Expression profiling of ABA pathway transcripts indicates crosstalk between abiotic and biotic stress responses in Arabidopsis

Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes

Covering: up to 2023Specialized metabolite (SM) modifications and/or decorations, corresponding to the addition or removal of functional groups (e.g. hydroxyl, methyl, glycosyl or acyl group) to SM structures, contribute to the huge diversity of structures, activities and functions of seed and plant SMs. This review summarizes available knowledge (up to 2023) on SM modifications in Brassicaceae and their contribution to SM plasticity. We give a comprehensive overview on enzymes involved in the addition or removal of these functional groups. Brassicaceae, including model (Arabidopsis thaliana) and crop (Brassica napus, Camelina sativa) plant species, present a large diversity of plant and seed SMs, which makes them valuable models to study SM modifications. In this review, particular attention is given to the environmental plasticity of SM and relative modification and/or decoration enzymes. Furthermore, a spotlight is given to SMs and related modification enzymes in seeds of Brassicaceae species. Seeds constitute a large reservoir of beneficial SMs and are one of the most important dietary sources, providing more than half of the world's intake of dietary proteins, oil and starch. The seed tissue- and stage-specific expressions of A. thaliana genes involved in SM modification are presented and discussed in the context of available literature. Given the major role in plant phytochemistry, biology and ecology, SM modifications constitute a subject of study contributing to the research and development in agroecology, pharmaceutical, cosmetics and food industrial sectors.

Predicted roles of long non-coding RNAs in abiotic stress tolerance responses of plants

The plant genome exhibits a significant amount of transcriptional activity, with most of the resulting transcripts lacking protein-coding potential. Non-coding RNAs play a pivotal role in the development and regulatory processes in plants. Long non-coding RNAs (lncRNAs), which exceed 200 nucleotides, may play a significant role in enhancing plant resilience to various abiotic stresses, such as excessive heat, drought, cold, and salinity. In addition, the exogenous application of chemicals, such as abscisic acid and salicylic acid, can augment plant defense responses against abiotic stress. While how lncRNAs play a role in abiotic stress tolerance is relatively well-studied in model plants, this review provides a comprehensive overview of the current understanding of this function in horticultural crop plants. It also delves into the potential role of lncRNAs in chemical priming of plants in order to acquire abiotic stress tolerance, although many limitations exist in proving lncRNA functionality under such conditions.

Genome-wide characterization of cytochrome P450 genes reveals the potential roles in fruit ripening and response to cold stress in tomato

Plant cytochrome P450 (CYP) superfamily, the largest enzyme metabolism family, has been identified in many species and plays a vital role in plant development and stress response via secondary metabolite biosynthesis. A comprehensive identification and functional investigation of CYPs in tomato plants would contribute to deeper understanding of their biological significance. In this study, 268 tomato CYP genes were identified and found to be unevenly located on 12 chromosomes. Based on the phylogenetic analysis, these 268 SlCYPs were classed into two distinct clades (A-type and non-A-type) and nine clans, including 48 families. Moreover, 67 tandem and 22 WGD (whole genome duplication)/segmental duplication events were detected, of which 12 SlCYP genes experienced both WGD/segmental and tandem duplication events, indicating that tandem duplication plays a major role in the expansion of the SlCYP family. Besides, 48 pairs containing 41 SlCYP and 44 AtCYP genes were orthologous, while 216 orthologous pairs were obtained between tomato and potato. The expression level of all SlCYP genes in tomato tissues at different development stages was analyzed, and most expressed SlCYPs showed a tissue-specific pattern. Meanwhile, 143 differentially expressed SlCYPs were identified under cold stress. Furthermore, the RT-qPCR results indicated that SlCYPs may be involved in fruit ripening and cold tolerance in tomato seedlings. These findings provide valuable insights into the evolutionary relationships and functional characteristics of SlCYPs, which can be utilized for further investigation of fruit metabolic pathways and cold tolerance in tomato.

Meta-analysis of public RNA sequencing data of abscisic acid-related abiotic stresses in Arabidopsis thaliana

Abiotic stresses such as drought, salinity, and cold negatively affect plant growth and crop productivity. Understanding the molecular mechanisms underlying plant responses to these stressors is essential for stress tolerance in crops. The plant hormone abscisic acid (ABA) is significantly increased upon abiotic stressors, inducing physiological responses to adapt to stress and regulate gene expression. Although many studies have examined the components of established stress signaling pathways, few have explored other unknown elements. This study aimed to identify novel stress-responsive genes in plants by performing a meta-analysis of public RNA sequencing (RNA-Seq) data in Arabidopsis thaliana, focusing on five ABA-related stress conditions (ABA, Salt, Dehydration, Osmotic, and Cold). The meta-analysis of 216 paired datasets from five stress conditions was conducted, and differentially expressed genes were identified by introducing a new metric, called TN [stress-treated (T) and non-treated (N)] score. We revealed that 14 genes were commonly upregulated and 8 genes were commonly downregulated across all five treatments, including some that were not previously associated with these stress responses. On the other hand, some genes regulated by salt, dehydration, and osmotic treatments were not regulated by exogenous ABA or cold stress, suggesting that they may be involved in the plant response to dehydration independent of ABA. Our meta-analysis revealed a list of candidate genes with unknown molecular mechanisms in ABA-dependent and ABA-independent stress responses. These genes could be valuable resources for selecting genome editing targets and potentially contribute to the discovery of novel stress tolerance mechanisms and pathways in plants.

Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes

Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.

Cytochrome P450 Gene Families: Role in Plant Secondary Metabolites Production and Plant Defense

Cytochrome P450s (CYPs) are the most prominent family of enzymes involved in NADPH- and O2-dependent hydroxylation processes throughout all spheres of life. CYPs are crucial for the detoxification of xenobiotics in plants, insects, and other organisms. In addition to performing this function, CYPs serve as flexible catalysts and are essential for producing secondary metabolites, antioxidants, and phytohormones in higher plants. Numerous biotic and abiotic stresses frequently affect the growth and development of plants. They cause a dramatic decrease in crop yield and a deterioration in crop quality. Plants protect themselves against these stresses through different mechanisms, which are accomplished by the active participation of CYPs in several biosynthetic and detoxifying pathways. There are immense potentialities for using CYPs as a candidate for developing agricultural crop species resistant to biotic and abiotic stressors. This review provides an overview of the plant CYP families and their functions to plant secondary metabolite production and defense against different biotic and abiotic stresses.

Comparative Analysis of the PYL Gene Family in Three Ipomoea Species and the Expression Profiling of IbPYL Genes during Abiotic Stress Response in Sweetpotato

Abscisic acid (ABA), a critical phytohormone that regulates plant development and stress response, is sensed by the ABA receptors PYR/PYL/RCAR (PYLs). The PYL genes have been widely studied in multiple plant species, while a systematic analysis of PYL genes in the genus Ipomoea remains unperformed. Here, a total of 13, 14, and 14 PYLs were identified in Ipomoea batatas, Ipomoea trifida, and Ipomoea triloba, respectively. Fragment duplication was speculated to play prominent roles in Ipomoea PYL gene expansions. These Ipomoea PYLs were classified into three subfamilies via phylogenetic analysis, which was supported by exon-intron structures and conserved motif analyses. Additionally, the interspecies collinearity analysis further depicted a potential evolutionary relationship between them. Moreover, qRT-PCR analysis showed that multiple IbPYLs are highly and differentially responsive to abiotic stress treatments, suggesting their potential roles in sweetpotato stress responses. Taken together, these data provide valuable insights into the PYLs in the genus Ipomoea, which may be useful for their further functional analysis of their defense against environmental changes.

Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica

Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.

Integrated metabolomics and transcriptomics analysis during seed germination of waxy corn under low temperature stress

BACKGROUND

Waxy corn has a short growth cycle and high multiple cropping index. However, after being planted in early spring, late autumn and winter, it is susceptible to low temperature (LT), which reduces the emergence rate and yield. Therefore, it is important to analyze the response mechanism of waxy corn under LT stress.

RESULTS

All phenotype indexes of waxy corn inbred lines N28 were significantly higher than waxy corn inbred lines N67 under LT. With the increase of LT stress time, all physiological indexes showed an upward trend in N28 and N67. Differentially expressed genes (DEGs) 16,017 and 14,435 were identified in N28 and N67 compared with nongerminated control under LT germination, respectively, and differential metabolites 127 and 93 were detected in N28 and N67, respectively. In addition, the expression level of some genes involved in plant hormones and mitogen activated protein kinase (MAPK) signaling pathways was significantly up-regulated in N28. Compared with N67, flavonoid metabolites were also significantly enriched in N28 under LT germination.

CONCLUSION

Under LT stress, the inbred lines N28 was significantly higher than the inbred lines N67 in the phenotypic and physiological indices of cold resistance. Compared with N67, the expression levels of some genes involved in the plant hormones and MAPK pathways were significantly up-regulated in N28, and flavonoid metabolites were also significantly enriched in N28 under LT stress. These genes and metabolites may help N28 to improve cold resistance and may be as potential target genes for cold resistance breeding in waxy corn.

'Garlic-lipo'4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum)

Recently, environmentally friendly crop improvements using next-generation plant biostimulants (PBs) come to the forefront in agriculture, regardless of whether they are used by scientists, farmers, or industries. Various organic and inorganic solutions have been investigated by researchers and producers, focusing on tolerance to abiotic and biotic stresses, crop quality, or nutritional deficiency. Garlic has been considered a universal remedy ever since antiquity. A supercritical carbon dioxide garlic extract encapsulated in nanoscale liposomes composed of plant-derived lipids was examined as a possible PB agent. The present study focused on the characterization of the genes associated with the pathways involved in defense response triggered by the liposome nanoparticles that were loaded with supercritical garlic extracts. This material was applied to Triticum aestivum in greenhouse experiments using foliar spraying. The effects were examined in a large-scale genome-wide transcriptional profiling experiment by collecting the samples four times (0 min, used as a control, and 15 min, 24 h, and 48 h after spraying). Based on a time-course expression analysis, the dynamics of the cellular response were determined by examining differentially expressed genes and applying a cluster analysis. The results suggested an enhanced expression of abscisic acid (ABA) pathway and pathogenesis-related (PR) genes, of which positive regulation was found for the AP2-, C2H2-, HD-ZIP-, and MYB-related transcription factor families.

Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis)

BACKGROUND

Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress.  RESULTS: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway.

CONCLUSION

F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.

NAC transcription factor TgNAP promotes tulip petal senescence

Petal senescence is a crucial determinant for ornamental quality and economic value of floral crops. Salicylic acid (SA) and reactive oxygen species (ROS) are two prominent factors involved in plant senescence regulation. In this study, tulip TgNAP (NAC-like, activated by APETALA3/PISTILLATA) was characterized as positively regulating tulip petal senescence through dually regulating SA biosynthesis and ROS detoxification pathways. TgNAP was upregulated in senescing petals of tulip while exogenous SA and H2O2 treatments substantially promoted petal senescence in tulip. Silencing of TgNAP by VIGS assay delayed SA and H2O2-induced petal senescence in tulip, whereas overexpression of TgNAP promoted the senescence process in Arabidopsis (Arabidopsis thaliana) plants. Additionally, inhibition of SA biosynthesis prolonged the lifespan of TgNAP-silenced petal discs. Further evidence indicated that TgNAP activates the transcriptions of two key SA biosynthetic genes ISOCHORISMATE SYNTHASE 1 (TgICS1) and PHENYLALANINE AMMONIA-LYASE 1 (TgPAL1) through directly binding to their promoter regions. Meanwhile, TgNAP repressed ROS scavenging by directly inhibiting PEROXIDASE 12 (POD12) and POD17 expression. Taken together, these results indicate that TgNAP enhances SA biosynthesis and ROS accumulation to positively regulate petal senescence in tulip.

Abscisic Acid Signaling in the Regulation of Postharvest Physiological Deterioration of Sliced Cassava Tuberous Roots

Phytohormone abscisic acid (ABA) influences the shelf life of fruit, vegetables, and tubers after harvest. However, little is known about the core signaling module involved in ABA's control of the postharvest physiological process. Exogenous ABA alleviated postharvest physiological deterioration (PPD) symptoms of sliced cassava tuberous roots, increased endogenous ABA levels, and reduced endogenous H₂O₂ content. The specific ABA signaling module during the PPD process was identified as MePYL6-MePP2C16-MeSnRK2.1-MebZIP5/34. MebZIP5/MebZIP34 directly binds to and activates the promoters of MeGRX6/MeMDAR1 through ABRE elements. Exogenous ABA significantly induced the expression of genes involved in this module, glutaredoxin content, and monodehydroascorbate reductase activity. We presented a hypothesis suggesting that MePYL6-MePP2C16-MeSnRK2.1-MebZIP5/34-MeGRX6/MeMDAR1 is involved in ABA-induced antioxidative capacity, thus alleviating PPD symptoms in cassava tuberous roots. The identification of the specific signaling module involved in ABA's control of PPD provides a basis and potential targets for extending the shelf life of cassava tuberous roots.

Drought and global hunger: biotechnological interventions in sustainability and management

Drought may be efficiently managed using the following strategies: prevention, mitigation, readiness, recovery, and transformation. Biotechnological interventions may become highly important in reducing plants' drought stress in order to address key plant challenges such as population growth and climate change. Drought is a multidimensional construct with several triggering mechanisms or contributing factors working at various spatiotemporal scales, making it one of the known natural catastrophes. Drought is among the causes of hunger and malnutrition, decreasing agricultural output, and poor nutrition. Many deaths caused in children are due to hunger situations, and one in four children face stunted growth. All this hunger and malnutrition may be responsible for the reduction in agricultural productivity caused due to the drought situations affecting food security. Global Hunger Index has been accelerating due to under-nutrition and under-5 deaths. Drought has been covering more than 20% of the world's agricultural areas, leading to significantly less food production than what is required for consumption. Drought reduces soil fertility and adversely affects soil biological activity reducing the inherent capacity of the soil to support vegetation. Recent droughts have had a much greater effect on people's lives, even beyond causing poverty and hunger. Drought may have substantial financial consequences across the globe it may cause a severe impact on the world economy. It is a natural feature of the environment that will appear and disappear as it has in history. Due to increasing temperatures and growing vulnerabilities, it will undoubtedly occur more often and seriously in the coming years. To ensure sustainable socio-economic and social development, it is critical to reducing the effects of potential droughts worldwide using different biotechnological interventions. It's part of a long-term growth plan, and forecasting is essential for early warnings and global hunger management.

NUCLEAR TRANSPORT FACTOR 2-LIKE improves drought tolerance by modulating leaf water loss in alfalfa (Medicago sativa L.)

Drought is a major environmental factor that limits the production of alfalfa (Medicago sativa). In the present study, M. sativa NUCLEAR TRANSPORT FACTOR 2-LIKE (MsNTF2L) was identified as a nucleus-, cytoplasm-, and plasma membrane-localized protein. Its transcriptional expression was highly induced by ABA and drought stress. Overexpression of MsNTF2L in Arabidopsis resulted in hypersensitivity to ABA during both the seed germination and seedling growth stages. However, transgenic Arabidopsis plants exhibited enhanced tolerance to drought stress by reducing the levels of reactive oxygen species (ROS) and increasing the expression of stress/ABA-inducible genes. Consistently, analysis of MsNTF2L overexpression (OE) and RNA interference (RNAi) alfalfa plants revealed that MsNTF2L confers drought tolerance through promoting ROS scavenging, a decrease in stomatal density, ABA-induced stomatal closure, and epicuticular wax crystal accumulation. MsNTF2L highly affected epicuticular wax deposition, as a large group of wax biosynthesis and transport genes were influenced in the alfalfa OE and RNAi lines. Furthermore, transcript profiling of drought-treated alfalfa WT, OE, and RNAi plants showed a differential drought response for genes related to stress/ABA signaling, antioxidant defense, and photosynthesis. Taken together, these results reveal that MsNTF2L confers drought tolerance in alfalfa via modulation of leaf water loss (by regulating both stomata and wax deposition), antioxidant defense, and photosynthesis.

Genome-wide identification and expression analysis of the cucumber PP2C gene family

Background

Type 2C protein phosphatase (PP2C) is a negative regulator of ABA signaling pathway, which plays important roles in stress signal transduction in plants. However, little research on the PP2C genes family of cucumber (Cucumis sativus L.), as an important economic vegetable, has been conducted.

Results

This study conducted a genome-wide investigation of the CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results reveal that CsPP2C family genes showed different expression patterns under ABA, drought, salt, and cold treatment, and that CsPP2C3, 11–17, 23, 45, 54 and 55 responded significantly to the four stresses. By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements and drought response elements. Additionally, the expression patterns of CsPP2C genes were specific in different tissues.

Conclusions

The results of this study provide a reference for the genome-wide identification of the PP2C gene family in other species and provide a basis for future studies on the function of PP2C genes in cucumber.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08734-y.

OsMLP423 Is a Positive Regulator of Tolerance to Drought and Salt Stresses in Rice

Rice (Oryza sativa L.) is one of the main food crops for human survival, and its yield is often restricted by abiotic stresses. Drought and soil salinity are among the most damaging abiotic stresses affecting today’s agriculture. Given the importance of abscisic acid (ABA) in plant growth and abiotic stress responses, it is very important to identify new genes involved in ABA signal transduction. We screened a drought-inducing gene containing about 158 amino acid residues from the transcriptome library of rice exposed to drought treatment, and we found ABA-related cis-acting elements and multiple drought-stress-related cis-acting elements in its promoter sequence. The results of real-time PCR showed that OsMLP423 was strongly induced by drought and salt stresses. The physiological and biochemical phenotype analysis of transgenic plants confirmed that overexpression of OsMLP423 enhanced the tolerance to drought and salt stresses in rice. The expression of OsMLP423-GFP fusion protein indicated that OsMLP423 was located in both the cell membrane system and nucleus. Compared with the wild type, the overexpressed OsMLP423 showed enhanced sensitivity to ABA. Physiological analyses showed that the overexpression of OsMLP423 may regulate the water loss efficiency and ABA-responsive gene expression of rice plants under drought and salt stresses, and it reduces membrane damage and the accumulation of reactive oxygen species. These results indicate that OsMLP423 is a positive regulator of drought and salinity tolerance in rice, governing the tolerance of rice to abiotic stresses through an ABA-dependent pathway. Therefore, this study provides a new insight into the physiological and molecular mechanisms of OsMLP423-mediated ABA signal transduction participating in drought and salt stresses.

Physiological Responses to Drought, Salinity, and Heat Stress in Plants: A Review

On the world stage, the increase in temperatures due to global warming is already a reality that has become one of the main challenges faced by the scientific community. Since agriculture is highly dependent on climatic conditions, it may suffer a great impact in the short term if no measures are taken to adapt and mitigate the agricultural system. Plant responses to abiotic stresses have been the subject of research by numerous groups worldwide. Initially, these studies were concentrated on model plants, and, later, they expanded their studies in several economically important crops such as rice, corn, soybeans, coffee, and others. However, agronomic evaluations for the launching of cultivars and the classical genetic improvement process focus, above all, on productivity, historically leaving factors such as tolerance to abiotic stresses in the background. Considering the importance of the impact that abiotic stresses can have on agriculture in the short term, new strategies are currently being sought and adopted in breeding programs to understand the physiological, biochemical, and molecular responses to environmental disturbances in plants of agronomic interest, thus ensuring the world food security. Moreover, integration of these approaches is bringing new insights on breeding. We will discuss how water deficit, high temperatures, and salinity exert effects on plants.

Jasmonic acid biosynthetic genes TgLOX4 and TgLOX5 are involved in daughter bulb development in tulip (Tulipa gesneriana)

The tulip bulbs are modified underground stems which originate from axillary meristems of mother bulb scales. Hormones including jasmonic acids (JAs) play key roles in regulating tulip bulb development. Here, we compared variations of daughter bulb development through transcriptomic profiling analysis and characterized the functions of JA biosynthesis related genes during daughter bulb enlargement. The results showed that tulip varieties exhibited contrasting bulb size variations. Transcriptomic analyses revealed that genes involved in plant hormones and development were significantly changed following tulip bulb growth, including two lipoxygenase genes TgLOX4 and TgLOX5. Ectopic overexpression of TgLOX4 and TgLOX5 in Arabidopsis enhanced endogenous JA content, improved plant growth and increased lateral root numbers. Silencing of these two genes in tulip repressed the growth of daughter bulbs. Furthermore, exogenous JA treatment promoted tulip bulb growth, whereas JA biosynthesis inhibitor sodium diethyldithiocarbamate (DIECA) inhibited this process. This study offers supporting evidence for the involvement of tulip TgLOX4 and TgLOX5 in the regulation of daughter bulb growth and development.

A Comprehensive Evaluation of Salt Tolerance in Tomato (Var. Ailsa Craig): Responses of Physiological and Transcriptional Changes in RBOH's and ABA Biosynthesis and Signalling Genes

Salinity is a ubiquitous stressor, depleting osmotic potential and affecting the tomato seedlings’ development and productivity. Considering this critical concern, we explored the salinity response in tomato seedlings by evaluating them under progressive salt stress duration (0, 3, 6, and 12 days). Intriguingly, besides the adverse effect of salt stress on tomato growth the findings exhibited a significant role of tomato antioxidative system, RBOH genes, ABA biosynthesis, and signaling transcription factor for establishing tolerance to salinity stress. For instance, the activities of enzymatic and non-enzymatic antioxidants continued to incline positively with the increased levels of reactive oxygen species (O₂^•−, H₂O₂), MDA, and cellular damage, suggesting the scavenging capacity of tomato seedlings against salt stress. Notably, the RBOH transcription factors activated the hydrogen peroxide-mediated signalling pathway that induced the detoxification mechanisms in tomato seedlings. Consequently, the increased gene expression of antioxidant enzymes and the corresponding ratio of non-enzymatic antioxidants AsA-GSH suggested the modulation of antioxidants to survive the salt-induced oxidative stress. In addition, the endogenous ABA level was enhanced under salinity stress, indicating higher ABA biosynthesis and signalling gene expression. Subsequently, the upregulated transcript abundance of ABA biosynthesis and signalling-related genes suggested the ABA-mediated capacity of tomato seedlings to regulate homeostasis under salt stress. The current findings have revealed fascinating responses of the tomato to survive the salt stress periods, in order to improve the abiotic stress tolerance in tomato.

AtUSP17 negatively regulates salt stress tolerance through modulation of multiple signaling pathways in Arabidopsis

AtUSP17 is a multiple stress-inducible gene that encodes a universal stress protein (USP) in Arabidopsis thaliana. In the present study, we functionally characterized AtUSP17 using its knock-down mutant, Atusp17, and AtUSP17-overexpression lines (WTOE). The overexpression of AtUSP17 in wild-type and Atusp17 mutant Arabidopsis plants resulted in higher sensitivity to salt stress during seed germination than WT and Atusp17 mutant lines. In addition, the WTOE and FC lines exhibited higher abscisic acid (ABA) sensitivity than Atusp17 mutant during germination. The exogenous application of ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) was able to rescue the salt hypersensitive phenotype of WTOE lines. In contrast, AgNO₃ , an ethylene action inhibitor, further blocked the effect of ACC during germination. The addition of ACC under salt stress resulted in reduced reactive oxygen species (ROS) accumulation, expression of ABA-responsive genes, improved proline synthesis, increased expression of positive regulators of ethylene signaling and antioxidant defense genes with enhanced antioxidant enzyme activities. The WTOE lines exhibited salt sensitivity even at the adult plant stage, while Atusp17 mutant exhibited higher salt tolerance with higher chlorophyll, relative water content and lower electrolyte leakage as compared with WT. The BAR interaction viewer database and available literature mining identified AtUSP17-interacting proteins, which include RGS1, RACK1C and PRN1 involved in G-protein signaling, which play a crucial role in salt stress responses. Based on the present study and available literature, we proposed a model in which AtUSP17 negatively mediates salt tolerance in Arabidopsis through modulation of ethylene, ABA, ROS, and G-protein signaling and responses.

Integrated physiological and transcriptomic analyses of two warm- and cool-season turfgrass species in response to heat stress

Warm- and cool-season turfgrasses were originated from different locations with contrasting heat tolerance. The molecular mechanisms of heat tolerance have not been extensively studied in turfgrass species. In this study, transcriptomic analysis showed that bermudagrass was more tolerant to heat stress as evidenced by lower contents of H₂O₂, proline and glutathione than those in tall fescue after heat treatment. RNA sequencing analysis revealed that 32.7% and 17.7% more genes were changed in tall fescue than in bermudagrass after 2 and 12h heat treatment, respectively. GO terms of redox were enriched in bermudagrass whereas metabolite transportation ones were over-represented in tall fescue after 2h treatment. Ubiquitin dependent degradation pathways were commonly regulated in both grass species. CdF-box and FaF-box transgenic Arabidopsis exhibited improved tolerance to heat stress. Regulatory elements analysis revealed that four ABA-responsive elements present in CdF-box promoter, indicating CdF-box could be potentially regulated by ABRE binding factors (ABFs). All these findings provide evidences for understanding heat stress response in warm- and cool-season grass species.

Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress

Water dropwort (Liyang Baiqin, Oenanthe javanica (BI.) DC.) is an aquatic perennial plant from the Apiaceae family with abundant protein, dietary fiber, vitamins, and minerals. It usually grows in wet soils and can even grow in water. Here, whole-genome sequencing of O. javanica via HiSeq 2000 sequencing technology was reported for the first time. The genome size was 1.28 Gb, including 42,270 genes, of which 93.92% could be functionally annotated. An online database of the whole-genome sequences of water dropwort, Water dropwortDB, was established to share the results and facilitate further research on O. javanica (database homepage: http://apiaceae.njau.edu.cn/waterdropwortdb ). Water dropwortDB offers whole-genome and transcriptome sequences and a Basic Local Alignment Search Tool. Comparative analysis with other species showed that the evolutionary relationship between O. javanica and Daucus carota was the closest. Twenty-five gene families of O. javanica were found to be expanded, and some genetic factors (such as genes and miRNAs) related to phenotypic and anatomic differentiation in O. javanica under different water conditions were further investigated. Two miRNA and target gene pairs (miR408 and Oja15472, miR171 and Oja47040) were remarkably regulated by water stress. The obtained reference genome of O. javanica provides important information for future work, thus making in-depth genetic breeding and gene editing possible. The present study also provides a foundation for the understanding of the O. javanica response to water stress, including morphological, anatomical, and genetic differentiation.

Arabidopsis MADS-box factor AGL16 is a negative regulator of plant response to salt stress by downregulating salt-responsive genes

Sessile plants constantly experience environmental stresses in nature. They must have evolved effective mechanisms to balance growth with stress response. Here we report the MADS-box transcription factor AGL16 acting as a negative regulator in stress response in Arabidopsis. Loss-of-AGL16 confers resistance to salt stress in seed germination, root elongation and soil-grown plants, while elevated AGL16 expression confers the opposite phenotypes compared with wild-type. However, the sensitivity to abscisic acid (ABA) in seed germination is inversely correlated with AGL16 expression levels. Transcriptomic comparison revealed that the improved salt resistance of agl16 mutants was largely attributed to enhanced expression of stress-responsive transcriptional factors and the genes involved in ABA signalling and ion homeostasis. We further demonstrated that AGL16 directly binds to the CArG motifs in the promoter of HKT1;1, HsfA6a and MYB102 and represses their expression. Genetic analyses with double mutants also support that HsfA6a and MYB102 are target genes of AGL16. Taken together, our results show that AGL16 acts as a negative regulator transcriptionally suppressing key components in the stress response and may play a role in balancing stress response with growth.

Arabidopsis thaliana Ubiquitin-Associated Protein 1 (AtUAP1) Interacts with redundant RING Zinc Finger 1 (AtRZF1) to Negatively Regulate Dehydration Response

Ubiquitination, one of the most frequently occurring post-translational modifications, is essential for regulating diverse cellular processes in plants during abiotic stress. The E3 ubiquitin (Ub) ligase Arabidopsis thaliana really interesting new gene (RING) zinc finger 1 (AtRZF1) mutation is known to enhance drought tolerance in A. thaliana seedlings. To further investigate the function of AtRZF1 in osmotic stress, we isolated Ub-associated protein 1 (AtUAP1) which interacts with AtRZF1 using a yeast two-hybrid system. AtUAP1, a Ub-associated motif containing protein, increased the amount of Ub-conjugated AtRZF1. Moreover, AtUAP1 RNA interference lines were more tolerant to osmotic stress than wild type, whereas AtUAP1-overexpressing (OX) transgenic lines showed sensitive responses, including cotyledon greening, water loss, proline accumulation and changes in stress-related genes expression, indicating that AtUAP1 could negatively regulate dehydration-mediated signaling. In addition, AtUAP1-green fluorescent protein fusion protein was observed in the nuclei of root cells of transgenic seedlings. Genetic studies showed that the AtRZF1 mutation could rescue the sensitive phenotype of AtUAP1-OX lines in response to osmotic stress, suggesting that AtRZF1 was epistatic to AtUAP1 in dehydration signaling. Taken together, our findings describe a new component in the AtRZF1 ubiquitination pathway which controls the dehydration response in A. thaliana.

Combined Abiotic Stresses Repress Defense and Cell Wall Metabolic Genes and Render Plants More Susceptible to Pathogen Infection

Plants are frequently exposed to simultaneous abiotic and biotic stresses, a condition that induces complex responses, negatively affects crop productivity and is becoming more exacerbated with current climate change. In this study, we investigated the effects of individual and combined heat and osmotic stresses on Arabidopsis susceptibility to the biotrophic pathogen Pseudomonas syringae pv. tomato (Pst) and the necrotrophic pathogen Botrytiscinerea (Bc). Our data showed that combined abiotic and biotic stresses caused an enhanced negative impact on plant disease resistance in comparison with individual Pst and Bc infections. Pretreating plants with individual heat or combined osmotic-heat stress strongly reduced the expression of many defense genes including pathogenesis-related proteins (PR-1 and PR-5) and the TN-13 gene encoding the TIR-NBS protein, which are involved in disease resistance towards Pst. We also found that combined osmotic-heat stress caused high plant susceptibility to Bc infection and reduced expression of a number of defense genes, including PLANT DEFENSIN 1.3 (PDF1.3), BOTRYTIS SUSCEPTIBLE 1 (BOS1) and THIONIN 2.2 (THI2.2) genes, which are important for disease resistance towards Bc. The impaired disease resistance against both Pst and Bc under combined abiotic stress is associated with reduced expression of cell wall-related genes. Taken together, our data emphasize that the combination of global warming-associated abiotic stresses such as heat and osmotic stresses makes plants more susceptible to pathogen infection, thus threatening future global food security.

An Update on Crop ABA Receptors

The hormone abscisic acid (ABA) orchestrates the plant stress response and regulates sophisticated metabolic and physiological mechanisms essential for survival in a changing environment. Plant ABA receptors were described more than 10 years ago, and a considerable amount of information is available for the model plant Arabidopsis thaliana. Unfortunately, this knowledge is still very limited in crops that hold the key to feeding a growing population. In this review, we summarize genomic, genetic and structural data obtained in crop ABA receptors. We also provide an update on ABA perception in major food crops, highlighting specific and common features of crop ABA receptors.

Transcriptional variation analysis of Arabidopsis ecotypes in response to drought and salt stresses dissects commonly regulated networks

Salinity and drought conditions commonly result in osmotic and oxidative stresses, while salinity additionally causes ionic stress. In this study, we identified specific genes regulated by osmotic and ionic stresses in five Arabidopsis ecotypes. Shahdara (SHA) and C24 ecotypes were more tolerant to salt and drought stresses at the seedling growth stage, as evidenced by lower water loss rate, lower electrolyte leakage, and higher survival rate when compared to the other three ecotypes under drought and salinity conditions. Transcriptomic analysis revealed that 3700 and 2242 genes were differentially regulated by salt and osmotic stresses, respectively. Totally 78.1% of upregulated and 62.0% of downregulated genes by osmotic stress were also commonly regulated by salt stress. Gene ontology term enrichment analysis showed that auxin indole-3-acetic acid (IAA), abscisic acid, cytokinin, and gibberellic acid pathways were regulated by the osmotic stress, while IAA, jasmonic acid, and ethylene pathways were changed by the ionic stress. The nutrient and water uptake pathways were regulated by both the osmotic and ionic stresses, whereas ion transportation and kinase pathways were modulated by the ionic stress. Additionally, we characterized bHLH61 as a negative regulator in response to salt and drought stresses. This study provided new clues of plant responses to salt and drought stresses.

Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis

Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated under NaCl or polyethylene glycol (PEG) stress. Approximately 30.89 G subreads were generated and 31,195 unigenes were obtained by clustering the same isoforms by the PacBio RSII platform. A total of 15,466 differentially expressed genes (DEGs) were obtained under the two stresses using the Illumina platform. Among them, 9266 and 8390 DEGs were obtained under high concentrations of NaCl and PEG, respectively. In total, 3897 DEGs with the same expression pattern under the two stresses were obtained. The transcriptome expression profiles of I. lactea var. chinensis under NaCl or PEG stress obtained in this study may provide a resource for the same and different response mechanisms against different types of abiotic stress. Furthermore, the stress-related genes found in this study can provide data for future molecular breeding.

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the "protein processing in endoplasmic reticulum" and "plant hormone signal transduction" pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

How Do Novel M-Rootstock (Vitis Spp.) Genotypes Cope with Drought?

Most of the vineyards around the world are in areas characterized by seasonal drought, where water deficits and high temperatures represent severe constraints on the regular grapevine growth cycle. Although grapevines are well adapted to arid and semi-arid environments, water stress can cause physiological changes, from mild to irreversible. Screening of available Vitis spp. genetic diversity for new rootstock breeding programs has been proposed as a way for which new viticulture challenges may be faced. In 2014, novel genotypes (M-rootstocks) were released from the University of Milan. In this work, the behavior of M1, M3 and M4 in response to decreasing water availabilities (80%, 50% and 20% soil water content, SWC) was investigated at the physiological and gene expression levels, evaluating gas exchange, stem water potential and transcript abundances of key genes related to ABA (abscisic acid) biosynthesis (VvZEP, VvNCED1 and VvNCED2) and signaling (VvPP2C4, VvSnRK2.6 and VvABF2), and comparing them to those of cuttings of nine commercial rootstocks widely used in viticulture. M-rootstocks showed a change at physiological levels in severe water-stressed conditions (20% soil water content, SWC), reducing the stomatal conductance and stem water potential, but maintaining high photosynthetic activity. Water use efficiency was high in water-limiting conditions. The transcriptional changes were observed at 50% SWC, with an increment of transcripts of VvNCED1 and VvNCED2 genes. M-rootstocks showed similar behavior to 1103P and 110R rootstocks, two highly tolerant commercial genotypes. These rootstocks adopted a tolerant strategy to face water-stressed conditions.

Overexpression of AtNCED3 gene improved drought tolerance in soybean in greenhouse and field conditions

Water deficit is an important climatic problem that can impair agriculture yield and economy. Genetically modified soybean plants containing the AtNCED3 gene were obtained aiming drought-tolerance improvement. The NCED3 gene encodes a 9-cis-epoxycarotenoid dioxygenase (NCED, EC 1.13.11.51), an important enzyme in abscisic acid biosynthesis. ABA activates the expression of drought-responsive genes, in water-deficit conditions, targeting defense mechanisms and enabling plants to survive under low water availability. Results from greenhouse experiments showed that the transgene AtNCED3 and the endogenous genes GmAREB1, GmPP2C, GmSnRK2 and GmAAO3 presented higher expression under water deficit (WD) in the event 2Ha11 than in WT-plants. No significant correlation was observed between the plant materials and WD conditions for growth parameters; however, gas exchange measurements decreased in the GM event, which also showed 80% higher intrinsic water use when compared to WT plants. In crop season 2015/16, event 2Ha11 showed higher total number of pods, higher number of pods with seeds and yield than WT plants. ABA concentration was also higher in GM plants under WD. These results obtained in field screenings suggest that AtNCED3 soybean plants might outperform under drought, reducing economic and yield losses, thus being a good candidate line to be incorporated in the soybean-breeding program to develop drought-tolerant cultivars.

Role of Cytochrome P450 Enzymes in Plant Stress Response

Cytochrome P450s (CYPs) are the largest enzyme family involved in NADPH- and/or O₂-dependent hydroxylation reactions across all the domains of life. In plants and animals, CYPs play a central role in the detoxification of xenobiotics. In addition to this function, CYPs act as versatile catalysts and play a crucial role in the biosynthesis of secondary metabolites, antioxidants, and phytohormones in higher plants. The molecular and biochemical processes catalyzed by CYPs have been well characterized, however, the relationship between the biochemical process catalyzed by CYPs and its effect on several plant functions was not well established. The advent of next-generation sequencing opened new avenues to unravel the involvement of CYPs in several plant functions such as plant stress response. The expression of several CYP genes are regulated in response to environmental stresses, and they also play a prominent role in the crosstalk between abiotic and biotic stress responses. CYPs have an enormous potential to be used as a candidate for engineering crop species resilient to biotic and abiotic stresses. The objective of this review is to summarize the latest research on the role of CYPs in plant stress response.

Comparative Transcriptome Analysis of Halophyte Zoysia macrostachya in Response to Salinity Stress

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress. In the present study, we compared transcriptome of Z. macrostachya under normal conditions and salt stress (300 mmol/L NaCl, 24 h) aimed to identify transcriptome responses and molecular mechanisms under salt stress in Z. macrostachya. A total of 8703 differently expressed genes (DEGs) were identified, including 4903 up-regulated and 3800 down-regulated ones. Moreover, a series of molecular processes were identified by Gene Ontology (GO) analysis, and these processes were suggested to be closely related to salt tolerance in Z. macrostachya. The identified DEGs concentrated on regulating plant growth via plant hormone signal transduction, maintaining ion homeostasis via salt secretion and osmoregulatory substance accumulation and preventing oxidative damage via increasing the activity of ROS (reactive oxygen species) scavenging system. These changes may be the most important responses of Z. macrostachya under salt stress. Some key genes related to salt stress were identified meanwhile. Collectively, our findings provided valuable insights into the molecular mechanisms and genetic underpinnings of salt tolerance in Z. macrostachya.

Integrating physiological and metabolites analysis to identify ethylene involvement in petal senescence in Tulipa gesneriana

Flower senescence is classified into ethylene-dependent and ethylene-independent manners and determines the flower longevity which is valuable for ornamental plants. However, the manner of petal senescence in tulip is still less defined. In this study, we characterized the physiological indexes in the process of petal senescence, as well as metabolic and ethylene responses in tulip cultivar 'American Dream', and further identified the role of ethylene biosynthesis genes TgACS by transgenic and transient assays. Primary metabolites profiling revealed that sugars, amino acids and organic acids preferentially accumulated in senescent petals. Additionally, senescence-associated genes were identified and significantly up-regulated, coupled with increased ROS contents, rapid water loss and accelerated cell membrane breakdown. Moreover, ethylene production was stimulated as evidenced by increasing in ACS activity and ethylene biosynthesis-related genes expression. Exogenous treatment of cutting flowers with 1-MCP or ethephon resulted in delayed or enhanced petal senescence, respectively. Transient down-regulation of TgACS by VIGS assay in tulip petals delayed senescence, while over-expressed TgACS1 in tobacco promoted leaf senescence. Taken together, this study provides evidences to certify ethylene roles and TgACS functions during flower senescence in tulip.

Major Latex Protein MdMLP423 Negatively Regulates Defense against Fungal Infections in Apple

Major latex proteins (MLPs) play critical roles in plants defense and stress responses. However, the roles of MLPs from apple (Malus × domestica) have not been clearly identified. In this study, we focused on the biological role of MdMLP423, which had been previously characterized as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis indicated that MdMLP423 is a protein with a ‘Gly-rich loop’ (GXGGXG) domain belonging to the Bet v_1 subfamily. Gene expression profiles showed that MdMLP423 is mainly expressed in flowers. In addition, the expression of MdMLP423 was significantly inhibited by Botryosphaeria berengeriana f. sp. piricola (BB) and Alternaria alternata apple pathotype (AAAP) infections. Apple calli overexpressing MdMLP423 had lower expression of resistance-related genes, and were more sensitive to infection with BB and AAAP compared with non-transgenic calli. RNA-seq analysis of MdMLP423-overexpressing calli and non-transgenic calli indicated that MdMLP423 regulated the expression of a number of differentially expressed genes (DEGs) and transcription factors, including genes involved in phytohormone signaling pathways, cell wall reinforcement, and genes encoding the defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein, and ABI3. Taken together, our results demonstrate that MdMLP423 negatively regulates apple resistance to BB and AAAP infections by inhibiting the expression of defense- and stress-related genes and transcription factors.

Genome-wide phylogenetic and structural analysis reveals the molecular evolution of the ABA receptor gene family

The plant hormone abscisic acid (ABA) plays a crucial role during the plant life cycle as well as in adaptive responses to environmental stresses. The core regulatory components of ABA signaling in plants are the pyrabactin resistance1/PYR1-like/regulatory component of ABA receptor family (PYLs), which comprise the largest plant hormone receptor family known. They act as negative regulators of members of the protein phosphatase type 2C family. Due to the biological importance of PYLs, many researchers have focused on their genetic redundancy and consequent functional divergence. However, little is understood of their evolution and its impact on the generation of regulatory diversity. In this study, we identify positive selection and functional divergence in PYLs through phylogenetic reconstruction, gene structure and expression pattern analysis, positive selection analysis, functional divergence analysis, and structure comparison. We found the correlation of desensitization of PYLs under specific modifications in the molecular recognition domain with functional diversification. Hence, an interesting antagonistic co-evolutionary mechanism is proposed for the functional diversification of ABA receptor family proteins. We believe a compensatory evolutionary pathway may have occurred.

Barley ABI5 (Abscisic Acid INSENSITIVE 5) Is Involved in Abscisic Acid-Dependent Drought Response

ABA INSENSITIVE 5 (ABI5) is a basic leucine zipper (bZIP) transcription factor which acts in the abscisic acid (ABA) network and is activated in response to abiotic stresses. However, the precise role of barley (Hordeum vulgare) ABI5 in ABA signaling and its function under stress remains elusive. Here, we show that HvABI5 is involved in ABA-dependent regulation of barley response to drought stress. We identified barley TILLING mutants carrying different alleles in the HvABI5 gene and we studied in detail the physiological and molecular response to drought and ABA for one of them. The hvabi5.d mutant, carrying G1751A transition, was insensitive to ABA during seed germination, yet it showed the ability to store more water than its parent cv. "Sebastian" (WT) in response to drought stress. The drought-tolerant phenotype of hvabi5.d was associated with better membrane protection, higher flavonoid content, and faster stomatal closure in the mutant under stress compared to the WT. The microarray transcriptome analysis revealed up-regulation of genes associated with cell protection mechanisms in the mutant. Furthermore, HvABI5 target genes: HVA1 and HVA22 showed higher activity after drought, which may imply better adaptation of hvabi5.d to stress. On the other hand, chlorophyll content in hvabi5.d was lower than in WT, which was associated with decreased photosynthesis efficiency observed in the mutant after drought treatment. To verify that HvABI5 acts in the ABA-dependent manner we analyzed expression of selected genes related to ABA pathway in hvabi5.d and its WT parent after drought and ABA treatments. The expression of key genes involved in ABA metabolism and signaling differed in the mutant and the WT under stress. Drought-induced increase of expression of HvNCED1, HvBG8, HvSnRK2.1, and HvPP2C4 genes was 2-20 times higher in hvabi5.d compared to "Sebastian". We also observed a faster stomatal closure in hvabi5.d and much higher induction of HvNCED1 and HvSnRK2.1 genes after ABA treatment. Together, these findings demonstrate that HvABI5 plays a role in regulation of drought response in barley and suggest that HvABI5 might be engaged in the fine tuning of ABA signaling by a feedback regulation between biosynthetic and signaling events. In addition, they point to different mechanisms of HvABI5 action in regulating drought response and seed germination in barley.

Bacillus amyloliquefaciens MBI600 differentially induces tomato defense signaling pathways depending on plant part and dose of application

The success of Bacillus amyloliquefaciens as a biological control agent relies on its ability to outgrow plant pathogens. It is also thought to interact with its plant host by inducing systemic resistance. In this study, the ability of B. amyloliquefaciens MBI600 to elicit defense (or other) responses in tomato seedlings and plants was assessed upon the expression of marker genes and transcriptomic analysis. Spray application of Serifel, a commercial formulation of MBI600, induced responses in a dose-dependent manner. Low dosage primed plant defense by activation of SA-responsive genes. Suggested dosage induced defense by mediating synergistic cross-talk between JA/ET and SA-signaling. Saturation of tomato roots or leaves with MBI600 elicitors activated JA/ET signaling at the expense of SA-mediated responses. The complex signaling network that is implicated in MBI600-tomato seedling interactions was mapped. MBI600 and flg22 (a bacterial flagellin peptide) elicitors induced, in a similar manner, biotic and abiotic stress responses by the coordinated activation of genes involved in JA/ET biosynthesis as well as hormone and redox signaling. This is the first study to suggest the activation of plant defense following the application of a commercial microbial formulation under conditions of greenhouse crop production.

Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare

Crassulacean acid metabolism (CAM) has evolved as a water-saving strategy, and its engineering into crops offers an opportunity to improve their water use efficiency. This requires a comprehensive understanding of the regulation of the CAM pathway. Here, we use the facultative CAM species Talinum triangulare as a model in which CAM can be induced rapidly by exogenous abscisic acid. RNA sequencing and metabolite measurements were employed to analyse the changes underlying CAM induction and identify potential CAM regulators. Non-negative matrix factorization followed by k-means clustering identified an early CAM-specific cluster and a late one, which was specific for the early light phase. Enrichment analysis revealed abscisic acid metabolism, WRKY-regulated transcription, sugar and nutrient transport, and protein degradation in these clusters. Activation of the CAM pathway was supported by up-regulation of phosphoenolpyruvate carboxylase, cytosolic and chloroplastic malic enzymes, and several transport proteins, as well as by increased end-of-night titratable acidity and malate accumulation. The transcription factors HSFA2, NF-YA9, and JMJ27 were identified as candidate regulators of CAM induction. With this study we promote the model species T. triangulare, in which CAM can be induced in a controlled way, enabling further deciphering of CAM regulation.

Selection of appropriate reference genes for RT-qPCR analysis under abiotic stress and hormone treatment in celery

Celery is one of the most important vegetable crop and its yield and quality is influenced by many environmental factors. Researches on gene expression not only help to unravel the molecular regulatory mechanism but also identify the key genes in the biological response. RT-qPCR is a commonly used technology to quantify the gene expression. Selecting an appropriate reference gene is an effective approach to improve the accuracy of RT-qPCR assay. To our knowledge, the evaluation of reference genes under different treatments in celery has not been reported yet. In this study, the expression stabilities of eight candidate reference genes (ACTIN, eIF-4α , GAPDH, TBP, TUB-A, UBC, TUB-B, and EF-1α ) under abiotic stresses (heat, cold, drought, and salt) and hormone treatments (SA, MeJA, GA, and ABA) were detected. The expression stabilities of candidate genes were compared and ranked by geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder programs. The results calculated by different programs were not completely consistent. Considering the comprehensive analysis results, ACTIN was the most stable reference gene and TUB-B showed the worst expression stabilities under the selected abiotic stress and hormone treatments in celery. The reliability of reference genes was further confirmed by the normalization of CAT1 gene under drought stress. This study presented evidences and basis to select the appropriate reference genes under different treatments in celery.

Transcript and metabolic adjustments triggered by drought in Ilex paraguariensis leaves

Abscisic acid is involved in the drought response of Ilex paraguariensis. Acclimation includes root growth stimulation, stomatal closure, osmotic adjustment, photoprotection, and regulation of nonstructural carbohydrates and amino acid metabolisms. Ilex paraguariensis (yerba mate) is cultivated in the subtropical region of South America, where the occurrence of drought episodes limit yield. To explore the mechanisms that allow I. paraguariensis to overcome dehydration, we investigated (1) how gene expression varied between water-stressed and non-stressed plants and (2) in what way the modulation of gene expression was linked to physiological status and metabolite composition. A total of 4920 differentially expressed transcripts were obtained through RNA-Seq after water deprivation. Drought induced the expression of several transcripts involved in the ABA-signalling pathway. Stomatal closure and leaf osmotic adjustments were promoted to minimize water loss, and these responses were accompanied by a high transcriptional remodeling of stress perception, signalling and transcriptional regulation, the photoprotective and antioxidant systems, and other stress-responsive genes. Simultaneously, significant changes in metabolite contents were detected. Glutamine, phenylalanine, isomaltose, fucose, and malate levels were shown to be positively correlated with dehydration. Principal component analysis showed differences in the metabolic profiles of control and stressed leaves. These results provide a comprehensive overview of how I. paraguariensis responds to dehydration at transcriptional and metabolomic levels and provide further characterization of the molecular mechanisms associated with drought response in perennial subtropical species.

Genome-wide identification and characterization of ABA receptor PYL/RCAR gene family reveals evolution and roles in drought stress in Nicotiana tabacum

BACKGROUND

Abscisic acid (ABA) is an important phytohormone for plant growth, development and responding to stresses such as drought, salinity, and pathogen infection. Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component of ABA Receptor (RCAR) (hereafter referred to as PYLs) has been identified as the ABA receptors. The PYL family members have been well studied in many plants. However, the members of PYL family have not been systematically identified at genome level in cultivated tobacco (Nicotiana tabacum) and its two ancestors. In this study, the phylogenic relationships, chromosomal distribution, gene structures, conserved motifs/regions, and expression profiles of NtPYLs were analyzed.

RESULTS

We identified 29, 11, 16 PYLs in the genomes of allotetraploid N. tabacum, and its two diploid ancestors N. tomentosiformis and N. sylvestris, respectively. The phylogenetic analysis revealed that NtPYLs can be divided into three subfamilies, and each NtPYL has one counterpart in N. sylvestris or N. tomentosiformis. Based on microarray analysis of NtPYL transcripts, four NtPYLs (from subfamily II, III), and five NtPYLs (from subfamily I) are highlighted as potential candidates for further functional characterization in N. tabacum seed development, response to ABA, and germination, and resistance to abiotic stresses, respectively. Interestingly, the expression profiles of members in the same NtPYL subfamily showed somehow similar patterns in tissues at different developmental stages and in leaves of seedlings under drought stress, suggesting particular NtPYLs might have multiple functions in both plant development and drought stress response.

CONCLUSIONS

NtPYLs are highlighted for important functions in seed development, germination and response to ABA, and particular in drought tolerance. This work will not only shed light on the PYL family in tobacco, but also provides some valuable information for functional characterization of ABA receptors in N. tabacum.

Populus trichocarpa clade A PP2C protein phosphatases: their stress-induced expression patterns, interactions in core abscisic acid signaling, and potential for regulation of growth and development

Overexpression of the poplar PP2C protein phosphatase gene PtrHAB2 resulted in increased tree height and altered leaf morphology and phyllotaxy, implicating PP2C phosphatases as growth regulators functioning under favorable conditions. We identified and studied Populus trichocarpa genes, PtrHAB1 through PtrHAB15, belonging to the clade A PP2C family of protein phosphatases known to regulate abscisic acid (ABA) signaling. PtrHAB1 through PtrHAB3 and PtrHAB12 through PtrHAB15 were the most highly expressed genes under non-stress conditions. The poplar PP2C genes were differentially regulated by drought treatments. Expression of PtrHAB1 through PtrHAB3 was unchanged or downregulated in response to drought, while all other PtrHAB genes were weakly to strongly upregulated in response to drought stress treatments. Yeast two-hybrid assays involving seven ABA receptor proteins (PtrRCAR) against 12 PtrHAB proteins detected 51 interactions involving eight PP2Cs and all PtrRCAR proteins with 22 interactions requiring the addition of ABA. PtrHAB2, PtrHAB12, PtrHAB13 and PtrHAB14 also interacted with the sucrose non-fermenting related kinase 2 proteins PtrSnRK2.10 and PtrSnRK2.11, supporting conservation of a SnRK2 signaling cascade regulated by PP2C in poplar. Additionally, PtrHAB2, PtrHAB12, PtrHAB13 and PtrHAB14 interacted with the mitogen-activated protein kinase protein PtrMPK7. Due to its interactions with PtrSnRK2 and PtrMPK7 proteins, and its reduced expression during drought stress, PtrHAB2 was overexpressed in poplar to test its potential as a growth regulator under non-stress conditions. 35S::PtrHAB2 transgenics exhibited increased growth rate for a majority of transgenic events and alterations in leaf phyllotaxy and morphology. These results indicate that PP2Cs have additional roles which extend beyond canonical ABA signaling, possibly coordinating plant growth and development in response to environmental conditions.

Comparative physiological and metabolomic analyses reveal natural variations of tulip in response to storage temperatures

Three tulip cultivars were screened out with successful bloom after a short-term cold treatment, and the differential responses to postharvest cold treatment were analyzed between two contrasting tulip cultivars. Tulip is one of the most important ornamental bulbous plants in the world. A precious precooling treatment during bulb postharvest is required for optimal floral stalk elongation and flower development in tulip. In this study, the naturally growing and flowering variations of tulip to storage temperatures were analyzed after long-term cold (LTC) and short-term cold (STC) treatments. Three cultivars were screened out with successful blooming after STC, which included 'Dow Jones' (DJ), 'Van Eijk' (VE) and 'World's Favourite' (WF) (5 °C for 2 weeks). Comparative analysis revealed that DJ cultivar maintained normal and intact reproductive organs under STC condition, while the 'Orange Emperor' (OE) cultivar, which failed blooming after STC treatment, showed gradually destroyed reproductive organs under STC condition. In addition, the DJ cultivar accumulated lower ROS levels and higher antioxidant enzyme activities, as well as significantly higher contents of total primary metabolites than OE to maintain normal shoot growth and floral organ development under STC condition. The relative expression levels of genes involved in vernalization and/or flower time regulation in DJ were significantly higher than those in OE after STC treatment. This study provides new insights into understanding the underlying mechanism of natural variation of tulip cultivars during postharvest storage treatment.

Genome-wide identification, evolution, and molecular characterization of the PP2C gene family in woodland strawberry

The protein phosphatase 2C (PP2C) gene family is one of the momentous and conserved plant-specific gene families, known to participate in cellular processes via reversible protein phosphorylation and regulates signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and maize, however, the whole-genome analysis of PP2C in strawberry has not yet been reported. In the current research, we found 62 PP2C-encoding genes in total from the strawberry genome. Further, the phylogenetic analysis categorized FvPP2C genes into twelve subgroups with significant structural conservation based on conserved domain and amino acid sequence. Moreover, we observed a strong signature of purifying selection between the comparison of orthologous gene pairs of strawberry and Arabidopsis. The comparison of RNA-sequence (RNA-seq) data published on various vegetative and reproductive tissues of strawberry plant suggested the significant role of FvPP2C genes in organ development. The qRT-PCR validation of thirty FvPP2C genes indicated their critical tolerance-related role under abiotic stress stimuli in strawberry. Finally, the subcellular localization of FvPP2C51 gene proves that it resides and stimulates its function in the nucleus. Our findings provide an overview of the identification of strawberry FvPP2C gene family and demonstrate their critical role in tissue-specific response and abiotic stress-tolerance, thereby, intimating their significance in the strawberry molecular breeding for the resistant cultivars.

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.

Comparative Transcriptomic and Physiological Analyses of Medicago sativa L. Indicates that Multiple Regulatory Networks Are Activated during Continuous ABA Treatment

Alfalfa is the most extensively cultivated forage legume worldwide. However, the molecular mechanisms underlying alfalfa responses to exogenous abscisic acid (ABA) are still unknown. In this study, the first global transcriptome profiles of alfalfa roots under ABA treatments for 1, 3 and 12 h (three biological replicates for each time point, including the control group) were constructed using a BGISEQ-500 sequencing platform. A total of 50,742 isoforms with a mean length of 2541 bp were generated, and 4944 differentially expressed isoforms (DEIs) were identified after ABA deposition. Metabolic analyses revealed that these DEIs were involved in plant hormone signal transduction, transcriptional regulation, antioxidative defense and pathogen immunity. Notably, several well characterized hormone signaling pathways, for example, the core ABA signaling pathway, was activated, while salicylic acid, jasmonate and ethylene signaling pathways were mainly suppressed by exogenous ABA. Moreover, the physiological work showed that catalase and peroxidase activity and glutathione and proline content were increased after ABA deposition, which is in accordance with the dynamic transcript profiles of the relevant genes in antioxidative defense system. These results indicate that ABA has the potential to improve abiotic stress tolerance, but that it may negatively regulate pathogen resistance in alfalfa.

Comparative Proteomic and Physiological Analyses of Two Divergent Maize Inbred Lines Provide More Insights into Drought-Stress Tolerance Mechanisms

Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought stress tolerance based on their physiological and proteomic responses at the seedling stage. Our observations showed that divergent stress tolerance mechanisms exist between the two inbred-lines at physiological and proteomic levels, with YE8112 being comparatively more tolerant than MO17 owing to its maintenance of higher relative leaf water and proline contents, greater increase in peroxidase (POD) activity, along with decreased level of lipid peroxidation under stressed conditions. Using an iTRAQ (isobaric tags for relative and absolute quantification)-based method, we identified a total of 721 differentially abundant proteins (DAPs). Amongst these, we fished out five essential sets of drought responsive DAPs, including 13 DAPs specific to YE8112, 107 specific DAPs shared between drought-sensitive and drought-tolerant lines after drought treatment (SD_TD), three DAPs of YE8112 also regulated in SD_TD, 84 DAPs unique to MO17, and five overlapping DAPs between the two inbred lines. The most significantly enriched DAPs in YE8112 were associated with the photosynthesis antenna proteins pathway, whilst those in MO17 were related to C5-branched dibasic acid metabolism and RNA transport pathways. The changes in protein abundance were consistent with the observed physiological characterizations of the two inbred lines. Further, quantitative real-time polymerase chain reaction (qRT-PCR) analysis results confirmed the iTRAQ sequencing data. The higher drought tolerance of YE8112 was attributed to: activation of photosynthesis proteins involved in balancing light capture and utilization; enhanced lipid-metabolism; development of abiotic and biotic cross-tolerance mechanisms; increased cellular detoxification capacity; activation of chaperones that stabilize other proteins against drought-induced denaturation; and reduced synthesis of redundant proteins to help save energy to battle drought stress. These findings provide further insights into the molecular signatures underpinning maize drought stress tolerance.