Genome-Wide Association Mapping of Fertility Reduction upon Heat Stress Reveals Developmental Stage-Specific QTLs in Arabidopsis thaliana

Mechanisms of plant acclimation to multiple abiotic stresses

Plants frequently encounter a range of abiotic stresses and their combinations. Even though stresses rarely occur in isolation, research on plant stress resilience typically focuses on single environmental stressors. Plant responses to abiotic stress combinations are often distinct from corresponding individual stresses. Factors determining the outcomes of combined stresses are complex and multifaceted. In this review, we summarize advancements in our understanding of the mechanisms underlying plant responses to co-occurring (combined and sequential) abiotic stresses, focusing on morphological, physiological, developmental, and molecular aspects. Comprehensive understanding of plant acclimation, including the signaling and response mechanisms to combined and individual stresses, can contribute to the development of strategies for enhancing plant resilience in dynamic environments.

Plant proximity reduces seed yield in Arabidopsis plants by decreasing the number of ovule primordia

Proximity of vegetation, which is influenced by planting density, significantly impacts plant development. In Arabidopsis thaliana, it is well established that simulated shade, which mimics the proximity of other plants, triggers hypocotyl and petiole elongation, accelerates flowering and suppresses axillary bud growth. Although there is evidence that simulated shade affects reproduction beyond accelerating flowering, its impact on the development of reproductive tissues after plant architecture establishment (i.e., once flowering has begun) remains poorly explored. Here, we report that simulated shade promotes silique and pedicel elongation while reducing seed production, primarily by decreasing ovule number formation. Shade perception triggers rapid changes in gene expression in reproductive tissues, with some genes showing tissue-specific responses and others being induced in both seedlings and reproductive tissues, highlighting a conserved core of shade-responsive genes associated with light perception, photosynthesis and hormone regulation. However, while shade-induced elongation responses occur rapidly, reduction in ovule number requires prolonged shade exposure, suggesting distinct regulatory pathways for these responses. These findings shed light on the complex interplay between common (e.g., elongation and core gene expression) and tissue-specific responses (e.g., ovule formation and specialized gene expression) to shade, contributing to the developmental plasticity of Arabidopsis. Furthermore, they enhance our understanding of how external signals, indicative of vegetation proximity, can modulate seed production, a genetically determined process.

A systematic review on the implications of concurrent heat and drought stress in modulating floral development in plants

The continuous change in climate, along with irregular rainfall patterns, poses a significant threat to sustainable agricultural productivity worldwide. Both high temperatures and drought stress are key factors limiting crop growth, and with global climate change, the occurrence of combined heat and drought stress is expected to rise. This will further exacerbate the vulnerability of agricultural yield. Simultaneous heat and drought stress is prevalent in field conditions, and while extensive research has been done on the individual effects of heat and drought stress on plants, little is known about the molecular mechanisms underlying plant acclimation to a combination of these stressors. The reproductive stage, especially the flowering phase, has been identified as the most sensitive to both heat and drought stress, leading to sterility in plants. However, our understanding of the combined stress response in commonly used crop plants is still limited. Hence, it is crucial to study and comprehend the effects and interactions between high temperatures and drought stress during the reproductive stages of crops. This review delves into the morpho-physiological changes in reproductive organs of various plant species under combined heat and drought stress and also details the molecular regulation of the mechanism of combined stress tolerance in plants. Notably, the article incorporates expression analyses of candidate genes in rice flowers, emphasizing the utilization of modern biotechnological methods to enhance stress tolerance in plants. Overall, the review provides a comprehensive insight into the regulation of floral development in plants following concurrent heat and drought stress.

Bivariate GWA mapping reveals associations between aliphatic glucosinolates and plant responses to thrips and heat stress

Although plants harbor a huge phytochemical diversity, only a fraction of plant metabolites is functionally characterized. In this work, we aimed to identify the genetic basis of metabolite functions during harsh environmental conditions in Arabidopsis thaliana. With machine learning algorithms we predicted stress-specific metabolomes for 23 (a)biotic stress phenotypes of 300 natural Arabidopsis accessions. The prediction models identified several aliphatic glucosinolates (GLSs) and their breakdown products to be implicated in responses to heat stress in siliques and herbivory by Western flower thrips, Frankliniella occidentalis. Bivariate GWA mapping of the metabolome predictions and their respective (a)biotic stress phenotype revealed genetic associations with MAM, AOP, and GS-OH, all three involved in aliphatic GSL biosynthesis. We, therefore, investigated thrips herbivory on AOP, MAM, and GS-OH loss-of-function and/or overexpression lines. Arabidopsis accessions with a combination of MAM2 and AOP3, leading to 3-hydroxypropyl dominance, suffered less from thrips feeding damage. The requirement of MAM2 for this effect could, however, not be confirmed with an introgression line of ecotypes Cvi and Ler, most likely due to other, unknown susceptibility factors in the Ler background. However, AOP2 and GS-OH, adding alkenyl or hydroxy-butenyl groups, respectively, did not have major effects on thrips feeding. Overall, this study illustrates the complex implications of aliphatic GSL diversity in plant responses to heat stress and a cell-content-feeding herbivore.

GRABSEEDS: extraction of plant organ traits through image analysis

BACKGROUND

Phenotyping of plant traits presents a significant bottleneck in Quantitative Trait Loci (QTL) mapping and genome-wide association studies (GWAS). Computerized phenotyping using digital images promises rapid, robust, and reproducible measurements of dimension, shape, and color traits of plant organs, including grain, leaf, and floral traits.

RESULTS

We introduce GRABSEEDS, which is specifically tailored to extract a comprehensive set of features from plant images based on state-of-the-art computer vision and deep learning methods. This command-line enabled tool, which is adept at managing varying light conditions, background disturbances, and overlapping objects, uses digital images to measure plant organ characteristics accurately and efficiently. GRABSEED has advanced features including label recognition and color correction in a batch setting.

CONCLUSION

GRABSEEDS streamlines the plant phenotyping process and is effective in a variety of seed, floral and leaf trait studies for association with agronomic traits and stress conditions. Source code and documentations for GRABSEEDS are available at: https://github.com/tanghaibao/jcvi/wiki/GRABSEEDS .

Temperature-dependent jumonji demethylase modulates flowering time by targeting H3K36me2/3 in Brassica rapa

Global warming has a severe impact on the flowering time and yield of crops. Histone modifications have been well-documented for their roles in enabling plant plasticity in ambient temperature. However, the factor modulating histone modifications and their involvement in habitat adaptation have remained elusive. In this study, through genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we reveal that BrJMJ18 is a candidate gene for a QTL regulating thermotolerance in thermotolerant B. rapa subsp. chinensis var. parachinensis (or Caixin, abbreviated to Par). BrJMJ18 encodes an H3K36me2/3 Jumonji demethylase that remodels H3K36 methylation across the genome. We demonstrate that the BrJMJ18 allele from Par (BrJMJ18Par) influences flowering time and plant growth in a temperature-dependent manner via characterizing overexpression and CRISPR/Cas9 mutant plants. We further show that overexpression of BrJMJ18Par can modulate the expression of BrFLC3, one of the five BrFLC orthologs. Furthermore, ChIP-seq and transcriptome data reveal that BrJMJ18Par can regulate chlorophyll biosynthesis under high temperatures. We also demonstrate that three amino acid mutations may account for function differences in BrJMJ18 between subspecies. Based on these findings, we propose a working model in which an H3K36me2/3 demethylase, while not affecting agronomic traits under normal conditions, can enhance resilience under heat stress in Brassica rapa.

XBAT31 regulates reproductive thermotolerance through controlling the accumulation of HSFB2a/B2b under heat stress conditions

Heat shock transcription factors (HSFs) play a crucial role in heat stress tolerance in vegetative tissues. However, their involvement in reproductive tissues and their post-translational modifications are not well understood. In this study, we identify the E3 ligase XB3 ORTHOLOG 1 IN ARABIDOPSIS THALIANA (XBAT31) as a key player in the ubiquitination and degradation of HSFB2a/B2b. Our results show that the xbat31 mutant exhibits a higher percentage of unfertile siliques and decreased expression of HSPs in flowers under heat stress conditions compared to the wild type. Conversely, the hsfb2a hsfb2b double mutant displays improved reproductive thermotolerance. We find that XBAT31 interacts with HSFB2a/B2b and mediates their ubiquitination. Furthermore, HSFB2a/B2b ubiquitination is reduced in the xbat31-1 mutant, resulting in higher accumulation of HSFB2a/B2b in flowers under heat stress conditions. Overexpression of HSFB2a or HSFB2b leads to an increase in unfertile siliques under heat stress conditions. Thus, our results dissect the important role of the XBAT31-HSFB2a/B2b module in conferring reproductive thermotolerance in plants.

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.

Heat stress during reproductive stages reduces camelina seed productivity and changes seed composition

Camelina (Camelina sativa L. Crantz) is a low-input oilseed crop with great potential in bioenergy and industrial oils. Improving tolerance to high temperatures is essential for camelina agronomic sustainability. Two genotypes, Suneson and Pryzeth, were exposed to a transient 14-day heat stress at 37 °C during the reproductive stages. Four cohorts of pods along the main stem, which were at different stages from fully developed pods (C1), young pods (C2), open flowers (C3) and flowering buds (C4) at the time of heat treatment, were examined for morphological and seed quality traits at maturity. The main stem length was shortened in both genotypes. Pods and seeds in all cohorts were negatively affected by heat, resulting in lower seed yield and reduced oil content. Seed size and seed weight had the greatest reduction in C1, pod size reduction was found the most in C3, and the number of fertile pods that contain at least one seed was reduced in C3 and C4. These results suggest that heat stress effects are developmental stage specific. Heat stress significantly reduced fertility during flowering and inhibited storage product biosynthesis and accumulation during seed filling which resulted in smaller and lighter seeds. Analyzing seed composition indicated that oil content decreased while protein content increased in seeds from heat treated plants. In addition, fatty acid composition was altered with the reduction of omega-3 α-linolenic acid and concomitantly increased omega-6 linoleic acid being the most significantly affected. Our results also revealed the different responses in the two genotypes examined, suggesting genetic variation in camelina germplasm which can be explored to improve heat tolerance. This study provides resources and guidance for future studies to understand genetic and physiological mechanisms of heat stress and to assist in improving the sustainability of camelina production facing climate change.

Arabidopsis CML13 and CML14 Have Essential and Overlapping Roles in Plant Development

Calmodulin (CaM)-like proteins (CMLs) are the largest family of calcium-binding proteins in plants, yet the functions of most CMLs are unknown. Arabidopsis CML13 and CML14 are closely related paralogs that interact with the isoleucine-glutamine (IQ) domains of myosins, IQ-domain proteins and CaM-binding transcription activators (CAMTAs). Here, we explored the physiological roles of CML13 and CML14 during development by using dexamethasone (Dex)-inducible RNA silencing to suppress either CML13 or CML14 transcript levels. In the absence of inducible suppression, CML13- and CML14-RNA-interference lines were indistinguishable from wild-type (WT) plants throughout development. In contrast, induction of silencing treatment led to rapid increases in RNA-hairpin production that correlated with a targeted reduction in CML13 or CML14 transcript levels and a range of developmental and morphological effects. RNA-suppression treatment did not impair the germination of CML13- or 14-RNA-interference lines, but these seedlings were chlorotic, displayed high mortality and failed to achieve seedling establishment. Under Dex treatment, seeds of CML13- and CML14-RNA-interference lines exhibited differential sensitivity to exogenous ABA compared to WT seeds. Induced RNA suppression of mature plants led to reduced silique length, shorter roots and rapid leaf senescence in CML13- and 14-RNA-interference plants, which correlated with increased gene expression of the senescence marker Senescence-Associated Gene13 (SAG13). Plants induced for RNA suppression at 2 weeks post-germination exhibited a much stronger phenotype than treatment of 3-, 4- or 5-week-old plants. Collectively, our data indicate that both CML13 and CML14 are essential for normal development and function across a broad range of tissues and developmental stages.

NFXL1 functions as a transcriptional activator required for thermotolerance at reproductive stage in Arabidopsis

Plants are highly susceptible to abiotic stresses, particularly heat stress during the reproductive stage. However, the specific molecular mechanisms underlying this sensitivity remain largely unknown. In the current study, we demonstrate that the Nuclear Transcription Factor, X-box Binding Protein 1-Like 1 (NFXL1), directly regulates the expression of DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 2A (DREB2A), which is crucial for reproductive thermotolerance in Arabidopsis. NFXL1 is upregulated by heat stress, and its mutation leads to a reduction in silique length (seed number) under heat stress conditions. RNA-Seq analysis reveals that NFXL1 has a global impact on the expression of heat stress responsive genes, including DREB2A, Heat Shock Factor A3 (HSFA3) and Heat Shock Protein 17.6 (HSP17.6) in flower buds. Interestingly, NFXL1 is enriched in the promoter region of DREB2A, but not of either HSFA3 or HSP17.6. Further experiments using electrophoretic mobility shift assay have confirmed that NFXL1 directly binds to the DNA fragment derived from the DREB2A promoter. Moreover, effector-reporter assays have shown that NFXL1 activates the DREB2A promoter. The DREB2A mutants are also heat stress sensitive at the reproductive stage, and DEREB2A is epistatic to NFXL1 in regulating thermotolerance in flower buds. It is known that HSFA3, a direct target of DREB2A, regulates the expression of heat shock proteins genes under heat stress conditions. Thus, our findings establish NFXL1 as a critical upstream regulator of DREB2A in the transcriptional cassette responsible for heat stress responses required for reproductive thermotolerance in Arabidopsis.

LHT1/MAC7 contributes to proper alternative splicing under long-term heat stress and mediates variation in the heat tolerance of Arabidopsis

Natural genetic variation has facilitated the identification of genes underlying complex traits such as stress tolerances. We here evaluated the long-term (L-) heat tolerance (37°C for 5 days) of 174 Arabidopsis thaliana accessions and short-term (S-) heat tolerance (42°C, 50 min) of 88 accessions and found extensive variation, respectively. Interestingly, L-heat-tolerant accessions are not necessarily S-heat tolerant, suggesting that the tolerance mechanisms are different. To elucidate the mechanisms underlying the variation, we performed a chromosomal mapping using the F2 progeny of a cross between Ms-0 (a hypersensitive accession) and Col-0 (a tolerant accession) and found a single locus responsible for the difference in L-heat tolerance between them, which we named Long-term Heat Tolerance 1 (LHT1). LHT1 is identical to MAC7, which encodes a putative RNA helicase involved in mRNA splicing as a component of the MOS4 complex. We found one amino acid deletion in LHT1 of Ms-0 that causes a loss of function. Arabidopsis mutants of other core components of the MOS4 complex-mos4-2, cdc5-1, mac3a mac3b, and prl1 prl2-also showed hypersensitivity to L-heat stress, suggesting that the MOS4 complex plays an important role in L-heat stress responses. L-heat stress induced mRNA processing-related genes and compromised alternative splicing. Loss of LHT1 function caused genome-wide detrimental splicing events, which are thought to produce nonfunctional mRNAs that include retained introns under L-heat stress. These findings suggest that maintaining proper alternative splicing under L-heat stress is important in the heat tolerance of A. thaliana.

Natural variation of warm temperature-induced raffinose accumulation identifies TREHALOSE-6-PHOSPHATE SYNTHASE 1 as a modulator of thermotolerance

High-temperature stress limits plant growth and reproduction. Exposure to high temperature, however, also elicits a physiological response, which protects plants from the damage evoked by heat. This response involves a partial reconfiguration of the metabolome including the accumulation of the trisaccharide raffinose. In this study, we explored the intraspecific variation of warm temperature-induced raffinose accumulation as a metabolic marker for temperature responsiveness with the aim to identify genes that contribute to thermotolerance. By combining raffinose measurements in 250 Arabidopsis thaliana accessions following a mild heat treatment with genome-wide association studies, we identified five genomic regions that were associated with the observed trait variation. Subsequent functional analyses confirmed a causal relationship between TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) and warm temperature-dependent raffinose synthesis. Moreover, complementation of the tps1-1 null mutant with functionally distinct TPS1 isoforms differentially affected carbohydrate metabolism under more severe heat stress. While higher TPS1 activity was associated with reduced endogenous sucrose levels and thermotolerance, disruption of trehalose 6-phosphate signalling resulted in higher accumulation of transitory starch and sucrose and was associated with enhanced heat resistance. Taken together, our findings suggest a role of trehalose 6-phosphate in thermotolerance, most likely through its regulatory function in carbon partitioning and sucrose homoeostasis.

Transcriptional Regulators of Plant Adaptation to Heat Stress

Heat stress (HS) is becoming an increasingly large problem for food security as global warming progresses. As sessile species, plants have evolved different mechanisms to cope with the disruption of cellular homeostasis, which can impede plant growth and development. Here, we summarize the mechanisms underlying transcriptional regulation mediated by transcription factors, epigenetic regulators, and regulatory RNAs in response to HS. Additionally, cellular activities for adaptation to HS are discussed, including maintenance of protein homeostasis through protein quality control machinery, and autophagy, as well as the regulation of ROS homeostasis via a ROS-scavenging system. Plant cells harmoniously regulate their activities to adapt to unfavorable environments. Lastly, we will discuss perspectives on future studies for improving urban agriculture by increasing crop resilience to HS.

Heat stress responses vary during floret development in European spring barley cultivars

The Poaceae, or grasses, include many agriculturally important cereal crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare) and bread wheat (Triticum aestivum). Barley is a widely grown cereal crop used for stock feed, malting and brewing. Abiotic stresses, particularly global warming, are the major causes of crop yield losses by affecting fertility and seed set. However, effects of heat stress on reproductive structures and fertility in barley have not been extensively investigated. In this study we examined three commercial European spring barley varieties under high temperature conditions to investigate the effects on floret development. Using a combination of fertility assays, X-ray micro computed tomography, 3-dimensional modelling, cytology and immunolabelling, we observed that male reproductive organs are severely impacted by increased temperature, while the female reproductive organs are less susceptible. Importantly, the timing of stress relative to reproductive development had a significant impact on fertility in a cultivar-dependent manner, this was most significant at pollen mitosis stage with fertility ranged from 31.6-56.0% depending on cultivar. This work provides insight into how heat stress, when applied during male pollen mother cell meiosis and pollen mitosis, affects barley fertility and seed set, and also describes complementary invasive and non-invasive techniques to investigate floret development. This information will be used to identify and study barley cultivars that are less susceptible to heat stress at specific stages of floral development.

Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.

Ovule initiation: the essential step controlling offspring number in Arabidopsis

Seed is the offspring of angiosperms. Plants produce large numbers of seeds to ensure effective reproduction and survival in varying environments. Ovule is a fundamentally important organ and is the precursor of the seed. In Arabidopsis and other plants characterized by multi-ovulate ovaries, ovule initiation determines the maximal ovule number, thus greatly affecting seed number per fruit and seed yield. Investigating the regulatory mechanism of ovule initiation has both scientific and economic significance. However, the genetic and molecular basis underlying ovule initiation remains unclear due to technological limitations. Very recently, rules governing the multiple ovules initiation from one placenta have been identified, the individual functions and crosstalk of phytohormones in regulating ovule initiation have been further characterized, and new regulators of ovule boundary are reported, therefore expanding the understanding of this field. In this review, we present an overview of current knowledge in ovule initiation and summarize the significance of ovule initiation in regulating the number of plant offspring, as well as raise insights for the future study in this field that provide potential routes for the improvement of crop yield.

Genome-Wide Association Mapping Reveals Novel Putative Gene Candidates Governing Reproductive Stage Heat Stress Tolerance in Rice

Temperature rise predicted for the future will severely affect rice productivity because the crop is highly sensitive to heat stress at the reproductive stage. Breeding tolerant varieties is an economically viable option to combat heat stress, for which the knowledge of target genomic regions associated with the reproductive stage heat stress tolerance (RSHT) is essential. A set of 192 rice genotypes of diverse origins were evaluated under natural field conditions through staggered sowings for RSHT using two surrogate traits, spikelet fertility and grain yield, which showed significant reduction under heat stress. These genotypes were genotyped using a 50 k SNP array, and the association analysis identified 10 quantitative trait nucleotides (QTNs) for grain yield, of which one QTN (qHTGY8.1) was consistent across the different models used. Only two out of 10 MTAs coincided with the previously reported QTLs, making the remaing eight novel. A total of 22 QTNs were observed for spikelet fertility, among which qHTSF5.1 was consistently found across three models. Of the QTNs identified, seven coincided with previous reports, while the remaining QTNs were new. The genes near the QTNs were found associated with the protein–protein interaction, protein ubiquitination, stress signal transduction, and so forth, qualifying them to be putative for RSHT. An in silico expression analysis revealed the predominant expression of genes identified for spikelet fertility in reproductive organs. Further validation of the biological relevance of QTNs in conferring heat stress tolerance will enable their utilization in improving the reproductive stage heat stress tolerance in rice.

Global identification and integrated analysis of heat-responsive long non-coding RNAs in contrasting rice cultivars

Identified 2743 rice lncRNAs LncRNAs in response to heat stress Function prediction of HRLs Network among HRLs, genes and miRNAs co-localization of HRLs with QTLs Significant motifs in HRL sequences Long non-coding RNAs (lncRNAs) play vital roles in plant responses to environmental challenges. A better understanding of the gene regulation mediated by lncRNAs and their systematic identification would provide great benefits for modern agriculture. In this study, we performed strand-specific RNA sequencing for two rice varieties, heat-tolerant ZS97B and heat-susceptible SYD2 under heat stress. In total, 2743 putative lncRNAs were identified, and their expression profiles in response to heat treatments were established. We identified 231 differentially expressed lncRNAs (DELs) under heat stress, including 31 DELs common to both varieties and 103 and 97 specific to ZS97B and SYD2, respectively, all defined as heat-responsive lncRNAs (HRLs). The target-coding genes of HRLs were predicted, and GO and KEGG annotations of HRL targets revealed functions in which HRLs might be involved. The interaction network between HRLs, target genes and relevant miRNAs was constructed. The HRLs and their targets were compared with publicly available QTLs for rice seedling growth under heat stimulus. Ten HRLs and twelve target genes were linked with five heat stress-relevant QTLs. Sequence analysis revealed several motifs significantly enriched within the 231 HRL sequences. Our findings provide a valuable resource for further characterization of lncRNAs in terms of heat response and plant heat tolerance improvement.

bZIP17 regulates heat stress tolerance at reproductive stage in Arabidopsis

High temperature elicits a well-conserved response called the unfolded protein response (UPR) to bring protein homeostasis in the endoplasmic reticulum (ER). Two key UPR regulators bZIP28 and bZIP60 have been shown to be essential for maintaining fertility under heat stress conditions in Arabidopsis, however, the function of transcriptional activator bZIP17, a paralog of bZIP28, in heat stress response at reproductive stage is not reported. Here we found that bzip17 mutant plants were sensitive to heat stress in terms of silique length and fertility comparing to that of wildtype (WT) Arabidopsis plants, and transcriptomic analysis showed that 1380 genes were specifically up-regulated and 493 genes were specifically down-regulated by heat stress in the flowers of WT plants comparing to that in bzip17 mutant plants. These bZIP17-dependent up-regulated genes were enriched in responses to abiotic stresses such as water deprivation and salt stress. Further chromatin immuno-precipitation coupled with high-throughput sequencing (ChIP-Seq) uncovered 1645 genes that were direct targets of bZIP17 in MYC-bZIP17 expressing seedlings subjected to heat stress. Among these 1645 genes, ERSE-II cis-element was enriched in the binding peaks of their promoters, and the up-regulation of 113 genes by heat stress in flowers was dependent on bZIP17. Our results revealed direct targets of bZIP17 in flowers during heat stress responses and demonstrated the important role of bZIP17 in maintaining fertility upon heat stress in plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00062-1.

Long-Term High-Temperature Stress Impacts on Embryo and Seed Development in Brassica napus

Brassica napus (rapeseed) is the second most important oilseed crop worldwide. Global rise in average ambient temperature and extreme weather severely impact rapeseed seed yield. However, fewer research explained the phenotype changes caused by moderate-to-high temperatures in rapeseed. To investigate these events, we determined the long-term response of three spring cultivars to different temperature regimes (21/18°C, 28/18°C, and 34/18°C) mimicking natural temperature variations. The analysis focused on the plant appearance, seed yield, quality and viability, and embryo development. Our microscopic observations suggest that embryonic development is accelerated and defective in high temperatures. Reduced viable seed yield at warm ambient temperature is due to a reduced fertilization rate, increased abortion rate, defective embryonic development, and pre-harvest sprouting. Reduced auxin levels in young seeds and low ABA and auxin levels in mature seeds may cause embryo pattern defects and reduced seed dormancy, respectively. Glucosinolates and oil composition measurements suggest reduced seed quality. These identified cues help understand seed thermomorphogenesis and pave the way to developing thermoresilient rapeseed.

Genetic and Physiological Responses to Heat Stress in Brassica napus

Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.

Opportunities and limits of controlled-environment plant phenotyping for climate response traits

Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.

Holistic insights from pollen omics: co-opting stress-responsive genes and ER-mediated proteostasis for male fertility

Sexual reproduction in flowering plants takes place without an aqueous environment. Sperm are carried by pollen through air to reach the female gametophyte, though the molecular basis underlying the protective strategy of the male gametophyte is poorly understood. Here we compared the published transcriptomes of Arabidopsis thaliana pollen, and of heat-responsive genes, and uncovered insights into how mature pollen (MP) tolerates desiccation, while developing and germinating pollen are vulnerable to heat stress. Germinating pollen expresses molecular chaperones or "heat shock proteins" in the absence of heat stress. Furthermore, pollen tubes that grew through pistils at basal temperature showed induction of the endoplasmic reticulum (ER) stress response, which is a characteristic of stressed vegetative tissues. Recent studies show MP contains mRNA-protein (mRNP) aggregates that resemble "stress" granules triggered by heat or other stresses to protect cells. Based on these observations, we postulate that mRNP particles are formed in maturing pollen in response to developmentally programmed dehydration. Dry pollen can withstand harsh conditions as it is dispersed in air. We propose that, when pollen lands on a compatible pistil and hydrates, mRNAs stored in particles are released, aided by molecular chaperones, to become translationally active. Pollen responds to osmotic, mechanical, oxidative, and peptide cues that promote ER-mediated proteostasis and membrane trafficking for tube growth and sperm discharge. Unlike vegetative tissues, pollen depends on stress-protection strategies for its normal development and function. Thus, heat stress during reproduction likely triggers changes that interfere with the normal pollen responses, thereby compromising male fertility. This holistic perspective provides a framework to understand the basis of heat-tolerant strains in the reproduction of crops.

Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures

BACKGROUND

Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown.

RESULTS

Multigenerational exposure of Arabidopsis MA (mutation accumulation) lines and MA populations to extreme heat and moderate warming results in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observe distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition and transversion frequencies. Mutation occurs more frequently in intergenic regions, coding regions, and transposable elements in plants grown under elevated temperatures. At elevated temperatures, more mutations accumulate in genes associated with defense responses, DNA repair, and signaling. Notably, the distribution patterns of mutations among all progeny differ between MA populations and MA lines, suggesting that stronger selection effects occurred in populations. Methylation is observed more frequently at mutation sites, indicating its contribution to the mutation process at elevated temperatures. Mutations occurring within the same genome under elevated temperatures are significantly biased toward low gene density regions, special trinucleotides, tandem repeats, and adjacent simple repeats. Additionally, mutations found in all progeny overlap significantly with genetic variations reported in 1001 Genomes, suggesting non-uniform distribution of de novo mutations through the genome.

CONCLUSION

Collectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.

A genome-wide association study reveals cytokinin as a major component in the root defense responses against Ralstonia solanacearum

Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host's root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated with the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a genome-wide association study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role for cytokinin in root immunity, paving the way for future research that will help in understanding the mechanisms underpinning root defenses.

Regulation of DNA (de)Methylation Positively Impacts Seed Germination during Seed Development under Heat Stress

Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression, and methylation on three stages of seed development. Notably, Arabidopsis Col-0 plants under heat stress presented a decrease in germination capacity as well as a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms including the activation of the ABA pathway. By analyzing candidate epigenetic markers using the mutants’ physiological assays, we observed that the lack of DNA demethylation by the ROS1 gene impaired seed germination by affecting germination-related gene expression. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in the promoters and gene sequences of germination-related genes. To conclude, our results indicate that DNA (de)methylation could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress.

Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat

Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.

Arabidopsis immune-associated nucleotide-binding genes repress heat tolerance at the reproductive stage by inhibiting the unfolded protein response and promoting cell death

Plants are vulnerable to heat stress, especially during reproductive development. The heat shock response (HSR) in the cytosol and nucleus, as well as the unfolded protein response (UPR) in the endoplasmic reticulum (ER), are two mechanisms that enable plants to survive heat stress. Excessive heat or ER stresses lead to cell death when the UPR cannot repair stress damage, but the means by which cell survival or death is determined remains unclear. In this study, we used a genome-wide association study (GWAS) to identify that a cluster of five Immune-associated nucleotide-binding protein (IAN) genes (IAN2 to IAN6) is responsible for variation in heat tolerance at the reproductive stage in Arabidopsis thaliana. These IAN genes have both unique and overlapping functions in the negative regulation of heat tolerance, and their loss of function singly or in combination confers increased heat tolerance, measured by a lower number of barren siliques and a higher seedling survival rate under heat. The loss of rice IAN1 gene function also leads to enhanced heat tolerance, suggesting a conserved function of plant IANs. Transcriptome analysis revealed enhanced expression of HSR and UPR genes, as well as reduced cell death, under heat and ER stress in the mutant of IAN6, a major effect member in Arabidopsis. Furthermore, the IAN proteins were found to promote cell death induced by heat stress, ER stress, and cell death-inducing molecules. Thus, the Arabidopsis IAN genes repress heat tolerance, probably through the HSR and UPR and by enhancing the cell death pathway. The IAN2 to IAN6 proteins are partially localized to the ER, suggesting a direct role in the UPR and UPR-mediated cell death. In addition, a natural IAN6 variant from more heat-tolerant Arabidopsis accessions confers greater heat tolerance and induces less cell death compared with the natural variant from less heat-tolerant accessions. The heat-tolerant IAN6 variant is associated with a higher maximum temperature of the warmest month at its collection sites compared with the heat-sensitive variant. Taken together, these results reveal an important role of Arabidopsis IAN2 to IAN6 genes in the regulation of the HSR, UPR, and cell death, and suggest that their natural variations have adaptive functions in heat tolerance.

DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis

Background

High-throughput phenotyping based on non-destructive imaging has great potential in plant biology and breeding programs. However, efficient feature extraction and quantification from image data remains a bottleneck that needs to be addressed. Advances in sensor technology have led to the increasing use of imaging to monitor and measure a range of plants including the model Arabidopsis thaliana. These extensive datasets contain diverse trait information, but feature extraction is often still implemented using approaches requiring substantial manual input.

Results

The computational detection and segmentation of individual fruits from images is a challenging task, for which we have developed DeepPod, a patch-based 2-phase deep learning framework. The associated manual annotation task is simple and cost-effective without the need for detailed segmentation or bounding boxes. Convolutional neural networks (CNNs) are used for classifying different parts of the plant inflorescence, including the tip, base, and body of the siliques and the stem inflorescence. In a post-processing step, different parts of the same silique are joined together for silique detection and localization, whilst taking into account possible overlapping among the siliques. The proposed framework is further validated on a separate test dataset of 2,408 images. Comparisons of the CNN-based prediction with manual counting (R² = 0.90) showed the desired capability of methods for estimating silique number.

Conclusions

The DeepPod framework provides a rapid and accurate estimate of fruit number in a model system widely used by biologists to investigate many fundemental processes underlying growth and reproduction

Activation tagging identifies Arabidopsis transcription factor AtMYB68 for heat and drought tolerance at yield determining reproductive stages

Heat stress occurring at reproductive stages can result in significant and permanent damage to crop yields. However, previous genetic studies in understanding heat stress response and signaling were performed mostly on seedling and plants at early vegetative stages. Here we identify, using a developmentally defined, gain-of-function genetic screen with approximately 18 000 Arabidopsis thaliana activation-tagged lines, a mutant that maintained productive seed set post-severe heat stress during flowering. Genome walking indicated this phenotype was caused by the insertion of 35S enhancers adjacent to a nuclear localized transcription factor AtMYB68. Subsequent overexpression analysis confirmed that AtMYB68 was responsible for the reproductive heat tolerance of the mutant. Furthermore, these transgenic Arabidopsis plants exhibited enhanced abscisic acid sensitivity at and post-germination, reduced transpirational water loss during a drought treatment, and enhanced seed yield under combined heat and drought stress during flowering. Ectopic expression of AtMYB68 in Brassica napus driven either by 35S or by heat-inducible promoter recapitulated the enhanced reproductive heat stress and drought tolerance phenotypes observed in the transgenic Arabidopsis. The improvement to heat stress is likely due to enhanced pollen viability observed in the transgenic plants. More importantly, the transgenic canola showed significant yield advantages over the non-transgenic controls in multiple locations, multiple season field trials under various drought and heat stress conditions. Together these results suggest that AtMYB68 regulate plant stress tolerance at the most important yield determining stage of plant development, and is an effective target for crop yield protection under current global climate volatility.

Molecular genetic analyses of abiotic stress responses during plant reproductive development

Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.

ERdj3B-Mediated Quality Control Maintains Anther Development at High Temperatures

Pollen development is highly sensitive to heat stress, which impairs cellular proteostasis by causing misfolded proteins to accumulate. Therefore, each cellular compartment possesses a dedicated protein quality control system. An elaborate quality control system involving molecular chaperones, including immunoglobulin-binding protein (BiP), heat shock protein70, and regulatory J domain-containing cochaperones (J proteins), allows the endoplasmic reticulum (ER) to withstand a large influx of proteins. Here, we found that Arabidopsis (Arabidopsis thaliana) mutants of ER-localized DnaJ family 3B (ERdj3B), one of three ER-resident J proteins involved in ER quality control, produced few seeds at high temperatures (29°C) due to defects in anther development. This temperature-sensitive fertility defect is specific to the defective interactions of BiP with ERdj3B but not with the other two J proteins, indicating functional differences between ERdj3B and the other J proteins. RNA sequencing analysis revealed that heat stress affects pollen development in both wild-type and mutant buds, but the erdj3b mutant is more susceptible, possibly due to defects in ER quality control. Our results highlight the importance of a specific ER quality control factor, ERdj3B, for plant reproduction, particularly anther development, at high temperatures.

Plant abiotic stress response and nutrient use efficiency

Abiotic stresses and soil nutrient limitations are major environmental conditions that reduce plant growth, productivity and quality. Plants have evolved mechanisms to perceive these environmental challenges, transmit the stress signals within cells as well as between cells and tissues, and make appropriate adjustments in their growth and development in order to survive and reproduce. In recent years, significant progress has been made on many fronts of the stress signaling research, particularly in understanding the downstream signaling events that culminate at the activation of stress- and nutrient limitation-responsive genes, cellular ion homeostasis, and growth adjustment. However, the revelation of the early events of stress signaling, particularly the identification of primary stress sensors, still lags behind. In this review, we summarize recent work on the genetic and molecular mechanisms of plant abiotic stress and nutrient limitation sensing and signaling and discuss new directions for future studies.

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

KEY MESSAGE

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

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf-level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large-scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water-use strategies, namely, C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci mapping and validation through near-isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13 C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf-level traits.

Genome-wide association study reveals novel players in defense hormone crosstalk in Arabidopsis

Jasmonic acid (JA) regulates plant defenses against necrotrophic pathogens and insect herbivores. Salicylic acid (SA) and abscisic acid (ABA) can antagonize JA-regulated defenses, thereby modulating pathogen or insect resistance. We performed a genome-wide association (GWA) study on natural genetic variation in Arabidopsis thaliana for the effect of SA and ABA on the JA pathway. We treated 349 Arabidopsis accessions with methyl JA (MeJA), or a combination of MeJA and either SA or ABA, after which expression of the JA-responsive marker gene PLANT DEFENSIN1.2 (PDF1.2) was quantified as a readout for GWA analysis. Both hormones antagonized MeJA-induced PDF1.2 in the majority of the accessions but with a large variation in magnitude. GWA mapping of the SA- and ABA-affected PDF1.2 expression data revealed loci associated with crosstalk. GLYI4 (encoding a glyoxalase) and ARR11 (encoding an Arabidopsis response regulator involved in cytokinin signalling) were confirmed by T-DNA insertion mutant analysis to affect SA-JA crosstalk and resistance against the necrotroph Botrytis cinerea. In addition, At1g16310 (encoding a cation efflux family protein) was confirmed to affect ABA-JA crosstalk and susceptibility to Mamestra brassicae herbivory. Collectively, this GWA study identified novel players in JA hormone crosstalk with potential roles in the regulation of pathogen or insect resistance.

KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis

Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.

To defend or to grow: lessons from Arabidopsis C24

The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterization of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding of how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) are a great asset to understand the mechanisms of multiple stress tolerances. One natural variant in Arabidopsis is the accession C24, and here we provide an overview of the increasing research interest in this accession. C24 is highlighted as a source of tolerance for multiple abiotic and biotic stresses, and a key accession to understand the basis of basal immunity to infection, high water use efficiency, and water productivity. Multiple biochemical, physiological, and phenological mechanisms have been attributed to these traits in C24, and none of them constrains productivity. Based on the uniqueness of C24, we postulate that the use of variation derived from natural selection in undomesticated species provides opportunities to better understand how complex environmental stress tolerances and resource use efficiency are co-ordinated.

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.

Natural variation of life-history traits, water use, and drought responses in Arabidopsis

The ability of plants to acquire and use water is critical in determining life-history traits such as growth, flowering, and allocation of biomass into reproduction. In this context, a combination of functionally linked traits is essential for plants to respond to environmental changes in a coordinated fashion to maximize resource use efficiency. We analyzed different water-use traits in Arabidopsis ecotypes to identify functionally linked traits that determine water use and plant growth performance. Water-use traits measured were (i) leaf-level water-use efficiency (WUE i ) to evaluate the amount of CO 2 fixed relative to water loss per leaf area and (ii) short-term plant water use at the vegetative stage (VWU) as a measure of whole-plant transpiration. Previously observed phenotypic variance in VWU, WUE i and life-history parameters, highlighted C24 as a valuable ecotype that combined drought tolerance, preferential reproductive biomass allocation, high WUE i , and reduced water use. We therefore screened 35 Arabidopsis ecotypes for these parameters, in order to assess whether the phenotypic combinations observed in C24 existed more widely within Arabidopsis ecotypes. All parameters were measured on a short dehydration cycle. A segmented regression analysis was carried out to evaluate the plasticity of the drought response and identified the breakpoint as a reliable measure of drought sensitivity. VWU was largely dependent on rosette area, but importantly the drought sensitivity and plasticity measures were independent of the transpiring leaf surface. A breakpoint at high rSWC indicated a more drought-sensitive plant that closed stomata early during the dehydration cycle and consequently showed stronger plasticity in leaf-level WUE i parameters. None of the sensitivity, plasticity, or water-use measurements were able to predict the overall growth performance; however, there was a general trade-off between vegetative and reproductive biomass. PCA and hierarchical clustering revealed that C24 was unique among the 35 ecotypes in uniting all the beneficial water use and stress tolerance traits, while also maintaining above average plant growth. We propose that a short dehydration cycle, measuring drought sensitivity and VWU is a fast and reliable screen for plant water use and drought response strategies.

Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance

Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress.

SIEVE ELEMENT-LINING CHAPERONE1 Restricts Aphid Feeding on Arabidopsis during Heat Stress

The role of phloem proteins in plant resistance to aphids is still largely elusive. By genome-wide association mapping of aphid behavior on 350 natural Arabidopsis thaliana accessions, we identified the small heat shock-like SIEVE ELEMENT-LINING CHAPERONE1 (SLI1). Detailed behavioral studies on near-isogenic and knockout lines showed that SLI1 impairs phloem feeding. Depending on the haplotype, aphids displayed a different duration of salivation in the phloem. On sli1 mutants, aphids prolonged their feeding sessions and ingested phloem at a higher rate than on wild-type plants. The largest phenotypic effects were observed at 26°C, when SLI1 expression is upregulated. At this moderately high temperature, sli1 mutants suffered from retarded elongation of the inflorescence and impaired silique development. Fluorescent reporter fusions showed that SLI1 is confined to the margins of sieve elements where it lines the parietal layer and colocalizes in spherical bodies around mitochondria. This localization pattern is reminiscent of the clamp-like structures observed in previous ultrastructural studies of the phloem and shows that the parietal phloem layer plays an important role in plant resistance to aphids and heat stress.

Multilevel Regulation of Abiotic Stress Responses in Plants

The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.

Quantitative Disease Resistance under Elevated Temperature: Genetic Basis of New Resistance Mechanisms to Ralstonia solanacearum

In the context of climate warming, plants will be facing an increased risk of epidemics as well as the emergence of new highly aggressive pathogen species. Although a permanent increase of temperature strongly affects plant immunity, the underlying molecular mechanisms involved are still poorly characterized. In this study, we aimed to uncover the genetic bases of resistance mechanisms that are efficient at elevated temperature to the Ralstonia solanacearum species complex (RSSC), one of the most harmful phytobacteria causing bacterial wilt. To start the identification of quantitative trait loci (QTLs) associated with natural variation of response to R. solanacearum, we adopted a genome wide association (GWA) mapping approach using 176 worldwide natural accessions of Arabidopsis thaliana inoculated with the R. solanacearum GMI1000 strain. Following two different procedures of root-inoculation (root apparatus cut vs. uncut), plants were grown either at 27 or 30°C, with the latter temperature mimicking a permanent increase in temperature. At 27°C, the RPS4/RRS1-R locus was the main QTL of resistance detected regardless of the method of inoculation used. This highlights the power of GWA mapping to identify functionally important loci for resistance to the GMI1000 strain. At 30°C, although most of the accessions developed wilting symptoms, we identified several QTLs that were specific to the inoculation method used. We focused on a QTL region associated with response to the GMI1000 strain in the early stages of infection and, by adopting a reverse genetic approach, we functionally validated the involvement of a strictosidine synthase-like 4 (SSL4) protein that shares structural similarities with animal proteins known to play a role in animal immunity.

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.

Arabidopsis Transcription Factors SPL1 and SPL12 Confer Plant Thermotolerance at Reproductive Stage

Plant reproductive organs are vulnerable to heat, but regulation of heat-shock responses in inflorescence is largely uncharacterized. Here, we report that two of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcriptional factors in Arabidopsis, SPL1 and SPL12, act redundantly in thermotolerance at the reproductive stage. The spl1-1 spl12-1 inflorescences displayed hypersensitivity to heat stress, whereas overexpression of SPL1 or SPL12 enhanced the thermotolerance in both Arabidopsis and tobacco. RNA sequencing revealed 1939 upregulated and 1479 downregulated genes in wild-type inflorescence upon heat stress, among which one-quarter (1,040) was misregulated in spl1-1 spl12-1, indicating that SPL1 and SPL12 contribute greatly to the heat-triggered transcriptional reprogramming in inflorescence. Notably, heat stress induced a large number of abscisic acid (ABA) responsive genes, of which ∼39% were disturbed in heat induction in spl1-1 spl12-1 inflorescence. Preapplication of ABA and overexpression of SPL1 restored the inflorescence thermotolerance in spl1-1 spl12-1 and in the ABA biosynthesis mutant aba2-1, but not in the pyl sextuple mutant defective in ABA receptors PYR1/PYL1/PYL2/PYL4/PYL5/PYL8. Thus, inflorescence thermotolerance conferred by SPL1 and SPL2 involves PYL-mediated ABA signaling. The molecular network consisting of SPL1 and SPL12 illustrated here shed new light on the mechanisms of plant thermotolerance at the reproductive stage.

Tissue-Specific Transcriptomics Reveals an Important Role of the Unfolded Protein Response in Maintaining Fertility upon Heat Stress in Arabidopsis

High temperatures have a great impact on plant reproductive development and subsequent fruit and seed set, but the underlying molecular mechanisms are not well understood. We used transcriptome profiling to investigate the effect of heat stress on reproductive development of Arabidopsis thaliana plants and observed distinct response patterns in vegetative versus reproductive tissues. Exposure to heat stress affected reproductive developmental programs, including early phases of anther/ovule development and meiosis. Also, genes participating in the unfolded protein response (UPR) were enriched in the reproductive tissue-specific genes that were upregulated by heat. Moreover, we found that the UPR-deficient bzip28 bzip60 double mutant was sensitive to heat stresses and had reduced silique length and fertility. Comparison of heat-responsive wild type versus bzip28 bzip60 plants identified 521 genes that were regulated by bZIP28 and bZIP60 upon heat stress during reproductive stages, most of which were noncanonical UPR genes. Chromatin immunoprecipitation coupled with high-throughput sequencing analyses revealed 133 likely direct targets of bZIP28 in Arabidopsis seedlings subjected to heat stress, including 27 genes that were also upregulated by heat during reproductive development. Our results provide important insights into heat responsiveness in Arabidopsis reproductive tissues and demonstrate the protective roles of the UPR for maintaining fertility upon heat stress.

Mapping quantitative trait loci for heat tolerance of reproductive traits in tomato (Solanum lycopersicum)

Global warming has become a worldwide concern due to its adverse effects on agricultural output. In particular, long-term mildly high temperatures interfere with sexual reproduction and thus fruit and seed set. To uncover the genetic basis of observed variation in tolerance against heat, a bi-parental F2 mapping population from two contrasting cultivars, i.e. Nagcarlang and NCHS-1, was generated and phenotyped under continuous mild heat conditions for a number of traits underlying reproductive success, i.e. pollen viability, pollen number, style length, anther length, style protrusion, female fertility and flowering characteristics, i.e. inflorescence number and flowers per inflorescence. Quantitative trait loci (QTLs) were identified for most of these traits, including a single, highly significant one for pollen viability, which accounted for 36% of phenotypic variation in the population and modified pollen viability under high temperature with around 20%. QTLs for some traits colocalised, indicating trait dependency or pleiotropic-effect loci. We conclude that a limited set of major genes determines differences in performance of reproductive traits under continuous mild heat in tomato. The results contribute to our fundamental understanding of pollen thermotolerance and may support development of more heat-tolerant tomato varieties.