Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize

Drought stress in maize: stress perception to molecular response and strategies for its improvement

Given the future demand for food crops, increasing crop productivity in drought-prone rainfed areas has become essential. Drought-tolerant varieties are warranted to solve this problem in major crops, with drought tolerance as a high-priority trait for future research. Maize is one such crop affected by drought stress, which limits production, resulting in substantial economic losses. It became a more serious issue due to global climate change. The most drought sensitive among all stages of maize is the reproductive stages and the most important for overall maize production. The exact molecular basis of reproductive drought sensitivity remains unclear due to genes' complex regulation of drought stress. Understanding the molecular biology and signaling of the unexplored area of reproductive drought tolerance will provide an opportunity to develop climate-smart drought-tolerant next-generation maize cultivars. In recent decades, significant progress has been made in maize to understand the drought tolerance mechanism. However, improving maize drought tolerance through breeding is ineffective due to the complex nature and multigenic control of drought traits. With the help of advanced breeding techniques, molecular genetics, and a precision genome editing approach like CRISPR-Cas, candidate genes for drought-tolerant maize can be identified and targeted. This review summarizes the effects of drought stress on each growth stage of maize, potential genes, and transcription factors that determine drought tolerance. In addition, we discussed drought stress sensing, its molecular mechanisms, different approaches to developing drought-resistant maize varieties, and how molecular breeding and genome editing will help with the current unpredictable climate change.

Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa

Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.

Maize Transcription Factor ZmHsf28 Positively Regulates Plant Drought Tolerance

Identification of central genes governing plant drought tolerance is fundamental to molecular breeding and crop improvement. Here, maize transcription factor ZmHsf28 is identified as a positive regulator of plant drought responses. ZmHsf28 exhibited inducible gene expression in response to drought and other abiotic stresses. Overexpression of ZmHsf28 diminished drought effects in Arabidopsis and maize. Gene silencing of ZmHsf28 via the technology of virus-induced gene silencing (VIGS) impaired maize drought tolerance. Overexpression of ZmHsf28 increased jasmonate (JA) and abscisic acid (ABA) production in transgenic maize and Arabidopsis by more than two times compared to wild-type plants under drought conditions, while it decreased reactive oxygen species (ROS) accumulation and elevated stomatal sensitivity significantly. Transcriptomic analysis revealed extensive gene regulation by ZmHsf28 with upregulation of JA and ABA biosynthesis genes, ROS scavenging genes, and other drought related genes. ABA treatment promoted ZmHsf28 regulation of downstream target genes. Specifically, electrophoretic mobility shift assays (EMSA) and yeast one-hybrid (Y1H) assay indicated that ZmHsf28 directly bound to the target gene promoters to regulate their gene expression. Taken together, our work provided new and solid evidence that ZmHsf28 improves drought tolerance both in the monocot maize and the dicot Arabidopsis through the implication of JA and ABA signaling and other signaling pathways, shedding light on molecular breeding for drought tolerance in maize and other crops.

Drought-Induced Responses in Maize under Different Vapor Pressure Deficit Conditions

Water stress in plants depends on the soil water level and the evaporative demand. In this study, the physiological, biochemical, and molecular response of maize were examined under three evaporative demand conditions (low—1.00 kPa, medium—2.2 kPa, and high—4.00 kPa Vapor pressure deficit (VPD)) at three different soil water content (SWC); well-watered, 45%, and 35% SWC. Plants grown at 35% SWC under high VPD had significant (p < 0.01) lower leaf weight, leaf area, and leaf number than low VPD. Plants under low, medium, and high VPD with drought stress (45% and 35% SWC) showed a 30 to 60% reduction in their leaf area compared to well-watered plants. Gas exchange parameters including photosynthesis, stomatal conductance, and water use efficiency exhibited significant differences (p < 0.01) between treatments, with the highest reduction occuring at 35% SWC and high VPD. Both drought and VPD significantly (p < 0.01) increased C4 enzyme levels and some transcription factors with increased stress levels. Transcription factors primarily related to Abssisic Acid (ABA) synthesis were upregulated under drought, which might be related to high ABA levels. In summary, severe drought levels coupled with high VPD had shown a significant decrease in plant development by modifying enzymes, ABA, and transcription factors.

Reference quality genome sequence of Indian pomegranate cv. 'Bhagawa' (Punica granatum L.)

Pomegranate is an important fruit crop for ensuring livelihood and nutrition security in fragile semi-arid regions of the globe having limited irrigation resources. This is a high-value, nutritionally rich, and export-oriented agri-commodity that ensures high returns on investment to growers across the world. Although it is a valuable fruit crop, it has received only a limited genomics research outcome. To fast-track the pomegranate improvement program, de novo whole-genome sequencing of the main Indian cultivar 'Bhagawa' was initiated by the Indian Council of Agricultural Research-National Research Center on Pomegranate (ICAR-NRCP). We have demonstrated that a combination of commercially available technologies from Illumina, PacBio, 10X Genomics, and BioNano Genomics could be used efficiently for sequencing and reference-grade de novo assembly of the pomegranate genome. The research led to a final reference-quality genome assembly for 'Bhagawa' of 346.08 Mb in 342 scaffolds and an average N50 of 16.12 Mb and N90 of 1088.62 Kb. This assembly covered more than 98% of the estimated pomegranate genome size, 352.54 Mb. The LTR assembly index (LAI) value of 10 and 93.68% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score over the 1,440 ortholog genes of the completed pomegranate genome indicates the quality of the assembled pomegranate genome. Furthermore, 29,435 gene models were discovered with a mean transcript length of 2,954 bp and a mean coding sequence length 1,090 bp. Four transcript data samples of pomegranate tissues were mapped over the assembled 'Bhagawa' genome up to 95% significant matches, indicating the high quality of the assembled genome. We have compared the 'Bhagawa' genome with the genomes of the pomegranate cultivars 'Dabenzi' and 'Taishanhong.' We have also performed whole-genome phylogenetic analysis using Computational Analysis of Gene Family Evolution (CAFE) and found that Eucalyptus grandis and pomegranate diverged 64 (60-70) million years ago. About 1,573 protein-coding resistance genes identified in the 'Bhagawa' genome were classified into 32 domains. In all, 314 copies of miRNA belonging to 26 different families were identified in the 'Bhagawa' genome. The reference-quality genome assembly of 'Bhagawa' is certainly a significant genomic resource for accelerated pomegranate improvement.

Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance

Globally, sodicity is one of the major abiotic stresses limiting the wheat productivity in arid and semi-arid regions. With due consideration, an investigation of the complex gene network associated with sodicity stress tolerance is required to identify transcriptional changes in plants during abiotic stress conditions. For this purpose, we sequenced the flag leaf transcriptome of a highly tolerant bread wheat germplasm (KRL 3-4) in order to extend our knowledge and better understanding of the molecular basis of sodicity tolerance. A total of 1,980 genes were differentially expressed in the flag leaf due to sodicity stress. Among these genes, 872 DEGs were upregulated and 1,108 were downregulated. Furthermore, annotation of DEGs revealed that a total of 1,384 genes were assigned to 2,267 GO terms corresponding to 502 (biological process), 638 (cellular component), and 1,127 (molecular function). GO annotation also revealed the involvement of genes related to several transcription factors; the important ones are expansins, peroxidase, glutathione-S-transferase, and metal ion transporters in response to sodicity. Additionally, from 127 KEGG pathways, only 40 were confidently enriched at a p-value <0.05 covering the five main KEGG categories of metabolism, i.e., environmental information processing, genetic information processing, organismal systems, and cellular processes. Most enriched pathways were prioritized using MapMan software and revealed that lipid metabolism, nutrient uptake, and protein homeostasis were paramount. We have also found 39 SNPs that mapped to the important sodicity stress-responsive genes associated with various pathways such as ROS scavenging, serine/threonine protein kinase, calcium signaling, and metal ion transporters. In a nutshell, only 19 important candidate genes contributing to sodicity tolerance in bread wheat were identified, and these genes might be helpful for better understanding and further improvement of sodicity tolerance in bread wheat.

Physiological and Transcriptome Indicators of Salt Tolerance in Wild and Cultivated Barley

Barley is used as a model cereal to decipher salt tolerance mechanisms due to its simpler genome than wheat and enhanced salt tolerance compared to rice and wheat. In the present study, RNA-Seq based transcriptomic profiles were compared between salt-tolerant wild (Hordeum spontaneum, genotype no. 395) genotype and salt-sensitive cultivated (H. vulgare, 'Mona' cultivar) subjected to salt stress (300 mM NaCl) and control (0 mM NaCl) conditions. Plant growth and physiological attributes were also evaluated in a separate experiment as a comparison. Wild barley was significantly less impacted by salt stress than cultivated barley in growth and physiology and hence was more stress-responsive functionally. A total of 6,048 differentially expressed genes (DEGs) including 3,025 up-regulated and 3,023 down-regulated DEGs were detected in the wild genotype in salt stress conditions. The transcripts of salt-stress-related genes were profoundly lower in the salt-sensitive than the tolerant barley having a total of 2,610 DEGs (580 up- and 2,030 down-regulated). GO enrichment analysis showed that the DEGs were mainly enriched in biological processes associated with stress defenses (e.g., cellular component, signaling network, ion transporter, regulatory proteins, reactive oxygen species (ROS) scavenging, hormone biosynthesis, osmotic homeostasis). Comparison of the candidate genes in the two genotypes showed that the tolerant genotype contains higher functional and effective salt-tolerance related genes with a higher level of transcripts than the sensitive one. In conclusion, the tolerant genotype consistently exhibited better tolerance to salt stress in physiological and functional attributes than did the sensitive one. These differences provide a comprehensive understanding of the evolved salt-tolerance mechanism in wild barley. The shared mechanisms between these two sub-species revealed at each functional level will provide more reliable insights into the basic mechanisms of salt tolerance in barley species.

Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L

Capsicum annuum L. is one of the most cultivated Solanaceae species, and in the open field, water limitation leading to drought stress affects its fruit quality, fruit setting, fruit size and ultimately yield. We identified stage-specific and a common core set of differentially expressed genes, following RNA-seq transcriptome analyses of a breeding line subjected to acute drought stress followed by recovery (rewatering), at three stages of plant development. Among them, two NAC transcription factor (TF) genes, i.e., CaNAC072 and CaNAC104, were always upregulated after drought stress and downregulated after recovery. The two TF proteins were observed to be localized in the nucleus following their transient expression in Nicotiana benthamiana leaves. The expression of the two NACs was also induced by NaCl, polyethylene glycol (PEG) and abscisic acid (ABA) treatments, suggesting that CaNAC072 is an early, while CaNAC104 is a late abiotic stress-responsive gene. Virus-induced gene silencing (VIGS) of CaNAC104 did not affect the pepper plantlet’s tolerance to drought stress, while VIGS of CaNAC072 increased drought tolerance. Heterologous expression of CaNAC072 in Arabidopsis thaliana as well as in plants mutated for its homolog ANAC072 did not increase drought stress tolerance. This highlights a different role of the two NAC homologs in the two species. Here, we discuss the complex role of NACs as transcriptional switches in the response to drought stress in bell pepper.

The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance

Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.

Comparative transcriptomic and physiological analyses of contrasting hybrid cultivars ND476 and ZX978 identify important differentially expressed genes and pathways regulating drought stress tolerance in maize

BACKGROUND

Drought is the major abiotic stress factor that negatively influences growth and yield in cereal grain crops such as maize (Zea mays L.). A multitude of genes and pathways tightly modulate plant growth, development and responses to environmental stresses including drought. Therefore, crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought responses.

OBJECTIVE

Here, we sought to elucidate the molecular and physiological mechanisms underpinning maize drought stress tolerance.

METHODS

We therefore applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at the late vegetative (V12) growth stage and performed a large-scale RNA sequencing (RNA-seq) transcriptome analysis of the leaf tissues.

RESULTS

A comparative analysis of the two genotypes leaf transcriptomes and physiological parameters revealed the key differentially expressed genes (DEGs) and metabolic pathways that respond to drought in a genotype-specific manner. A total of 3114 DEGs were identified, with 21 DEGs being specifically expressed in tolerant genotype ND476 in response to drought stress. Of these, genes involved in secondary metabolites biosynthesis, transcription factor regulation, detoxification and stress defense were highly expressed in ND476. Physiological analysis results substantiated our RNA-seq data, with ND476 exhibiting better cell water retention, higher soluble protein content and guaiacol peroxidase activity, along with low lipid peroxidation extent than the sensitive cultivar ZX978 under drought conditions.

CONCLUSION

Our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Additionally, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.

Overexpression of Arabidopsis aspartic protease APA1 gene confers drought tolerance

Drought is an environmental stress that severely affects plant growth and crop production. Different studies have focused on drought responses but the molecular bases that regulate these mechanisms are still unclear. We report the participation of Aspartic Protease (APA1) in drought tolerance. Overexpressing APA1 Arabidopsis plants (OE-APA1), showed a phenotype more tolerant to drought compared with WT. On the contrary, apa1 insertional lines were more sensitive to this stress compared to WT plants. Morphological and physiological differences related with the water loss were observed between leaves of OE- APA1 and WT plants. OE-APA1 leaves showed lower stomata index and stomata density as well as a smaller of the stomatic aperture compared to WT plants. qPCR analysis in OE-APA1 leaves, showed higher expression levels of genes related to ABA signaling and synthesis. Analysis of plant lines expressing APA1 promoter fused to GUS showed that APA1 is expressed in epidermal and stomata cells. In summary, this work suggests that APA1 is involved in ABA-dependent response that its overexpression confers drought tolerance in Arabidopsis.

Physiological, biochemical and gene-expressional responses to water deficit in apple subjected to partial root-zone drying (PRD)

Water scarcity is one of the major factors limiting apple production. Partial root-zone drying (PRD) is a water-saving irrigation technique necessary to improve the efficiency of irrigation techniques to optimize the amount of fruit produced with the volume of water used. The apple trees cv. Red Delicious were exposed to four treatments, including (1) control with 100% of the crop evapotranspiration (ETc) needs; (2) alternate partial root-zone drying with 75% of the ETc needs (APRD75); (3) fixed partial root-zone drying with 75% of the ETc needs (FPRD75); (4) fixed partial root-zone irrigation with 50% of the ETc needs (FPRD50) in a semiarid region of Iran. Results showed that leaf water potential (Ψ _leaf), and chlorophyll were significantly decreased in FPRD50 compared to control and other PRD treatments. APRD75 and FPRD75 treatments significantly enhanced (+) -catechin (+C), epicatechin (EC), chlorogenic acid (CGA), caffeic acid (CA) as well as increased water use efficiency (WUE) (by 30-40% compared to control) without significant reduction of yield. PRD reduced gibberellic acid (GA3) and kinetin, while, increased the abscisic acid (ABA) and salicylic acid (SA) levels. The abiotic stress-responsive transcription factors (TFs) MdoMYB121, MdoMYB155, MdbZIP2, and MdbZIP48 were highly expressed in all PRD treatments. Our results demonstrated that APRD75 and FPRD75 have the potential to stimulate antioxidant defense mechanisms, hormonal signaling pathways, and expression of drought-tolerance TFs to improve WUE while maintaining crop yield. Therefore, APRD75andFPRD75 with water savings as compared to full irrigation might be a suitable strategy for irrigation apple trees under water scarcity.

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.