological outcomes. Impact of elevated heavy metal and water deficit exposure extends beyond growth and development, influencing the biodiversity of the microenvironment including the rhizosphere nutrient profile and microbiome. These findings have significant implications for plant-stress interactions and ecosystem functioning that prompt immediate action in order to eliminate effect of pollution and address global environmental issues to promote sustainable tolerance for multiple stress combinations in plants. Here, we review plant tolerance against stress combinations, highlighting the need for interdisciplinary approaches and advanced technologies, such as omics and molecular tools, to achieve a comprehensive understanding of underlying stress tolerance mechanisms. To accelerate progress towards developing stress-tolerance in plants against multiple environmental stressors, future research in plant stress tolerance should adopt a collaborative approach, involving researchers from multiple disciplines with diverse expertise and resources.

The resistance of the jujube (Ziziphus jujuba) to the devastating insect pest Apolygus lucorum (Hemiptera, Insecta) involves the jasmonic acid signaling pathway

Apolygus lucorum (Hemiptera, Insecta), cosmopolitan true bug, is a major pest of the Chinese jujube (Ziziphus jujuba). To propose control measures of A. lucorum, we investigated the molecular mechanisms of resistance in two varieties of jujube (wild jujube and winter jujube) with different sensitivities to this pest. We monitored changes of two species of jujube in the transcriptome, jasmonic acid (JA) and salicylic acid (SA) content, and the expression of genes involved in signaling pathways. The preference of A. lucorum for jujube with exogenous SA and methyl jasmonate (MeJA) were also examined. The results showed that wild jujube leaves infested by A. lucorum showed stronger resistance and non-selectivity to A. lucorum than winter jujube. By comparing data from the A. lucorum infested plants with the control, A total of 438 and 796 differentially expressed genes (DEGs) were found in winter and wild jujube leaves, respectively. GO analysis revealed that biological process termed "plant-pathogen interactions", "plant hormone transduction" and "phenylpropanoid biosynthesis". Most of DEGs enriched in JA pathways were upregulated, while most DEGs of SA pathways were downregulated. A. lucorum increased the JA content but decreased the SA content in jujube. Consistently, the JA and SA contents in winter jujube were lower than those in wild jujube leaves. The key genes ZjFAD3, ZjLOX, ZjAOS, ZjAOC3 and ZjAOC4 involved in JA synthesis of jujube leaves were significantly up-regulated after A. lucorum infestation, especially the expression and up-regulation ratio of ZjFAD3, ZjLOX and ZjAOS in wild jujube were significantly higher than those in winter jujube. MeJA-treated jujube showed an obvious repellent effect on A. lucorum. Based on these findings, we conclude that A. lucorum infestation of jujube induced the JA pathway and suppressed the SA pathway. In jujube leaves the ZjFAD3, ZjLOX and ZjAOS played important roles in increasing of JA content in jujube leaves. Thus, JA played an important role in repelling and resisting against A. lucorum in jujube.

Proteomic Insights of Cowpea Response to Combined Biotic and Abiotic Stresses

The co-occurrence of biotic and abiotic stresses in agricultural areas severely affects crop performance and productivity. Drought is one of the most adverse environmental stresses, and its association with root-knot nematodes further limits the development of several economically important crops, such as cowpea. Plant responses to combined stresses are complex and require novel adaptive mechanisms through the induction of specific biotic and abiotic signaling pathways. Therefore, the present work aimed to identify proteins involved in the resistance of cowpea to nematode and drought stresses individually and combined. We used the genotype CE 31, which is resistant to the root-knot nematode Meloidogyne spp. And tolerant to drought. Three biological replicates of roots and shoots were submitted to protein extraction, and the peptides were evaluated by LC-MS/MS. Shotgun proteomics revealed 2345 proteins, of which 1040 were differentially abundant. Proteins involved in essential biological processes, such as transcriptional regulation, cell signaling, oxidative processes, and photosynthesis, were identified. However, the main defense strategies in cowpea against cross-stress are focused on the regulation of hormonal signaling, the intense production of pathogenesis-related proteins, and the downregulation of photosynthetic activity. These are key processes that can culminate in the adaptation of cowpea challenged by multiple stresses. Furthermore, the candidate proteins identified in this study will strongly contribute to cowpea genetic improvement programs.

Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression

In the plant sciences, results of laboratory studies often do not translate well to the field. To help close this lab-field gap, we developed a strategy for studying the wiring of plant traits directly in the field, based on molecular profiling and phenotyping of individual plants. Here, we use this single-plant omics strategy on winter-type Brassica napus (rapeseed). We investigate to what extent early and late phenotypes of field-grown rapeseed plants can be predicted from their autumnal leaf gene expression, and find that autumnal leaf gene expression not only has substantial predictive power for autumnal leaf phenotypes but also for final yield phenotypes in spring. Many of the top predictor genes are linked to developmental processes known to occur in autumn in winter-type B. napus accessions, such as the juvenile-to-adult and vegetative-to-reproductive phase transitions, indicating that the yield potential of winter-type B. napus is influenced by autumnal development. Our results show that single-plant omics can be used to identify genes and processes influencing crop yield in the field.

Water availability and plant-herbivore interactions

Water is essential to plant growth and drives plant evolution and interactions with other organisms such as herbivores. However, water availability fluctuates, and these fluctuations are intensified by climate change. How plant water availability influences plant-herbivore interactions in the future is an important question in basic and applied ecology. Here we summarize and synthesize the recent discoveries on the impact of water availability on plant antiherbivore defense ecology and the underlying physiological processes. Water deficit tends to enhance plant resistance and escape traits (i.e. early phenology) against herbivory but negatively affects other defense strategies, including indirect defense and tolerance. However, exceptions are sometimes observed in specific plant-herbivore species pairs. We discuss the effect of water availability on species interactions associated with plants and herbivores from individual to community levels and how these interactions drive plant evolution. Although water stress and many other abiotic stresses are predicted to increase in intensity and frequency due to climate change, we identify a significant lack of study on the interactive impact of additional abiotic stressors on water-plant-herbivore interactions. This review summarizes critical knowledge gaps and informs possible future research directions in water-plant-herbivore interactions.

Genome-wide association study reveals WRKY42 as a novel plant transcription factor that influences oviposition preference of Pieris butterflies

Insect herbivores are amongst the most destructive plant pests, damaging both naturally occurring and domesticated plants. As sessile organisms, plants make use of structural and chemical barriers to counteract herbivores. However, over 75% of herbivorous insect species are well adapted to their host's defenses and these specialists are generally difficult to ward off. By actively antagonizing the number of insect eggs deposited on plants, future damage by the herbivore's offspring can be limited. Therefore, it is important to understand which plant traits influence attractiveness for oviposition, especially for specialist insects that are well adapted to their host plants. In this study, we investigated the oviposition preference of Pieris butterflies (Lepidoptera: Pieridae) by offering them the choice between 350 different naturally occurring Arabidopsis accessions. Using a genome-wide association study of the oviposition data and subsequent fine mapping with full genome sequences of 164 accessions, we identified WRKY42 and AOC1 as candidate genes that are associated with the oviposition preference observed for Pieris butterflies. Host plant choice assays with Arabidopsis genotypes impaired in WRKY42 or AOC1 function confirmed a clear role for WRKY42 in oviposition preference of female Pieris butterflies, while for AOC1 the effect was mild. In contrast, WRKY42-impaired plants, which were preferred for oviposition by butterflies, negatively impacted offspring performance. These findings exemplify that plant genotype can have opposite effects on oviposition preference and caterpillar performance. This knowledge can be used for breeding trap crops or crops that are unattractive for oviposition by pest insects.

Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.

Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity

Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.

Integrated Transcriptome and Metabolome Analysis to Identify Sugarcane Gene Defense against Fall Armyworm (Spodoptera frugiperda) Herbivory

Sugarcane is the most important sugar crop, contributing ≥80% to total sugar production around the world. Spodoptera frugiperda is one of the main pests of sugarcane, potentially causing severe yield and sugar loss. The identification of key defense factors against S. frugiperda herbivory can provide targets for improving sugarcane resistance to insect pests by molecular breeding. In this work, we used one of the main sugarcane pests, S. frugiperda, as the tested insect to attack sugarcane. Integrated transcriptome and metabolomic analyses were performed to explore the changes in gene expression and metabolic processes that occurred in sugarcane leaf after continuous herbivory by S. frugiperda larvae for 72 h. The transcriptome analysis demonstrated that sugarcane pest herbivory enhanced several herbivory-induced responses, including carbohydrate metabolism, secondary metabolites and amino acid metabolism, plant hormone signaling transduction, pathogen responses, and transcription factors. Further metabolome analysis verified the inducement of specific metabolites of amino acids and secondary metabolites by insect herbivory. Finally, association analysis of the transcriptome and metabolome by the Pearson correlation coefficient method brought into focus the target defense genes against insect herbivory in sugarcane. These genes include amidase and lipoxygenase in amino acid metabolism, peroxidase in phenylpropanoid biosynthesis, and pathogenesis-related protein 1 in plant hormone signal transduction. A putative regulatory model was proposed to illustrate the sugarcane defense mechanism against insect attack. This work will accelerate the dissection of the mechanism underlying insect herbivory in sugarcane and provide targets for improving sugarcane variety resistance to insect herbivory by molecular breeding.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Plant defense strategies against attack by multiple herbivores

Plants may effectively tailor defenses by recognizing their attackers and reprogramming their physiology. Although most plants are under attack by a large diversity of herbivores, surprisingly little is known about the physiological capabilities of plants to deal with attack by multiple herbivores. Studies on dual herbivore attack identified that defense against one attacker may cause energetic and physiological constraints to deal with a second attacker. How these constraints shape plant plasticity in defense to their full community of attackers is a major knowledge gap in plant science. Here, we provide a framework for plant defense to multiherbivore attack by defining the repertoire of plastic defense strategies that may allow plants to optimize their defenses against a multitude of stressors.

Network organization of the plant immune system: from pathogen perception to robust defense induction

The plant immune system has been explored essentially through the study of qualitative resistance, a simple form of immunity, and from a reductionist point of view. The recent identification of genes conferring quantitative disease resistance revealed a large array of functions, suggesting more complex mechanisms. In addition, thanks to the advent of high-throughput analyses and system approaches, our view of the immune system has become more integrative, revealing that plant immunity should rather be seen as a distributed and highly connected molecular network including diverse functions to optimize expression of plant defenses to pathogens. Here, we review the recent progress made to understand the network complexity of regulatory pathways leading to plant immunity, from pathogen perception, through signaling pathways and finally to immune responses. We also analyze the topological organization of these networks and their emergent properties, crucial to predict novel immune functions and test them experimentally. Finally, we report how these networks might be regulated by environmental clues. Although system approaches remain extremely scarce in this area of research, a growing body of evidence indicates that the plant response to combined biotic and abiotic stresses cannot be inferred from responses to individual stresses. A view of possible research avenues in this nascent biology domain is finally proposed.

Developing climate-resilient crops: improving plant tolerance to stress combination

Global warming and climate change are driving an alarming increase in the frequency and intensity of different abiotic stresses, such as droughts, heat waves, cold snaps, and flooding, negatively affecting crop yields and causing food shortages. Climate change is also altering the composition and behavior of different insect and pathogen populations adding to yield losses worldwide. Additional constraints to agriculture are caused by the increasing amounts of human-generated pollutants, as well as the negative impact of climate change on soil microbiomes. Although in the laboratory, we are trained to study the impact of individual stress conditions on plants, in the field many stresses, pollutants, and pests could simultaneously or sequentially affect plants, causing conditions of stress combination. Because climate change is expected to increase the frequency and intensity of such stress combination events (e.g., heat waves combined with drought, flooding, or other abiotic stresses, pollutants, and/or pathogens), a concentrated effort is needed to study how stress combination is affecting crops. This need is particularly critical, as many studies have shown that the response of plants to stress combination is unique and cannot be predicted from simply studying each of the different stresses that are part of the stress combination. Strategies to enhance crop tolerance to a particular stress may therefore fail to enhance tolerance to this specific stress, when combined with other factors. Here we review recent studies of stress combinations in different plants and propose new approaches and avenues for the development of stress combination- and climate change-resilient crops.

The Genomic Architecture of Competitive Response of Arabidopsis thaliana Is Highly Flexible Among Plurispecific Neighborhoods

Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.

Global Warming, Climate Change, and Environmental Pollution: Recipe for a Multifactorial Stress Combination Disaster

Global warming, climate change, and environmental pollution present plants with unique combinations of different abiotic and biotic stresses. Although much is known about how plants acclimate to each of these individual stresses, little is known about how they respond to a combination of many of these stress factors occurring together, namely a multifactorial stress combination. Recent studies revealed that increasing the number of different co-occurring multifactorial stress factors causes a severe decline in plant growth and survival, as well as in the microbiome biodiversity that plants depend upon. This effect should serve as a dire warning to our society and prompt us to decisively act to reduce pollutants, fight global warming, and augment the tolerance of crops to multifactorial stress combinations.

Defining the combined stress response in wild Arachis

Nematodes and drought are major constraints in tropical agriculture and often occur simultaneously. Plant responses to these stresses are complex and require crosstalk between biotic and abiotic signaling pathways. In this study, we explored the transcriptome data of wild Arachis species subjected to drought (A-metaDEG) and the root-knot nematode Meloidogyne arenaria (B-metaDEG) via meta-analysis, to identify core-stress responsive genes to each individual and concurrent stresses in these species. Transcriptome analysis of a nematode/drought bioassay (cross-stress) showed that the set of stress responsive DEGs to concurrent stress is distinct from those resulting from overlapping A- and B-metaDEGs, indicating a specialized and unique response to combined stresses in wild Arachis. Whilst individual biotic and abiotic stresses elicit hormone-responsive genes, most notably in the jasmonic and abscisic acid pathways, combined stresses seem to trigger mainly the ethylene hormone pathway. The overexpression of a cross-stress tolerance candidate gene identified here, an endochitinase-encoding gene (AsECHI) from Arachis stenosperma, reduced up to 30% of M. incognita infection and increased post-drought recovery in Arabidopsis plants submitted to both stresses. The elucidation of the network of cross-stress responsive genes in Arachis contributes to better understanding the complex regulation of biotic and abiotic responses in plants facilitating more adequate crop breeding for combined stress tolerance.

Using single-plant-omics in the field to link maize genes to functions and phenotypes

Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.

Ménage à Trois: Unraveling the Mechanisms Regulating Plant-Microbe-Arthropod Interactions

Plant-microbe-arthropod (PMA) three-way interactions have important implications for plant health. However, our poor understanding of the underlying regulatory mechanisms hampers their biotechnological applications. To this end, we searched for potential common patterns in plant responses regarding taxonomic groups or lifestyles. We found that most signaling modules regulating two-way interactions also operate in three-way interactions. Furthermore, the relative contribution of signaling modules to the final plant response cannot be directly inferred from two-way interactions. Moreover, our analyses show that three-way interactions often result in the activation of additional pathways, as well as in changes in the speed or intensity of defense activation. Thus, detailed, basic knowledge of plant-microbe-arthropod regulation will be essential for the design of environmentally friendly crop management strategies.

Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions

Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (Φ_PSII ) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in Φ_PSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in Φ_PSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.

Identifying Vitamin E Biosynthesis Genes in Elaeis guineensis by Genome-Wide Association Study

Elaeis guineensis is a tropical oil crop and has the highest oil yield per unit area. Palm oil has high palmitic acid content and is also rich in vitamins, including vitamin E. We conducted genome-wide association studies in a diversity panel of 161 E. guineensis accessions to identify single-nucleotide polymorphisms (SNPs) linked with vitamin E and validated candidate genes in these marker-associated intervals. Based on the SNPs reported in our previous research, 47 SNP markers were detected to be significantly associated with the variation of tocopherol and tocotrienol content at a cutoff P value of 6.3 × 10^-7. A total of 656 candidate genes in the flanking regions of the 47 SNPs were identified, followed by pathway enrichment analysis. Of these candidate genes, EgHGGT (homogentisate geranylgeranyl transferase) involved in the biosynthesis of tocotrienols had a higher expression level in the mesocarp compared to other tissues. Expression of the EgHGGT gene was positively correlated with the variation in α-tocotrienol content. Induced overexpression of the gene in Arabidopsis caused a significant increase in vitamin E content and production of α-tocotrienols compared to wild Arabidopsis.

Plant immunity in signal integration between biotic and abiotic stress responses

Plants constantly monitor and cope with the fluctuating environment while hosting a diversity of plant-inhabiting microbes. The mode and outcome of plant-microbe interactions, including plant disease epidemics, are dynamically and profoundly influenced by abiotic factors, such as light, temperature, water and nutrients. Plants also utilize associations with beneficial microbes during adaptation to adverse conditions. Elucidation of the molecular bases for the plant-microbe-environment interactions is therefore of fundamental importance in the plant sciences. Following advances into individual stress signaling pathways, recent studies are beginning to reveal molecular intersections between biotic and abiotic stress responses and regulatory principles in combined stress responses. We outline mechanisms underlying environmental modulation of plant immunity and emerging roles for immune regulators in abiotic stress tolerance. Furthermore, we discuss how plants coordinate conflicting demands when exposed to combinations of different stresses, with attention to a possible determinant that links initial stress response to broad-spectrum stress tolerance or prioritization of specific stress tolerance.

Dynamics of plant responses to combinations of air pollutants

The focus of this review is on how plants respond to combinations of multiple air pollutants. Global pollution trends, plant physiological responses and ecological perspectives in natural and agricultural systems are all discussed. In particular, we highlight the importance of studying sequential or simultaneous exposure of plants to pollutants, rather than exposure to individual pollutants in isolation, and explore how these responses may interfere with the way plants interact with their biotic community. Air pollutants can alter the normal physiology and metabolic functioning of plants. Here we describe how the phenotypic and molecular changes in response to multiple pollutants can differ compared to those elicited by single pollutants, and how different responses have been observed between plants in the field and in controlled laboratory conditions and between trees and crop plants. From an ecological perspective, we discuss how air pollution can result in greater susceptibility to biotic stressors and in direct or indirect effects on interactions with organisms that occupy higher trophic levels. Finally, we provide an overview of the potential uses of plants to mitigate air pollution, exploring the feasibility for pollution removal via the processes of bio-accumulation and phytoremediation. We conclude by proposing some new directions for future research in the field.

Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation

The molecular mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using Arabidopsis thaliana accessions, we analyzed RGR variation under combinatorial mineral nutrient deficiencies involving phosphorus (P), iron (Fe), and zinc (Zn). While -P stimulated early RGR of most accessions, -Fe or -Zn reduced it. The combination of either -P-Fe or -P-Zn led to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, root growth responses of the reference accession Columbia (Col-0) were not representative of the species under -P nor -Zn. Using a systems approach that combines GWAS, network-based candidate identification, and reverse genetic screen, we identified new genes that regulate root growth in -P-Fe: VIM1, FH6, and VDAC3. Our findings provide a framework to systematically identifying favorable allelic variations to improve root growth, and to better understand how plants sense and respond to multiple environmental cues.

Plants thrive in highly heterogenous soils. How they compute a multitude of contrasting stimuli and mount an adaptive response without a centralized information processing unit is an intriguing question. For instance, below ground, roots can sense and respond to the single or multiple nutrient stresses, and adjust its growth rate accordingly. Nevertheless, the genetic architecture of root growth responses under single and combined stress remains poorly understood. To fill this gap in our understanding about such crucial phenomenon for plant survival, we explored the natural variation of root growth rate (RGR) in Arabidopsis grown under single and combined nutritional stress, including deficiencies of iron (-Fe), zinc (-Zn), phosphate and iron (-P-Fe) and phosphate and zinc (-P-Zn). Our GWAS revealed distinct genetic architectures underlying root growth responses to single or combined nutrient stresses. By integrating GWAS and coexpression networks, we identified and validated genes controlling the variation of root growth to combined nutrient-deficiency, namely VARIANT IN METHYLATION 1, FORMIN-LIKE-PROTEIN-6 and VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 3. Our findings provide a framework to accelerate future research aiming at better understanding how plants sense and respond to multiple environmental inputs, and promise to help designing new agronomical and biotechnological strategies to improve root growth.

Evolutionary constraint on low elevation range expansion: Defense-abiotic stress-tolerance trade-off in crosses of the ecological model Boechera stricta

Most transplant experiments across species geographic range boundaries indicate that adaptation to stressful environments outside the range is often constrained. However, the mechanisms of these constraints remain poorly understood. We used extended generation crosses from diverged high and low elevation populations. In experiments across low elevation range boundaries, there was selection on the parental lines for abiotic stress-tolerance and resistance to herbivores. However, in support of a defense-tolerance trade-off, extended generation crosses showed nonindependent segregation of these traits in the laboratory across a drought-stress gradient and in the field across the low elevation range boundary. Genotypic variation in a marker from a region of the genome containing a candidate gene (MYC2) was associated with change in the genetic trade-off. Thus, using crosses and forward genetics, we found experimental genetic and molecular evidence for a pleiotropic trade-off that could constrain the evolution of range expansion.

QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana

BACKGROUND

Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability.

RESULTS

Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus.

CONCLUSION

We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .

The plant immune system in heterogeneous environments

The plant immune system inhibits pathogen growth and contributes to shaping a healthy microbial community in the plant body. Plants must appropriately respond to both microbial signals and abiotic factors that are diverse in time and space, and thus, proper integration of these inputs at local and systemic levels is of crucial importance for optimal plant responses and fitness in nature. Here, we review our current knowledge of three properties of the plant immune system, resilience, tunability, and balance, which enable plants to deal with complex cocktails of environmental factors. We also discuss future challenges on the path towards a comprehensive understanding of the interactions between plant immunity and pathogenic, non-pathogenic, and beneficial microbes.

Molecular Interactions Between Plants and Insect Herbivores

Diverse molecular processes regulate the interactions between plants and insect herbivores. Here, we review genes and proteins that are involved in plant-herbivore interactions and discuss how their discovery has structured the current standard model of plant-herbivore interactions. Plants perceive damage-associated and, possibly, herbivore-associated molecular patterns via receptors that activate early signaling components such as Ca²⁺, reactive oxygen species, and MAP kinases. Specific defense reprogramming proceeds via signaling networks that include phytohormones, secondary metabolites, and transcription factors. Local and systemic regulation of toxins, defense proteins, physical barriers, and tolerance traits protect plants against herbivores. Herbivores counteract plant defenses through biochemical defense deactivation, effector-mediated suppression of defense signaling, and chemically controlled behavioral changes. The molecular basis of plant-herbivore interactions is now well established for model systems. Expanding molecular approaches to unexplored dimensions of plant-insect interactions should be a future priority.

Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana

BACKGROUND

Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context, Arabidopsis trichomes provide an excellent system to discern the roles of natural variation and a key gene, GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1 and gl1-2) and 17 natural accessions of Arabidopsis thaliana to two localities in Switzerland and Japan.

RESULTS

Fifteen insect species inhabited the plant accessions, with the insect community composition significantly attributed to variations among plant accessions. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both field sites, while glucosinolates had variable effects on leaf chewers between the sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher on gl1-1 and gl1-2 than on their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in the GLABRA1 gene significantly decreased the resistance of plants to the two predominant chewers; flea beetles and turnip sawflies.

CONCLUSIONS

Overall, our results indicate that insect community composition significantly varies among A. thaliana accessions across two distant field sites, with GLABRA1 playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide effect of a single plant gene on crucifer-feeding insects in the field.

Mining the natural genetic variation in Arabidopsis thaliana for adaptation to sequential abiotic and biotic stresses

In this genome-wide association study, we obtained novel insights into the genetic basis of the effect of herbivory or drought stress on the level of resistance against the fungus Botrytis cinerea. In nature, plants function in complex environments where they encounter different biotic and abiotic stresses individually, sequentially or simultaneously. The adaptive response to a single stress does not always reflect how plants respond to such a stress in combination with other stresses. To identify genetic factors that contribute to the plant's ability to swiftly adapt to different stresses, we investigated the response of Arabidopsis thaliana to infection by the necrotrophic fungus B. cinerea when preceded by Pieris rapae herbivory or drought stress. Using 346 natural A. thaliana accessions, we found natural genetic variation in the level of resistance against single B. cinerea infection. When preceded by herbivory or drought stress, the level of B. cinerea resistance was differentially influenced in the 346 accessions. To study the genetic factors contributing to the differential adaptation of A. thaliana to B. cinerea infection under multi-stress conditions, we performed a genome-wide association study supported by quantitative trait loci mapping and fine mapping with full genome sequences of 164 accessions. This yielded several genes previously associated with defense to B. cinerea and additional candidate genes with putative roles in the plant's adaptive response to a combination of herbivory, drought and B. cinerea infection.

A new regulator of seed size control in Arabidopsis identified by a genome-wide association study

Organ size in plants is controlled by the interaction between genotype and the environment. Seed size, an important agronomic trait, largely determines yield and is an important focus of research. However, the genetic components underpinning natural variation of seed size in undomesticated species remain largely unidentified. Here we report a genome-wide association study (GWAS) of seed size in Arabidopsis thaliana, which identified 38 significantly associated loci, including one locus associated with CYCB1;4. Natural variations in CYCB1;4, which encodes a cyclin protein involved in the cell cycle, significantly influence seed size in A. thaliana. Transgenic plants with enhanced CYCB1;4 expression show normal development, exhibit increased seed size as a result of an accelerated cell cycle progression, and tend to produce higher yields. By contrast, cycb1;4 mutants have smaller seeds, and the effect is especially pronounced in a large-seed accession. The temporal and spatial expression pattern of CYCB1;4 suggests that this gene may function in both maternal tissues and zygotic tissues to coordinate the final size of seeds. Taken together, our results provide genetic insights into natural variation in seed size in Arabidopsis. Moreover, CYCB1;4 homologs in other crops could have great potential as targets for efforts aimed at yield improvement.

Linking genes with ecological strategies in Arabidopsis thaliana

Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.

Evolutionary and ecological functional genomics, from lab to the wild

Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.

Quantifying temporal change in plant population attributes: insights from a resurrection approach

Rapid evolution in annual plants can be quantified by comparing phenotypic and genetic changes between past and contemporary individuals from the same populations over several generations. Such knowledge will help understand the response of plants to rapid environmental shifts, such as the ones imposed by global climate change. To that end, we undertook a resurrection approach in Spanish populations of the annual plant Arabidopsis thaliana that were sampled twice over a decade. Annual weather records were compared to their historical records to extract patterns of climatic shifts over time. We evaluated the differences between samplings in flowering time, a key life-history trait with adaptive significance, with a field experiment. We also estimated genetic diversity and differentiation based on neutral nuclear markers and nucleotide diversity in candidate flowering time (FRI and FLC) and seed dormancy (DOG1) genes. The role of genetic drift was estimated by computing effective population sizes with the temporal method. Overall, two climatic scenarios were detected: intense warming with increased precipitation and moderate warming with decreased precipitation. The average flowering time varied little between samplings. Instead, within-population variation in flowering time exhibited a decreasing trend over time. Substantial temporal changes in genetic diversity and differentiation were observed with both nuclear microsatellites and candidate genes in all populations, which were interpreted as the result of natural demographic fluctuations. We conclude that drought stress caused by moderate warming with decreased precipitation may have the potential to reduce within-population variation in key life-cycle traits, perhaps as a result of stabilizing selection on them, and to constrain the genetic differentiation over time. Besides, the demographic behaviour of populations probably accounts for the substantial temporal patterns of genetic variation, while keeping rather constant those of phenotypic variation.

Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner

The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.

Genome-wide association mapping of the architecture of susceptibility to the root-knot nematode Meloidogyne incognita in Arabidopsis thaliana

Susceptibility to the root-knot nematode Meloidogyne incognita in plants is thought to be a complex trait based on multiple genes involved in cell differentiation, growth and defence. Previous genetic analyses of susceptibility to M. incognita have mainly focused on segregating dominant resistance genes in crops. It is not known if plants harbour significant genetic variation in susceptibility to M. incognita independent of dominant resistance. To study the genetic architecture of susceptibility to M. incognita, we analysed nematode reproduction on a highly diverse set of 340 natural inbred lines of Arabidopsis thaliana with genome-wide association mapping. We observed a surprisingly large variation in nematode reproduction among these lines. Genome-wide association mapping revealed four quantitative trait loci (QTLs) located on chromosomes 1 and 5 of A. thaliana significantly associated with reproductive success of M. incognita, none of which harbours typical resistance gene homologues. Mutant analysis of three genes located in two QTLs showed that the transcription factor BRASSINAZOLE RESISTANT1 and an F-box family protein may function as (co-)regulators of susceptibility to M. incognita in Arabidopsis. Our data suggest that breeding for loss-of-susceptibility, based on allelic variants critically involved in nematode feeding, could be used to make crops more resilient to root-knot nematodes.

Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes.

Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

Metabolic genome-wide association studies (mGWAS), whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309 Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two-condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08), 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between structural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.

Evolution of Hormone Signaling Networks in Plant Defense

Studies with model plants such as Arabidopsis thaliana have revealed that phytohormones are central regulators of plant defense. The intricate network of phytohormone signaling pathways enables plants to activate appropriate and effective defense responses against pathogens as well as to balance defense and growth. The timing of the evolution of most phytohormone signaling pathways seems to coincide with the colonization of land, a likely requirement for plant adaptations to the more variable terrestrial environments, which included the presence of pathogens. In this review, we explore the evolution of defense hormone signaling networks by combining the model plant-based knowledge about molecular components mediating phytohormone signaling and cross talk with available genome information of other plant species. We highlight conserved hubs in hormone cross talk and discuss evolutionary advantages of defense hormone cross talk. Finally, we examine possibilities of engineering hormone cross talk for improvement of plant fitness and crop production.

Towards engineering of hormonal crosstalk in plant immunity

Plant hormones regulate physiological responses in plants, including responses to pathogens and beneficial microbes. The last decades have provided a vast amount of evidence about the contribution of different plant hormones to plant immunity, and also of how they cooperate to orchestrate immunity activation, in a process known as hormone crosstalk. In this review we highlight the complexity of hormonal crosstalk in immunity and approaches currently being used to further understand this process, as well as perspectives to engineer hormone crosstalk for enhanced pathogen resistance and overall plant fitness.

Natural variation in life history strategy of Arabidopsis thaliana determines stress responses to drought and insects of different feeding guilds

Plants are sessile organisms and, consequently, are exposed to a plethora of stresses in their local habitat. As a result, different populations of a species are subject to different selection pressures leading to adaptation to local conditions and intraspecific divergence. The annual brassicaceous plant Arabidopsis thaliana is an attractive model for ecologists and evolutionary biologists due to the availability of a large collection of resequenced natural accessions. Accessions of A. thaliana display one of two different life cycle strategies: summer and winter annuals. We exposed a collection of 308 European Arabidopsis accessions, that have been genotyped for 250K SNPs, to a range of stresses: one abiotic stress (drought), four biotic stresses (Pieris rapae caterpillars, Plutella xylostella caterpillars, Frankliniella occidentalis thrips and Myzus persicae aphids) and two combined stresses (drought plus P. rapae and Botrytis cinerea fungus plus P. rapae). We identified heritable genetic variation for responses to the different stresses, estimated by narrow-sense heritability. We found that accessions displaying different life cycle strategies differ in their response to stresses. Winter annuals are more resistant to drought, aphids and thrips and summer annuals are more resistant to P. rapae and P. xylostella caterpillars. Summer annuals are also more resistant to the combined stresses of drought plus P. rapae and infection by the fungus Botryris cinerea plus herbivory by P. rapae. Adaptation to drought displayed a longitudinal gradient. Finally, trade-offs were recorded between the response to drought and responses to herbivory by caterpillars of the specialist herbivore P. rapae.

Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA) mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes). In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.