Extreme Abiotic Stress Research Articles

Abiotic Stress in Cotton: Insights into Plant Responses and Biotechnological Solutions

Climate change has rapidly increased incidences of frequent extreme abiotic stresses, such as heat, drought, salinity, and waterlogging. Each of these stressors negatively affects the cotton crop (Gossypium spp.) and results in significant yield decreases. Every stressful event causes specific changes in the metabolism and physiology of plants, which are linked to complex molecular alterations. Understanding the molecular mechanisms that regulate a plant’s response to stress is essential to developing stress-resistant cotton varieties that can withstand various stress factors. Gene expressions in response to multiple stresses have been studied and mapped. These genes include ion transporters and heat shock proteins, which are vital to allowing adaptive responses. These approaches showed the ability to employ advanced genome sequencing and multi-omics techniques to identify dynamic gene expression patterns and elucidate intricate regulatory networks. Using genetic variation in combination with molecular techniques, it would be possible to generate stress-resilient cotton varieties that would enable sustainable cotton output in the face of abiotic stresses. Here, we reviewed the effects of major abiotic stressors on cotton plants, such as heat, salinity, drought, heavy metals, and waterlogging. We also examine the vast network of proteins, genes, and stress-sensitive signaling pathways that help cotton tolerate abiotic stress.

Exploring Thinopyrum spp. Group 7 Chromosome Introgressions to Improve Durum Wheat Performance under Intense Daytime and Night-Time Heat Stress at Anthesis.

Durum wheat (DW) is one of the major crops grown in the Mediterranean area, a climate-vulnerable region where the increase in day/night (d/n) temperature is severely threatening DW yield stability. In order to improve DW heat tolerance, the introgression of chromosomal segments derived from the wild gene pool is a promising strategy. Here, four DW-Thinopyrum spp. near-isogenic recombinant lines (NIRLs) were assessed for their physiological response and productive performance after intense heat stress (IH, 37/27 °C d/n) had been applied for 3 days at anthesis. The NIRLs included two primary types (R5, R112), carriers (+) of a differently sized Th. ponticum 7el1L segment on the DW 7AL arm, and two corresponding secondary types (R69-9/R5, R69-9/R112), possessing a Th. elongatum 7EL segment distally inserted into the 7el1L ones. Their response to the IH stress was compared to that of corresponding non-carrier sib lines (-) and the heat-tolerant cv. Margherita. Overall, the R112+, R69-9/R5+ and R69-9/R112+ NIRLs exhibited a tolerant behaviour towards the applied stress, standing out for the maintenance of leaf relative water content but also for the accumulation of proline and soluble sugars in the flag leaf and the preservation of photosynthetic efficiency. As a result, all the above three NIRLs (R112+ > R69-9/R5+ > R69-9/R112+) displayed good yield stability under the IH, also in comparison with cv. Margherita. R112+ particularly relied on the strength of spike fertility/grain number traits, while R69-9/R5+ benefited from efficient compensation by the grain weight increase. This work largely confirmed and further substantiated the value of exploiting the wild germplasm of Thinopyrum species as a useful source for the improvement of DW tolerance to even extreme abiotic stress conditions, such as the severe heat treatment throughout day- and night-time applied here.

Transcriptome Analysis Identifies Key Genes Involved in Response and Recovery to High Heat Stress Induced by Fire in Schima superba.

Fire-resistant tree species play a crucial role in forest fire prevention, utilizing several physiological and molecular mechanisms to respond to extreme heat stress. Many transcription factors (TFs) and genes are known to be involved in the regulatory network of heat stress response in plants. However, their roles in response to high temperatures induced by fire remain less understood. In this study, we investigated Schima superba, a fire-resistant tree, to elucidate these mechanisms. Leaves of S. superba seedlings were exposed to fire stimulation for 10 s, 30 s, and 1 min, followed by a 24-h recovery period. Fifteen transcriptomes were assembled to identify key molecular and biological pathways affected by high temperatures. Differentially expressed genes (DEGs) analysis revealed essential candidate genes and TFs involved in the heat stress response, including members of the ethylene-responsive factors, WRKY, MYB, bHLH, and Nin-like families. Genes related to heat shock proteins/factors, lipid metabolism, antioxidant enzymes, dehydration responses, and hormone signal transduction were differentially expressed after heat stress and recovery, underscoring their roles in cellular process and recovery after heat stress. This study advances our understanding of plant response and defense strategies against extreme abiotic stresses.

Comparative effects of two elicitors on the essential oil biosynthesis of simulated hail-damaged rose geranium (Pelargonium graveolens L’Hér. cv. ‘BOURBON’)

Extreme abiotic stress factors such as hail, defoliation, salinity, and moisture stress can affect the biosynthesis of essential oils. To mitigate this, most commercial farmers globally use agricultural crop insurance; however, this is not the case for most smallholder and emerging farmers in southern Africa, as agricultural insurance tends to be expensive when included in the production system. Therefore, this study aimed to investigate the comparative effects between two elicitors: abscisic acid (ABA) and methyl jasmonate (MeJA) on essential oil biosynthesis of simulated hail-damaged rose geranium (Pelargonium graveolens L’Hér.) as an alternative strategy to improve the essential oil biosynthesis following severe hail damage of rose geranium. The study was conducted in a 72 m2 temperature-controlled greenhouse, using a 4 x 2 factorial treatment design arranged in a randomized complete block design. Treatments comprised four levels of two elicitors at 75 µM (ABA), 150 μM (ABA), 10 mM (MeJA), and 20 mM (MeJA), applied in two different application periods (daily application for either 7 or 14 days). The simulation of hail damage was through 100% defoliation, with decapitation of the terminal buds. A significant interaction was observed between the elicitor treatment, and length of the period of application on essential oil yield (mass), where the highest yield was observed when MeJA (10 mM) was applied for seven consecutive days compared to the 14-day treatment. Geraniol esters were partially improved by the application of MeJA at 10 mM. Application of the two elicitors improved citronellol, geraniol, and linalool, regardless of the length of the period of application. The citronellol to geraniol ratio, a determining factor of essential oil quality, was 2.7:1 when MeJA was applied at 10 mM, significantly better than any application level of ABA. Therefore, it could be concluded that the application of MeJA at 10 mM may improve the essential oil biosynthesis of hail-damaged rose geranium plants compared to ABA at any level, and this may be adopted as a possible mitigating strategy by the emerging farmers and growers in southern Africa for improving the biosynthesis of rose geranium post hail damage. On the other hand, where growers are interested in higher contents of linalool and citronellol, ABA may be used at any level. Key words: Defoliation, essential oil, yield, phytohormone, citronellol, geraniol, linalool

Genome-wide functional characterization of Canavalia rosea cysteine-rich trans-membrane module (CrCYSTM) genes to reveal their potential protective roles under extreme abiotic stress

Cysteine-rich transmembrane module (CYSTM) proteins constitute small molecular protein families and have been identified across eukaryotes, including yeast, humans, and several plant species. Plant CYSTMs play vital roles in growth regulation, development, phytohormone signal transduction, pathogen defense, environmental stress response, and even heavy metal binding and detoxification. Canavalia rosea (Sw.) DC is a perennial halophyte with great semi-arid and saline-alkali tolerance. In this study, the CrCYSTM family including 10 members were identified in the C. rosea genome, with the purpose of clarifying the possible roles of CrCYSTMs in C. rosea plants development and stress resistance. The phylogenetic relationships, exon–intron structure, domain structure, chromosomal localization, and putative cis-acting elements in promoter regions were predicted and analyzed. Transcriptome analysis combined with quantitative reverse transcription PCR showed that different CrCYSTM members exhibited varied expression patterns in different tissues and under different abiotic stress challenges. In addition, several CrCYSTMs were cloned and functionally characterized for their roles in abiotic stress tolerance with yeast expression system. Overall, these findings provide a foundation for functionally characterizing plant CYSTMs to unravel their possible roles in the adaptation of C. rosea to tropical coral reefs. Our results also lay the foundation for further research on the roles of plant CYSTM genes in abiotic stress signaling, especially for heavy metal detoxification.

Circadian Clock Contributes to Modulate Salinity Stress-Responsive Antioxidative Mechanisms and Chloroplast Proteome in Spinacia oleracea

Extreme abiotic stresses such as drought, salinity, and temperature reduce crop productivity significantly and pose a serious threat to the area of land used for agriculture. Therefore, there is a pressing need to create crops that can thrive in these circumstances. It has been noted that plants can maintain defense mechanisms during any environmental changes and anticipate diurnal patterns correct to a circadian-based clock. Therefore, the main aim of this study was to investigate the role of circadian core oscillators in response to salinity stress in an important vegetable crop, spinach, and obtain evidence to better understand salinity stress adaptation for crop productivity. Therefore, the current study was carried out to examine the circadian clock-based (morning–evening loop) salinity stress defense mechanism in spinach (Spinacia oleracea), a leafy vegetable crop with significant economic importance and health benefits. In the presence of dawn and dusk, the circadian clock-based defense mechanism was observed using the genotypes “Delhi Green” and “Malav Jyoti.” A photoperiodic rhythm consists of 4-h intervals for 12 h (morning–evening loop) in spinach was demonstrated under the salinity stress treatments (20 mM and 50 mM). The clock-controlled a large fraction of growth parameters such as plant height, biomass, and root-shoot ratio under salinity stress. Conversely, salinity stress resulted in upregulation of antioxidative parameters such as superoxide dismutase, ascorbate peroxidase, catalase, and other stress markers such as thiobarbituric acid reactive substances, proline content, and localizations of H2O2 and O2−1 but was altered and maintained at a certain photoperiodic time interval of the circadian clock. In distinction to results observed from antioxidative measurements performed with an early and late circadian duration of salt-treated plants, 10 am and 2 pm were revealed to be the rhythmic times for controlling salinity stress. Likewise, comprehensive measurements of the photosynthetic system under salinity stress at specific photoperiodic circadian time intervals, including net-photosynthetic rate, transpiration, stomatal conductance, PSII quantum yield, and stomata structure, were made at 10 am and 2 pm. The salinity stress response was down-streamed and the clock also regulated chloroplastic protein expression. Thus, according to our findings, photoperiodic circadian rhythms, particularly the morning–evening loop, enhanced plant survival rates by modulating cellular antioxidant mechanisms and chloroplastic proteins that further helped to reduce the effects of salinity stress.

Response of Pea Plants (Pisum sativum cv. Ran 1) to NaCl Treatment in Regard to Membrane Stability and Photosynthetic Activity.

Salinity is one of the most extreme abiotic stress factors that negatively affect the development and productivity of plants. The salt-induced injuries depend on the salt tolerance of the plant species, salt concentration, time of exposure and developmental stage. Here, we report on the response of pea plants (Pisum sativum L. cv Ran 1) to exposure to increasing salt concentrations (100, 150 and 200 mM NaCl) for a short time period (5 days) and the ability of the plants to recover after the removal of salt. The water content, membrane integrity, lipid peroxidation, pigment content and net photosynthetic rate were determined for the pea leaves of the control, treated and recovered plants. Salt-induced alterations in the primary photosynthetic reactions and energy transfer between the main pigment-protein complexes in isolated thylakoid membranes were evaluated. The pea plants were able to recover from the treatment with 100 mM NaCl, while at higher concentrations, concentration-dependent water loss, the disturbance of the membrane integrity, lipid peroxidation and an increase in the pigment content were detected. The net photosynthetic rate, electron transport through the reaction centers of PSII and PSII, activity of PSIIα centers and energy transfer between the pigment-protein complexes were negatively affected and were not restored after the removal of NaCl.

Optimizing machine learning-based site-specific nitrogen application recommendations for canola production

Machine learning approaches are attracting more attention in predicting the economic optimum nitrogen rate (EONR) for field crop production. However, the robustness in fertilizer recommendations appeared to be less responsive to extreme abiotic stress conditions, due to the lack of post-fertilization seasonal weather information. This study employed four machine learning models, namely, support vector machine (SVM), gradient boosting (GB), random forest (RF), and ridge regression (RR) to predict the site-specific EONR values of canola crops, based on a 22-site-year field study across eastern Canada. Model performance was assessed using the ‘leave-one-out’ approach under three scenarios, i.e., different combinations of input variables, including current seasonal weather data before N topdressing, 10-year historical weather records, and field management and crop traits. Results of this study showed that including historical weather data highly improved prediction accuracy for EONR in a variety of canola growing environments. The RF model outperformed other models in predicting site-specific EONRs, with a Pearson correlation coefficient of 0.9, a standard deviation of 23 kg N ha −1 and a relative error of 2%. For 16 of the 22 test environments, the EONR predicted using RF fell within its confidence range, indicating that the prediction has a 73% chance of being an acceptable recommendation. Overall, incorporating historical weather data is essential for successfully predicting crop N requirements under normal and stressful growing conditions. The results indicate that with a base fertilizer of 50 kg N ha −1 , the recommended topdressing application rate varied from 50 to 110 kg N ha −1 in moist seasons, but decreased to 20–50 kg N ha −1 in hot and dry years, for sustainable canola production in eastern Canada. Appropriately incorporating historical weather data and soil properties into machine learning-based algorithms can be used to precisely guide fertilizer N management on canola crops under diverse climatic stress conditions. This approach promises to optimize seed yield and reduce nitrogen losses to the environment for sustainable canola production in Canada. • Four machine learning models were compared to predict economic optimum nitrogen rate (EONR). • Historical weather conditions were essential to predict the site-specific EONR. • Random forest model performed the best in recommending EONR by integrating weather data, field management and crop features. • A rate of 50 kg N ha −1 at planting plus 20–110 kg N ha −1 at the 4–6 leaf stage is recommended for canola production.

Plant Growth Promoting and Abiotic Stress Tolerant Chickpea (Cicer arietinum L.) Rhizobial Isolates from Some Areas of South Wollo Zone, Ethiopia

Chickpea (Cicer arietinum L) is an important pulse crop prized for its high protein content and is grown as a food source worldwide, including Ethiopia. However, the yield of chickpea is low due to low soil fertility and the ever-changing abiotic stresses. Therefore, this study aimed at isolation, characterization, and selection of chickpea rhizobia effective in their nitrogen fixation and abiotic stress tolerance potential. As a result, 150 nodule samples were collected from three districts of chickpea-producing areas in South Wollo. The nodules were crushed, and the rhizobia were isolated and characterized by using standard microbiological procedures. Based on the presumptive tests conducted, 103 (68.7%) of the rhizobial isolates were tentatively categorized as Rhizobium species. Regarding phosphate solubilization, only 48 (46.7%) solubilized phosphate with a solubilization index ranging from 2.1 to 2.7 mm. Twenty-four (50%) of the isolates were found to be hydrogen cyanide producers. Among the rhizobial isolates tested under greenhouse conditions, 37 (77.1%) of them induced nodulation on their host plant (chickpea). Their symbiotic effectiveness evaluation test confirmed that 16(47.1%), 6(17.6%), 26.47%, and 3(8.8%) were highly effective, effective, low effective, and ineffective, respectively. Of the authenticated rhizobial isolates, 12 (35.5%) of them, including WuCR-15, 16, 17, 18, 19, 20, 23, 30, 31, 32, 36, 38, and 48, accumulated higher shoot dry matter than the positive control. Isolates WuCR- 11, 17, and 36 showed resistance to low and high extreme abiotic stresses of pH, temperature, and salt. Consequently, rhizobial isolates, WuCR- 11, 17, and 36, which were effective and competent in all the tested parameters, were recommended as good rhizobial candidates for applications under greenhouse and field conditions.

Transcriptomic and metabolomic landscape of quinoa during seed germination

BackgroundQuinoa (Chenopodium quinoa), a dicotyledonous species native to Andean region, is an emerging crop worldwide nowadays due to its high nutritional value and resistance to extreme abiotic stresses. Although it is well known that seed germination is an important and multiple physiological process, the network regulation of quinoa seed germination is largely unknown.ResultsHere, we performed transcriptomic study in five stages during transition from quinoa dry seed to seedling. Together with the GC–MS based metabolome analysis, we found that seed metabolism is reprogrammed with significant alteration of multiple phytohormones (especially abscisic acid) and other nutrients during the elongation of radicels. Cell-wall remodeling is another main active process happening in the early period of quinoa seed germination. Photosynthesis was fully activated at the final stage, promoting the biosynthesis of amino acids and protein to allow seedling growth. The multi-omics analysis revealed global changes in metabolic pathways and phenotype during quinoa seed germination.ConclusionThe transcriptomic and metabolomic landscape depicted here pave ways for further gene function elucidation and quinoa development in the future.

Review: Regulation of Phytohormones and Environmental Stresses to Increase the Production of Plant Secondary Metabolites

Secondary metabolites are synthesized by plants when subjected to abiotic and biotic stresses as a defense mechanism and play an ecologically vital role both as pollination attractants and as repellents. These compounds are not essential for the process of growth and development but provide a significant impact on human welfare in various aspects as pharmaceuticals and therapeutics, aroma and taste, biopesticides, and agrochemicals. This natural product has high economic and commercial value, so it is important to explore it along with the increasing needs of consumers and industry at a large scale. Various extensive studies were carried out to improve and increase the production and accumulation of secondary metabolites. One of the strategies adopted in this review is the role of exogenous phytohormones in triggering the production of important secondary metabolites based on their classification, namely terpenoids, phenols, and flavonoids, as well as alkaloids and nitrogen-containing compounds. Bioregulators work as elicitors to induce the production of secondary metabolites through up-regulation of specific gene expression. In some cases, the application of phytohormones combined with exposure to extreme abiotic stresses showed overexpression of secondary metabolite synthesis compared to treatment with only those subjected to phytohormone. The abiotic stress of irradiation, UV-B, temperature, drought, ultrasonic, salinity, and metal stress was discussed in this study. Oxidative conditions under environmental changes trigger the plant to produce reactive oxygen species (ROS), which induce various secondary metabolites as part of the regulation of antioxidant systems. Micropropagation of medicinal plants by the addition of exogenous growth regulators could enhance the production and accumulation of important secondary metabolites.

Bacterial Exopolysaccharides: Insight into Their Role in Plant Abiotic Stress Tolerance.

Various abiotic stressors like drought, salinity, temperature, and heavy metals are major environmental stresses that affect agricultural productivity and crop yields all over the world. Continuous changes in climatic conditions put selective pressure on the microbial ecosystem to produce exopolysaccharides. Apart from soil aggregation, exopolysaccharide (EPS) production also helps in increasing water permeability, nutrient uptake by roots, soil stability, soil fertility, plant biomass, chlorophyll content, root and shoot length, and surface area of leaves while also helping maintain metabolic and physiological activities during drought stress. EPS-producing microbes can impart salt tolerance to plants by binding to sodium ions in the soil and preventing these ions from reaching the stem, thereby decreasing sodium absorption from the soil and increasing nutrient uptake by the roots. Biofilm formation in high-salinity soils increases cell viability, enhances soil fertility, and promotes plant growth and development. The third environmental stressor is presence of heavy metals in the soil due to improper industrial waste disposal practices that are toxic for plants. EPS production by soil bacteria can result in the biomineralization of metal ions, thereby imparting metal stress tolerance to plants. Finally, high temperatures can also affect agricultural productivity by decreasing plant metabolism, seedling growth, and seed germination. The present review discusses the role of exopolysaccharide-producing plant growth-promoting bacteria in modulating plant growth and development in plants and alleviating extreme abiotic stress condition. The review suggests exploring the potential of EPS-producing bacteria for multiple abiotic stress management strategies.

Why Plants Harbor Complex Endophytic Fungal Communities: Insights From Perennial Bunchgrass Stipagrostis sabulicola in the Namib Sand Sea.

All perennial plants harbor diverse endophytic fungal communities, but why they tolerate these complex asymptomatic symbioses is unknown. Using a multi-pronged approach, we conclusively found that a dryland grass supports endophyte communities comprised predominantly of latent saprophytes that can enhance localized nutrient recycling after senescence. A perennial bunchgrass, Stipagrostis sabulicola, which persists along a gradient of extreme abiotic stress in the hyper-arid Namib Sand Sea, was the focal point of our study. Living tillers yielded 20 fungal endophyte taxa, 80% of which decomposed host litter during a 28-day laboratory decomposition assay. During a 6-month field experiment, tillers with endophytes decomposed twice as fast as sterilized tillers, consistent with the laboratory assay. Furthermore, profiling the community active during decomposition using next-generation sequencing revealed that 59–70% of the S. sabulicola endophyte community is comprised of latent saprophytes, and these dual-niche fungi still constitute a large proportion (58–62%) of the litter community more than a year after senescence. This study provides multiple lines of evidence that the fungal communities that initiate decomposition of standing litter develop in living plants, thus providing a plausible explanation for why plants harbor complex endophyte communities. Using frequent overnight non-rainfall moisture events (fog, dew, high humidity), these latent saprophytes can initiate decomposition of standing litter immediately after tiller senescence, thus maximizing the likelihood that plant-bound nutrients are recycled in situ and contribute to the nutrient island effect that is prevalent in drylands.

Comparative transcriptomic analysis provides insights into the coordinated mechanisms of leaves and roots response to cold stress in Common Vetch

Due to the stronger ability to grow in extreme abiotic stress conditions, common vetch (Vicia sativa L.) has been generally cultivated worldwide and commonly utilized in methane biofuel production and health-promoting foods, and considered as an important protein source to feed livestock and human consumption. Nevertheless, the comprehensive molecular mechanisms on how the aboveground and underground tissues of common vetch response to various abiotic stresses, especially in cold stress, remain largely elusive and unknown. In this study, a total of 30,525 non-redundant full-length transcripts were identified in common vetch, with an average length of 2,291.56 bp and N50 of 3,130 bp. Among these transcripts, 7,689 and 3,415 differentially expressed genes (DEGs) were identified in leaves and roots, respectively, and 1,560 DEGs were induced in both tissues. The Gene Ontology (GO) enrichment results displayed that the DEGs were significantly enriched in the photosynthetic related categories in leaves. Correspondingly, the “response to cold” category was significantly enriched in roots, and most of them were upregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed that Ca2+, redox, hormonal signalling, circadian clock, and photosynthesis-antenna proteins might play crucial roles through CBF dependent or independent transcriptional pathways to respond cold stress in common vetch. Besides, a total of 36 DEGs involved in ICE-CBF-COR signalling cascade and cold stress were identified. Furthermore, three cold response-related DEGs and three upregulated transcription factors were overexpressed in yeast and indicated their biological functions to confer the tolerance to cold. This work will advance the understanding of common and distinct intrinsic molecular mechanisms beneath the cold response in common vetch leaf and root tissues. The further investigation of the promising potential candidate genes identified in this study will serve as a valuable resource for next step functional genomics research and raise the possibility to improve the cold tolerance through a transgenic approach in common vetch.

Understanding the molecular mechanism of anther development under abiotic stresses.

The developmental stage of anther development is generally more sensitive to abiotic stress than other stages of growth. Specific ROS levels, plant hormones and carbohydrate metabolism are disturbed in anthers subjected to abiotic stresses. As sessile organisms, plants are often challenged to multiple extreme abiotic stresses, such as drought, heat, cold, salinity and metal stresses in the field, which reduce plant growth, productivity and yield. The development of reproductive stage is more susceptible to abiotic stresses than the vegetative stage. Anther, the male reproductive organ that generate pollen grains, is more sensitive to abiotic stresses than female organs. Abiotic stresses affect all the processes of anther development, including tapetum development and degradation, microsporogenesis and pollen development, anther dehiscence, and filament elongation. In addition, abiotic stresses significantly interrupt phytohormone, lipid and carbohydrate metabolism, alter reactive oxygen species (ROS) homeostasis in anthers, which are strongly responsible for the loss of pollen fertility. At present, the precise molecular mechanisms of anther development under adverse abiotic stresses are still not fully understood. Therefore, more emphasis should be given to understand molecular control of anther development during abiotic stresses to engineer crops with better crop yield.

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

BackgroundVviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq.ResultsA total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum, and E. necator. VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses.ConclusionsVviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis. Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae

Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.

Genome-wide computational prediction and experimental validation of quinoa (Chenopodium quinoa) microRNAs

MicroRNAs (miRNAs) are highly conserved, endogenous, short (21–24 nucleotides), non-coding RNA molecules that play significant roles in post-transcriptional gene silencing by directing target mRNA cleavage or translational inhibition. Nonetheless, highly nutritious “super grain” quinoa (Chenopodium quinoa) is an extreme abiotic stress tolerant Andean seed crop of many potential uses, with outstanding protein quality and a load of vitamins, minerals, as well as flavonoid antioxidants. In this study, applying genome-wide in silico approaches (referring to the recently published quinoa genome) and following a set of stringent filtering measures, a total of 22 potentially conserved microRNAs belonging to 18 families were characterized from quinoa and 11 randomly selected putative microRNAs (cqu-miR160a, cqu-miR162a, cqu-miR164a, cqu-miR166b, cqu-miR167a, cqu-miR172a, cqu-miR319a, cqu-miR390a, cqu-miR393a, cqu-miR394a, and cqu-miR398b) were validated successfully by RT-PCR. Using the psRNATarget tool, a sum of 59 potential miRNA targets, mostly transcription factors, were identified that are involved in biosynthesis, metabolic processes, and signal transduction. Among the detected targets, six target transcripts (F-Box proteins, TCP, MYB, WD protein, NAC, and CSD) were reported to have specific roles in both flavonoids biosynthesis and stress response signaling in some plants. To the best of our knowledge, this is the first report of quinoa microRNAs and their targets.

Genomic and transcriptomic insights into the survival of the subaerial cyanobacterium Nostoc flagelliforme in arid and exposed habitats.

The cyanobacterium Nostoc flagelliforme is an extremophile that thrives under extraordinary desiccation and ultraviolet (UV) radiation conditions. To investigate its survival strategies, we performed whole-genome sequencing of N. flagelliforme CCNUN1 and transcriptional profiling of its field populations upon rehydration in BG11 medium. The genome of N. flagelliforme is 10.23 Mb in size and contains 10 825 predicted protein-encoding genes, making it one of the largest complete genomes of cyanobacteria reported to date. Comparative genomics analysis among 20 cyanobacterial strains revealed that genes related to DNA replication, recombination and repair had disproportionately high contributions to the genome expansion. The ability of N. flagelliforme to thrive under extreme abiotic stresses is supported by the acquisition of genes involved in the protection of photosynthetic apparatus, the formation of monounsaturated fatty acids, responses to UV radiation, and a peculiar role of ornithine metabolism. Transcriptome analysis revealed a distinct acclimation strategy to rehydration, including the strong constitutive expression of genes encoding photosystem I assembly factors and the involvement of post-transcriptional control mechanisms of photosynthetic resuscitation. Our results provide insights into the adaptive mechanisms of subaerial cyanobacteria in their harsh habitats and have important implications to understand the evolutionary transition of cyanobacteria from aquatic environments to terrestrial ecosystems.

Nesting on high: reproductive and physiological consequences of breeding across an intertidal gradient

Nest site selection is a critical parental decision with profound fitness consequences, yet the physiological consequences of these decisions are rarely examined. Certain fishes and other aquatic organisms construct nests and provide parental care in the intertidal zone—an environment characterized by fluctuating water levels, which can exert intermittent and sometimes extreme abiotic stress on the animals that live there including dramatic changes in temperature and dissolved oxygen level. In this study, we used the plainfin midshipman fish, Porichthys notatus, to test whether (1) nest site preferences and reproductive success vary across an intertidal elevation gradient, and (2) fish that nest at higher elevations pay greater physiological costs due to prolonged exposure to more extreme abiotic conditions. We found that fish preferred nests lower in the intertidal zone, with larger males outcompeting smaller males for these sites. Broods at high elevations suffered greater offspring mortality than broods at lower elevations. The average microhabitat temperature of nests was also warmer and more variable at higher elevations compared to lower elevations. While isolated from the ocean during low tides, care-giving parents increased their use of anaerobic metabolism, and potentially draw upon oxygen reserves in the swim bladder. Our results suggest that the choice of nesting location can have profound effects on a parent’s physiology and may generate significant variation in reproductive success among individuals.