Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings

Transcriptomic analysis in tomato fruit reveals divergences in genes involved in cold stress response and fruit ripening

Cold storage is widely used to extend the postharvest life of most horticultural crops, including tomatoes, but this practice triggers cold stress and leads to the development of undesirable chilling injury (CI) symptoms. The underlying mechanisms of cold stress response and CI development in fruits remain unclear as they are often intermingled with fruit ripening changes. To gain insight into cold responses in fruits, we examined the effect of the potent ethylene signaling inhibitor 1-methylcyclopropene (1-MCP) on fruit ripening, CI occurrence and gene expression in mature green tomatoes during storage at 20°C and 5°C. 1-MCP treatments effectively inhibited ethylene production and peel color changes during storage at 20°C. Storage at 5°C also inhibited both ethylene production and peel color change; during rewarming at 20°C, 1-MCP treatments inhibited peel color change but failed to inhibit ethylene production. Furthermore, fruits stored at 5°C for 14 d developed CI symptoms (surface pitting and decay) during the rewarming period at 20°C regardless of 1-MCP treatment. Subsequent RNA-Seq analysis revealed that cold stress triggers a large-scale transcriptomic adjustment, as noticeably more genes were differentially expressed at 5°C (8,406) than at 20°C (4,814). More importantly, we have found some important divergences among genes involved in fruit ripening (up- or down-regulated at 20°C; inhibited by 1-MCP treatment) and those involved in cold stress (up- or down-regulated at 5°C; unaffected by 1-MCP treatment). Transcriptomic adjustments unique to cold stress response were associated with ribosome biogenesis, NcRNA metabolism, DNA methylation, chromatin formation/remodeling, and alternative splicing events. These data should foster further research into cold stress response mechanisms in fruits with the ultimate aim of improving tolerance to low temperature and reduction of CI symptoms during cold storage.

Modulation of the Berry Skin Transcriptome of cv. Tempranillo Induced by Water Stress Levels

Climate change in the Mediterranean area is making summers warmer and dryer. Grapevine (Vitis vinifera L.) is mostly important for wine production in Mediterranean countries, and the variety Tempranillo is one of the most cultivated in Spain and Portugal. Drought decreases yield and quality and causes important economic losses. As full irrigation has negative effects on quality and water is scarce in this region, deficit irrigation is often applied. In this research, we studied the effects of two deficit irrigation treatments, Sustained Deficit Irrigation (SDI) and Regulated Deficit Irrigation (RDI), on the transcriptome of grape berries at full maturation, through RNAseq. The expression of differentially regulated genes (DEGs) was also monitored through RT-qPCR along berry development. Most transcripts were regulated by water stress, with a similar distribution of up- and down-regulated transcripts within functional categories (FC). Primary metabolism was the more severely affected FC under water stress, followed by signaling and transport. Almost all DEGs monitored were significantly up-regulated by severe water stress at veraison. The modulation of an auxin response repression factor, AUX22D, by water stress indicates a role of this gene in the response to drought. Further, the expression of WRKY40, a TF that regulates anthocyanin biosynthesis, may be responsible for changes in grape quality under severe water stress.

Responses of sorghum to cold stress: A review focused on molecular breeding

Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.

Testing the chilling- before drought-tolerance hypothesis in Pooideae grasses

Temperate Pooideae are a large clade of economically important grasses distributed in some of the Earth's coldest and driest terrestrial environments. Previous studies have inferred that Pooideae diversified from their tropical ancestors in a cold montane habitat, suggesting that above-freezing cold (chilling) tolerance evolved early in the subfamily. By contrast, drought tolerance is hypothesized to have evolved multiple times independently in response to global aridification that occurred after the split of Pooideae tribes. To independently test predictions of the chilling-before-drought hypothesis in Pooideae, we assessed conservation of whole plant and gene expression traits in response to chilling vs. drought. We demonstrated that both trait responses are more similar across tribes in cold as compared to drought, suggesting that chilling responses evolved before, and drought responses after, tribe diversification. Moreover, we found significantly more overlap between drought and chilling responsive genes within a species than between drought responsive genes across species, providing evidence that chilling tolerance genes acted as precursors for the novel acquisition of increased drought tolerance multiple times independently, partially through the cooption of chilling responsive genes.

Natural variation MeMYB108 associated with tolerance to stress-induced leaf abscission linked to enhanced protection against reactive oxygen species in cassava

Natural variation of the MeMYB108 exon was associated with reactive oxygen scavengers led to alleviate leaf abscission under drought in cassava. The reactive oxygen scavengers play important roles in regulating the cassava (Manihot esculenta Crantz) leaf abscission induced by stresses. To date, the relationship between natural variations of MYB genes and reactive oxygen scavengers under drought in cassava genotypes remains unclear. Here, we reported the transcription factor MeMYB108 played an important role in regulating leaf abscission exposed to drought in cassava. The expression levels of MeMYB108 in abscission zones of cassava leaf pulvinus were higher in cassava genotype SC124, which were less easy to shed leaves under stress than cassava genotype SC8 when the leaf abscission induced by the same drought condition. Compared with wild type and interference expression plants, overexpression of MeMYB108 significantly reduced the drought-induced leaf abscission rate under drought. The consecutively 2-year analysis of reactive oxygen scavengers showed significant differences among different cassava genotypes under drought-induced leaf abscission, indicating the relevance between reactive oxygen scavengers and leaf abscission. Correlation analysis revealed the natural variation of the MeMYB108 exon was associated with reactive oxygen scavengers during drought-induced leaf abscission. Association analysis between pairwise LD of DNA polymorphism indicated the MeMYB108 allele enhanced the tolerance of cassava to drought-induced leaf abscission. Complementation transgenic lines containing the elite allele of MeMYB108 ^SC124 decreased the leaf abscission rate induced by drought conditions, demonstrating natural variation in MeMYB108 contributed to leaf abscission tolerance induced by drought in cassava. Further studies showed MeMYB108 played an active role in the tolerance of cassava to drought-induced leaf abscission by inducing scavenging of reactive oxygen species.

Insight into Carbohydrate Metabolism and Signaling in Grapevine Buds during Dormancy Progression

Perennial fruit crops enter dormancy to ensure bud tissue survival during winter. However, a faster phenological advancement caused by global warming exposes bud tissue to a higher risk of spring frost damage. Tissue dehydration and soluble sugars accumulation are connected to freezing tolerance, but non-structural carbohydrates also act as metabolic substrates and signaling molecules. A deepened understanding of sugar metabolism in the context of winter freezing resistance is required to gain insight into adaptive possibilities to cope with climate changes. In this study, the soluble sugar content was measured in a cold-tolerant grapevine hybrid throughout the winter season. Moreover, the expression of drought-responsive hexose transporters VvHT1 and VvHT5, raffinose synthase VvRS and grapevine ABA-, Stress- and Ripening protein VvMSA was analyzed. The general increase in sugars in December and January suggests that they can participate in protecting bud tissues against low temperatures. The modulation of VvHT5, VvINV and VvRS appeared consistent with the availability of the different sugar species; challenging results were obtained for VvHT1 and VvMSA, suggesting interesting hypotheses about their role in the sugar-hormone crosstalk. The multifaceted role of sugars on the intricate phenomenon, which is the response of dormant buds to changing temperature, is discussed.

Cyanogenesis in cassava and its molecular manipulation for crop improvement

While cassava is one of the most important staple crops worldwide, it has received the least investment per capita consumption of any of the major global crops. This is in part due to cassava being a crop of subsistence farmers that is grown in countries with limited resources for crop improvement. While its starchy roots are rich in calories, they are poor in protein and other essential nutrients. In addition, they contain potentially toxic levels of cyanogenic glycosides which must be reduced to safe levels before consumption. Furthermore, cyanogens compromise the shelf life of harvested roots due to cyanide-induced inhibition of mitochondrial respiration, and associated production of reactive oxygen species that accelerate root deterioration. Over the past two decades, the genetic, biochemical, and developmental factors that control cyanogen synthesis, transport, storage, and turnover have largely been elucidated. It is now apparent that cyanogens contribute substantially to whole-plant nitrogen metabolism and protein synthesis in roots. The essential role of cyanogens in root nitrogen metabolism, however, has confounded efforts to create acyanogenic varieties. This review proposes alternative molecular approaches that integrate accelerated cyanogen turnover with nitrogen reassimilation into root protein that may offer a solution to creating a safer, more nutritious cassava crop.

MeSPL9 attenuates drought resistance by regulating JA signaling and protectant metabolite contents in cassava

Analysis of drought-related genes in cassava shows the involvement of MeSPL9 in drought stress tolerance and overexpression of a dominant-negative form of this gene demonstrates its negative roles in drought stress resistance. Drought stress severely impairs crop yield and is considered a primary threat to food security worldwide. Although the SQUAMOSA promoter binding protein-like 9 (SPL9) gene participates extensively in numerous developmental processes and in plant response to abiotic stimuli, its role and regulatory pathway in cassava (Manihot esculenta) response to the drought condition remain elusive. In the current study, we show that cassava SPL9 (MeSPL9) plays negative roles in drought stress resistance. MeSPL9 expression was strongly repressed by drought treatment. Overexpression of a dominant-negative form of miR156-resistant MeSPL9, rMeSPL9-SRDX, in which a 12-amino acid repressor sequence was fused to rMeSPL9 at the C terminus, conferred drought tolerance without penalizing overall growth. rMeSPL9-SRDX-overexpressing lines not only exhibited increased osmoprotectant metabolites including proline and anthocyanin, but also accumulated more endogenous jasmonic acid (JA) and soluble sugars. Transcriptomic and real-time PCR analysis suggested that differentially expressed genes were involved in sugar or JA biosynthesis, signaling, and metabolism in transgenic cassava under drought conditions. Exogenous application of JA further confirmed that JA conferred improved drought resistance and promoted stomatal closure in cassava leaves. Taken together, our findings suggest that MeSPL9 affects drought resistance by modulating protectant metabolite levels and JA signaling, which have substantial implications for engineering drought tolerant crops.

Evaluation of curcuminoids, physiological adaptation, and growth of Curcuma longa under water deficit and controlled temperature

Turmeric (Curcuma longa L.; Zingiberaceae), an economically important crop and a major spice in Indian cuisine, produces natural yellow color (curcumin) as well as curcuminoids which are widely utilized in traditional and modern medicinal practices. During the turmeric culture, the fluctuations of precipitation and seasonal changes in the whole life cycle play a major role, especially water shortage and decreasing temperature (in winter season), leading to rhizome dormancy under extreme weather conditions. The objective of this investigation was to understand how the water deficit and reduced temperature affect turmeric growth, physiological adaptation, quantity, and quality of turmeric rhizomes. Four-month-old turmeric plants were subjected to four treatments, namely normal temperature and well-watered (RT-WW), or water-deficit (RT-WD) conditions in the greenhouse, 25 °C controlled temperature and well-watered (CT-WW), or water-deficit (CT-WD) conditions in glasshouse. Leaf osmotic potential considerably declined in 30 days CT-WD treatment, leading to chlorophyll degradation by 26.04%, diminution of maximum quantum yield of PSII (F_v/F_m) by 23.50%, photon yield of PSII (Φ_PSII) by 29.01%, and reduction of net photosynthetic rate (P_n) by 89.39% over CT-WW (control). After 30 days water withholding, fresh- and dry-weights of rhizomes of turmeric plants grown under CT-WD declined by 30-50% when compared with RT-WW conditions. Subsequently, curcuminoid content was reduced by 40% over RT-WW plants (control), whereas transcriptional expression levels of curcuminoids-related genes (CURS1, CURS2, CURS3, and DCS) were upregulated in CT-WD conditions. In summary, the water withholding and controlled temperature (constant at 25 °C day/night) negatively affected turmeric plants as abiotic stresses tend to limit overall plant growth performances and curcuminoid yield.

Problems and Prospects of Improving Abiotic Stress Tolerance and Pathogen Resistance of Oil Palm

Oil palm crops are the most important determinant of the agricultural economy within the segment of oilseed crops. Oil palm growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic that limit crop productivity and are major constraints to meeting global food demands. The stress-tolerant oil palm crops that mitigate the effects of abiotic stresses on crop productivity are crucially needed to sustain agricultural production. Basal stem rot threatens the development of the industry, and the key to solving the problem is to breed new oil palm varieties resistant to adversity. This has created a need for genetic improvement which involves evaluation of germplasm, pest and disease resistance, earliness and shattering resistance, quality of oil, varieties for different climatic conditions, etc. In recent years, insights into physiology, molecular biology, and genetics have significantly enhanced our understanding of oil palm response towards such stimuli as well as the reason for varietal diversity in tolerance. In this review, we explore the research progress, existing problems, and prospects of oil palm stress resistance-based physiological mechanisms of stress tolerance as well as the genes and metabolic pathways that regulate stress response.

Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

BACKGROUND

Common vetch (Vicia sativa L.) is an important self-pollinating annual forage legume and is of interest for drought prone regions as a protein source to feed livestock and human consumption. However, the development and production of common vetch are negatively affected by drought stress. Plants have evolved common or distinct metabolic pathways between the aboveground and underground in response to drought stress. Little is known regarding the coordinated response of aboveground and underground tissues of common vetch to drought stress.

RESULTS

Our results showed that a total of 30,427 full-length transcripts were identified in 12 samples, with an average length of 2278.89 bp. Global transcriptional profiles of the above 12 samples were then analysed via Illumina-Seq. A total of 3464 and 3062 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Gene Ontology (GO) enrichment analyses identified that the dehydrin genes and Δ¹-pyrroline-5-carboxylate synthase were induced for the biosynthesis of proline and water conservation. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that the DEGs were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism, and various drought response candidate genes were also identified. Abscisic acid (ABA; the AREB/ABF-SnRK2 pathway) regulates the activity of AMY3 and BAM1 to induce starch degradation in leaves and increase carbon export to roots, which may be associated with the drought stress responses in common vetch. Among the co-induced transcription factors (TFs), AREB/ABF, bHLH, MYB, WRKY, and AP2/ERF had divergent expression patterns and may be key in the crosstalk between leaves and roots during adaption to drought stress. In transgenic yeast, the overexpression of four TFs increased yeast tolerance to osmotic stresses.

CONCLUSION

The multipronged approach identified in the leaves and roots broadens our understanding of the coordinated mechanisms of drought response in common vetch, and further provides targets to improve drought resistance through genetic engineering.

A perspective on crassulacean acid metabolism photosynthesis evolution of orchids on different continents: Dendrobium as a case study

Members of the Orchidaceae, one of the largest families of flowering plants, evolved the crassulacean acid metabolism (CAM) photosynthesis strategy. It is thought that CAM triggers adaptive radiation into new niche spaces, yet very little is known about its origin and diversification on different continents. Here, we assess the prevalence of CAM in Dendrobium, which is one of the largest genera of flowering plants and found in a wide range of environments, from the high altitudes of the Himalayas to relatively arid habitats in Australia. Based on phylogenetic time trees, we estimated that CAM, as determined by δ 13C values less negative than -20.0‰, evolved independently at least eight times in Dendrobium. The oldest lineage appeared in the Asian clade during the middle Miocene, indicating the origin of CAM was associated with a pronounced climatic cooling that followed a period of aridity. Divergence of the four CAM lineages in the Asian clade appeared to be earlier than divergence of those in the Australasian clade. However, CAM species in the Asian clade are much less diverse (25.6%) than those in the Australasian clade (57.9%). These findings shed new light on CAM evolutionary history and the aridity levels of the paleoclimate on different continents.

Transcriptome analysis provides insights into the stress response crosstalk in apple (Malus × domestica) subjected to drought, cold and high salinity

Drought, cold, and high salinity are three major abiotic stresses effecting apple tree growth and fruit production. Understanding the genetic mechanisms of crosstalk between stress responses signalling networks and identifying the genes involved in apple has potential importance for crop improvement and breeding strategies. Here, the transcriptome profiling analysis of in vitro-grown apple plants subjected to drought, cold and high salinity stress, showed a total of 377 upregulated and 211 downregulated common differentially expressed genes (DEGs) to all 3 stress treatments compared with the control. Gene Ontology (GO) analysis indicated that these common DEGs were enriched in ‘metabolic process’ under the ‘biological process’ category, as well as in ‘binding’ and ‘catalytic activity’ under the ‘molecular function’ category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that common DEGs were mainly belong to the ‘biological functions’ category and 17 DEGs were identified in ‘environmental information processing’ sub-category which may act as signal transduction components in response crosstalk regulation. Overexpression of 5 upregulated genes individually, out of these 17 common DEGs in apple calli promoted the consistent upregulation of DREB6, CBF1 and ZAT10 and increased the mass weight and antioxidase ability, implying these five common DEGs involved in multiple pathways and improved comprehensive resistance to stress.

The regulatory effects of MeTCP4 on cold stress tolerance in Arabidopsis thaliana: A transcriptome analysis

Cassava (Manihot esculenta), an important food crop in tropical areas, is well-adapted to drought conditions, but is sensitive to cold. The expression of MeTCP4, a transcription factor involved in the regulation of plant development and abiotic stresses responses, was altered under cold stress. However, its biological function under abiotic stress responses is still unclear. Here, we show that increased MeTCP4 expression enhances cold stress tolerance in Arabidopsis (Arabidopsis thaliana). To better understand the biological role of MeTCP4, the mRNA from overexpression and wild-type (WT) plants was isolated for whole genome sequencing to identify MeTCP4-mediated cold-responsive genes. Our results identify 1341 and 797 differentially expressed genes (DEGs) affected by MeTCP4 overexpression under normal and cold conditions, respectively. Gene ontology analysis revealed that a portion of the DEGs were involved in reactive oxygen species (ROS) metabolism process after cold treatment. qRT-PCR analysis revealed that the expression of cold-responsive genes and ROS-scavenging-related genes were increased in MeTCP4 overexpression plant, which could be responsible for the reduced ROS levels and enhanced cold resistance observed in transgenic plant. The findings provide insight into mechanisms of MeTCP4-mediated cold stress response, and provide clues for development of low temperature-tolerant cassava cultivars.

Extensive Post-Transcriptional Regulation Revealed by Transcriptomic and Proteomic Integrative Analysis in Cassava under Drought

Cassava is a major tropical/subtropical food crop and its yield is greatly restrained by drought; however, the mechanism underlying the drought stress remains largely unknown. In this study, totally 1242 and 715 differentially expressed genes (DEGs), together with 237 and 307 differentially expressed proteins (DEPs), were respectively identified in cassava leaves and roots through RNA-seq and iTRAQ techniques. The majority of DEGs and DEPs were exclusively regulated at the mRNA and protein level, respectively, whereas only a few were commonly regulated, indicating the major involvement of post-transcriptional regulation under drought. Subsequently, the functions of these specifically or commonly regulated DEGs and DEPs were analyzed, and the post-transcriptional regulation of genes involved in heat shock protein, secondary metabolism biosynthesis, and hormone biosynthesis was extensively discussed. This is the first report on an integration of transcriptomic and proteomic analysis in cassava, and it provides new insights into the post-transcriptional regulation of cassava drought stress.

An optimized isolation protocol yields high-quality RNA from cassava tissues (Manihot esculenta Crantz)

We developed and modified a precise, rapid, and reproducible protocol isolating high-quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170-600 μg·g^-1) using low-cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A ₂₆₀ : A ₂₈₀ ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase-polymerase chain reaction or RNA sequencing) in cassava molecular breeding.

Full-length transcript sequencing and comparative transcriptomic analysis to evaluate the contribution of osmotic and ionic stress components towards salinity tolerance in the roots of cultivated alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa is the most extensively cultivated forage legume. Salinity is a major environmental factor that impacts on alfalfa's productivity. However, little is known about the molecular mechanisms underlying alfalfa responses to salinity, especially the relative contribution of the two important components of osmotic and ionic stress.

RESULTS

In this study, we constructed the first full-length transcriptome database for alfalfa root tips under continuous NaCl and mannitol treatments for 1, 3, 6, 12, and 24 h (three biological replicates for each time points, including the control group) via PacBio Iso-Seq. This resulted in the identification of 52,787 full-length transcripts, with an average length of 2551 bp. Global transcriptional changes in the same 33 stressed samples were then analyzed via BGISEQ-500 RNA-Seq. Totals of 8861 NaCl-regulated and 8016 mannitol-regulated differentially expressed genes (DEGs) were identified. Metabolic analyses revealed that these DEGs overlapped or diverged in the cascades of molecular networks involved in signal perception, signal transduction, transcriptional regulation, and antioxidative defense. Notably, several well characterized signalling pathways, such as CDPK, MAPK, CIPK, and PYL-PP2C-SnRK2, were shown to be involved in osmotic stress, while the SOS core pathway was activated by ionic stress. Moreover, the physiological shifts of catalase and peroxidase activity, glutathione and proline content were in accordance with dynamic transcript profiles of the relevant genes, indicating that antioxidative defense system plays critical roles in response to salinity stress.

CONCLUSIONS

Overall, our study provides evidence that the response to salinity stress in alfalfa includes both osmotic and ionic components. The key osmotic and ionic stress-related genes are candidates for future studies as potential targets to improve resistance to salinity stress via genetic engineering.

Physiological characterization of common bean (Phaseolus vulgaris L.) under abiotic stresses for breeding purposes

In the Brazilian wet and dry seasons, common beans (Phaseolus vulgaris L.) are grown under rainfed conditions with unexpected episodes of drought and high temperatures. The objective of this study was to evaluate the physiological mechanisms associated with drought adaptation traits in landraces and line/cultivars of beans from the Andean and Mesoamerican gene pools. Twenty-five genotypes, contrasting in terms of drought tolerance, were evaluated in a phenotyping platform under irrigated and rainfed conditions. Agronomic and physiological parameters such as grain yield, shoot structures, gas exchange, water potential, and osmotic adjustment were evaluated. The stress intensity was estimated to be 0.57, and the grain yield reduction ranged from 22 to 89%. Seven accessions, representative of the Andean and Mesoamerican germplasm (CF 200012, CF 240056, CF 250002, CF 900004, CNF 4497, CNF 7382, and SEA 5), presented superior performance in grain yield with and without stresses. The physiological responses under abiotic stresses were highly variable among the genotypes, and two Mesoamerican accessions (CF 200012 and SEA 5) showed more favorable adaptive responses. As the main secondary physiological traits, gas exchange and osmotic adjustment should be evaluated together with the grain yield to increase the selection efficiency of abiotic stresses-tolerant common bean lines.

Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L

Cultivated alfalfa (Medicago sativa L.) is one of the most important perennial legume forages in the world, and it has considerable potential as a valuable forage crop for livestock. However, the molecular mechanisms underlying alfalfa responses to cold stress are largely unknown. In this study, the transcriptome changes in alfalfa under cold stress at 4 °C for 2, 6, 24, and 48 h (three replicates for each time point) were analyzed using the high-throughput sequencing platform, BGISEQ-500, resulting in the identification of 50,809 annotated unigenes and 5283 differentially expressed genes (DEGs). Metabolic pathway enrichment analysis demonstrated that the DEGs were involved in carbohydrate metabolism, photosynthesis, plant hormone signal transduction, and the biosynthesis of amino acids. Moreover, the physiological changes of glutathione and proline content, catalase, and peroxidase activity were in accordance with dynamic transcript profiles of the relevant genes. Additionally, some transcription factors might play important roles in the alfalfa response to cold stress, as determined by the expression pattern of the related genes during 48 h of cold stress treatment. These findings provide valuable information for identifying and characterizing important components in the cold signaling network in alfalfa and enhancing the understanding of the molecular mechanisms underlying alfalfa responses to cold stress.

Transcriptome analysis reveals interplay between hormones, ROS metabolism and cell wall biosynthesis for drought-induced root growth in wheat

The ability of roots to grow under drought stress is an adaptive trait for crop plants especially under rain fed and restricted irrigation regime. To unravel the molecular mechanism of drought induced-root growth, root transcriptomes of two wheat genotypes viz. Raj3765 and HD2329, with contrasting root growth under drought stress were analyzed. Drought stress significantly enhanced total root length in Raj3765 as compared to that of HD2329. RNA-seq analysis led to the identification of 2783 and 2638 differentially expressed genes (DEGs) in Raj3765 and HD2329, respectively, under drought stress as compared with non-stress conditions. Functional annotation, gene ontology and MapMan analysis of the DEGs revealed differential regulation of genes for pathways associated with root growth and stress tolerance. Drought stress significantly upregulated auxin receptor (AFB2) and ABA responsive transcription factors (MYB78, WRKY18 and GBF3) in roots of Raj3765. Although certain genes for ethylene pathway were downregulated in both the genotypes, ACC oxidase and 2OG-Fe(II) oxygenase were upregulated only in Raj3765 which might contribute to maintenance of a basal ethylene level to maintain root growth. Several genes related to cell wall biosynthesis and ROS metabolism were significantly upregulated in Raj3765. Genes related to gibberellic acid, jasmonic acid and phenylpropanoid pathways were downregulated in roots of both the genotypes under drought stress. Our analysis suggests that a coordinated yet complex interplay between hormones, cellular tolerance, cell wall synthesis and ROS metabolism are required for drought induced root growth in wheat.

Stress cross-response of the antioxidative system promoted by superimposed drought and cold conditions in Coffea spp

The understanding of acclimation strategies to low temperature and water availability is decisive to ensure coffee crop sustainability, since these environmental conditions determine the suitability of cultivation areas. In this context, the impacts of single and combined exposure to drought and cold were evaluated in three genotypes of the two major cropped species, Coffea arabica cv. Icatu, Coffea canephora cv. Apoatã, and the hybrid Obatã. Crucial traits of plant resilience to environmental stresses have been examined: photosynthesis, lipoperoxidation and the antioxidant response. Drought and/or cold promoted leaf dehydration, which was accompanied by stomatal and mesophyll limitations that impaired leaf C-assimilation in all genotypes. However, Icatu showed a lower impact upon stress exposure and a faster and complete photosynthetic recovery. Although lipoperoxidation was increased by drought (Icatu) and cold (all genotypes), it was greatly reduced by stress interaction, especially in Icatu. In fact, although the antioxidative system was reinforced under single drought and cold exposure (e.g., activity of enzymes as Cu,Zn-superoxide dismutase, ascorbate peroxidase, APX, glutathione reductase and catalase, CAT), the stronger increases were observed upon the simultaneous exposure to both stresses, which was accompanied with a transcriptional response of some genes, namely related to APX. Complementary, non-enzyme antioxidant molecules were promoted mostly by cold and the stress interaction, including α-tocopherol (in C. arabica plants), ascorbate (ASC), zeaxanthin, and phenolic compounds (all genotypes). In general, drought promoted antioxidant enzymes activity, whereas cold enhanced the synthesis of both enzyme and non-enzyme antioxidants, the latter likely related to a higher need of antioxidative capability when enzyme reactions were probably quite repressed by low temperature. Icatu showed the wider antioxidative capability, with the triggering of all studied antioxidative molecules by drought (except CAT), cold, and, particularly, stress interaction (except ASC), revealing a clear stress cross-tolerance. This justified the lower impacts on membrane lipoperoxidation and photosynthetic capacity under stress interaction conditions, related to a better ROS control. These findings are also relevant to coffee water management, showing that watering in the cold season should be largely avoided.