Transcriptome Analysis of Tolerant and Susceptible Maize Genotypes Reveals Novel Insights about the Molecular Mechanisms Underlying Drought Responses in Leaves

Smart agriculture: utilizing machine learning and deep learning for drought stress identification in crops

Plant stress reduction research has advanced significantly with the use of Artificial Intelligence (AI) techniques, such as machine learning and deep learning. This is a significant step toward sustainable agriculture. Innovative insights into the physiological responses of plants mostly crops to drought stress have been revealed through the use of complex algorithms like gradient boosting, support vector machines (SVM), recurrent neural network (RNN), and long short-term memory (LSTM), combined with a thorough examination of the TYRKC and RBR-E3 domains in stress-associated signaling proteins across a range of crop species. Modern resources were used in this study, including the UniProt protein database for crop physiochemical properties associated with specific signaling domains and the SMART database for signaling protein domains. These insights were then applied to deep learning and machine learning techniques after careful data processing. The rigorous metric evaluations and ablation analysis that typified the study's approach highlighted the algorithms' effectiveness and dependability in recognizing and classifying stress events. Notably, the accuracy of SVM was 82%, while gradient boosting and RNN showed 96%, and 94%, respectively and LSTM obtained an astounding 97% accuracy. The study observed these successes but also highlights the ongoing obstacles to AI adoption in agriculture, emphasizing the need for creative thinking and interdisciplinary cooperation. In addition to its scholarly value, the collected data has significant implications for improving resource efficiency, directing precision agricultural methods, and supporting global food security programs. Notably, the gradient boosting and LSTM algorithm outperformed the others with an exceptional accuracy of 96% and 97%, demonstrating their potential for accurate stress categorization. This work highlights the revolutionary potential of AI to completely disrupt the agricultural industry while simultaneously advancing our understanding of plant stress responses.

Molecular mechanisms of heterosis under drought stress in maize hybrids Zhengdan7137 and Zhengdan7153

Maize is one of the most successful crops in utilizing heterosis which significantly improves maize stresses resistance and yield. Drought is a destructive abiotic stress that significantly reduces crop yield, particularly in maize. Drought stress and re-watering frequently occur during the growth and development of maize; however, the molecular mechanisms of heterosis under drought stress and re-watering have rarely been systematically investigated. Zhengdan7137 and Zhengdan7153 are two maize hybrid varieties with robust heterosis, and separately belongs to the SS×NSS and Reid×Tangsipingtou heterotic groups. 54 transcriptomes of these two hybrids and their parental inbred lines were analyzed under well-watering (WW), water-deficit (WD), and re-watering (RW) conditions using RNA-Seq. In this study, we identified 3,411 conserved drought response genes (CDRGs) and 3,133 conserved re-watering response genes (CRRGs) between Zhengdan7137 and Zhengdan7153. When comparing CDRGs and CRRGs to overdominance and underdominance genes, we identified 303 and 252 conservative drought response overdominance genes (DODGs) and underdominance genes (DUDGs), respectively, and 165 and 267 conservative re-watering response overdominance genes (RODGs) and underdominance genes (RUDGs), respectively. DODGs are involved in stress response-related processes, such as L-phenylalanine metabolism, carbohydrate metabolism, and heat response, whereas DUDGs are associated with glucose metabolism, pentose-phosphate shunt, and starch metabolism. RODGs and RUDGs contribute to the recovery of hybrids from drought stress by upregulating cell propagation and photosynthesis processes, and repressing stress response processes, respectively. It indicated overdominant and underdominant genes conservatively contributed to hybrid heterosis under drought stress. These results deepen our understanding of the molecular mechanisms of drought resistance, uncover conservative molecular mechanisms of heterosis under drought stress and re-watering, and provide potential targets for improving drought resistance in maize.

Comparative Physiological, Biochemical, and Leaf Proteome Responses of Contrasting Wheat Varieties to Drought Stress

Drought stress severely affects crop productivity and threatens food security. As current trends of global warming are predicted to exacerbate droughts, developing drought-resilient crops becomes urgent. Here, we used the drought-tolerant (BW35695) and drought-sensitive (BW4074) wheat varieties to investigate the physiological, biochemical, and leaf proteome responses underpinning drought tolerance. In response to drought, the tolerant variety had higher osmolyte accumulation and maintained higher leaf water content than the sensitive variety. BW35695 also had an enhanced antioxidant enzyme capacity and reduced reactive oxygen species (ROS), resulting in diminished membrane lipid damage, as reflected by malondialdehyde content. Proteomic analysis revealed that drought-induced differential expression of proteins involved in diverse biological processes in both wheat varieties, including primary and secondary metabolism, protein synthesis/folding/degradation, defense/ROS detoxification, energy, transcription, and cell structure. Notably, photosynthesis emerged as the most enriched biochemical process targeted for suppression in the drought-tolerant BW35695 wheat, but not in drought-sensitive BW4074, possibly as a survival strategy for averting cell damage inflicted by photosynthesis-derived ROS. Additionally, protein synthesis-related proteins were highly upregulated in BW35695, presumably to drive cell-wide stress-adaptive responses. The protein network identified here will be useful in further studies to understand the molecular basis for divergent drought response phenotypes in crops.

Genetic, molecular and physiological crosstalk during drought tolerance in maize (Zea mays): pathways to resilient agriculture

MAIN CONCLUSION

This review comprehensively elucidates maize drought tolerance mechanisms, vital for global food security. It highlights genetic networks, key genes, CRISPR-Cas applications, and physiological responses, guiding resilient variety development. Maize, a globally significant crop, confronts the pervasive challenge of drought stress, impacting its growth and yield significantly. Drought, an important abiotic stress, triggers a spectrum of alterations encompassing maize's morphological, biochemical, and physiological dimensions. Unraveling and understanding these mechanisms assumes paramount importance for ensuring global food security. Approaches like developing drought-tolerant varieties and harnessing genomic and molecular applications emerge as effective measures to mitigate the negative effects of drought. The multifaceted nature of drought tolerance in maize has been unfolded through complex genetic networks. Additionally, quantitative trait loci mapping and genome-wide association studies pinpoint key genes associated with drought tolerance, influencing morphophysiological traits and yield. Furthermore, transcription factors like ZmHsf28, ZmNAC20, and ZmNF-YA1 play pivotal roles in drought response through hormone signaling, stomatal regulation, and gene expression. Genes, such as ZmSAG39, ZmRAFS, and ZmBSK1, have been reported to be pivotal in enhancing drought tolerance through diverse mechanisms. Integration of CRISPR-Cas9 technology, targeting genes like gl2 and ZmHDT103, emerges as crucial for precise genetic enhancement, highlighting its role in safeguarding global food security amid pervasive drought challenges. Thus, decoding the genetic and molecular underpinnings of drought tolerance in maize sheds light on its resilience and paves the way for cultivating robust and climate-smart varieties, thus safeguarding global food security amid climate challenges. This comprehensive review covers quantitative trait loci mapping, genome-wide association studies, key genes and functions, CRISPR-Cas applications, transcription factors, physiological responses, signaling pathways, offering a nuanced understanding of intricate mechanisms involved in maize drought tolerance.

Leveraging Multiomics Insights and Exploiting Wild Relatives' Potential for Drought and Heat Tolerance in Maize

Climate change, particularly drought and heat stress, may slash agricultural productivity by 25.7% by 2080, with maize being the hardest hit. Therefore, unraveling the molecular nature of plant responses to these stressors is vital for the development of climate-smart maize. This manuscript's primary objective was to examine how maize plants respond to these stresses, both individually and in combination. Additionally, the paper delved into harnessing the potential of maize wild relatives as a valuable genetic resource and leveraging AI-based technologies to boost maize resilience. The role of multiomics approaches particularly genomics and transcriptomics in dissecting the genetic basis of stress tolerance was also highlighted. The way forward was proposed to utilize a bunch of information obtained through omics technologies by an interdisciplinary state-of-the-art forward-looking big-data, cyberagriculture system, and AI-based approach to orchestrate the development of climate resilient maize genotypes.

De novo transcriptomic analysis of Doum Palm (Hyphaene compressa) revealed an insight into its potential drought tolerance

BACKGROUND

Doum palms (Hyphaene compressa) perform a crucial starring role in the lives of Kenya's arid and semi-arid people for empowerment and sustenance. Despite the crop's potential for economic gain, there is a lack of genetic resources and detailed information about its domestication at the molecular level. Given the doum palm's vast potential as a widely distributed plant in semi-arid and arid climates and a source of many applications, coupled with the current changing climate scenario, it is essential to understand the molecular processes that provide drought resistance to this plant.

RESULTS

Assembly of the first transcriptome of doum palms subjected to water stress generated about 39.97 Gb of RNA-Seq data. The assembled transcriptome revealed 193,167 unigenes with an average length of 1655 bp, with 128,708 (66.63%) successfully annotated in seven public databases. Unigenes exhibited significant differentially expressed genes (DEGs) in well-watered and stressed-treated plants, with 45071 and 42457 accounting for up-regulated and down-regulated DEGs, respectively. GO term, KEGG, and KOG analysis showed that DEGs were functionally enriched cellular processes, metabolic processes, cellular and catalytic activity, metabolism, genetic information processing, signal transduction mechanisms, and posttranslational modification pathways. Transcription factors (TF), such as the MYB, WRKY, NAC family, FAR1, B3, bHLH, and bZIP, were the prominent TF families identified as doum palm DEGs encoding drought stress tolerance.

CONCLUSIONS

This study provides a complete understanding of DEGs involved in drought stress at the transcriptome level in doum palms. This research is, therefore, the foundation for the characterization of potential genes, leading to a clear understanding of its drought stress responses and providing resources for improved genetic modification.

Maize-Azospirillum brasilense interaction: accessing maize's miRNA expression under the effect of an inhibitor of indole-3-acetic acid production by the plant

MicroRNA (miRNA) is a class of non-coding RNAs. They play essential roles in plants' physiology, as in the regulation of plant development, response to biotic and abiotic stresses, and symbiotic processes. This work aimed to better understand the importance of maize's miRNA during Azospirillum-plant interaction when the plant indole-3-acetic acid (IAA) production was inhibited with yucasin, an inhibitor of the TAM/YUC pathway. Twelve cDNA libraries from a previous Dual RNA-Seq experiment were used to analyze gene expression using a combined analysis approach. miRNA coding genes (miR) and their predicted mRNA targets were identified among the differentially expressed genes. Statistical differences among the groups indicate that Azospirillum brasilense, yucasin, IAA concentration, or all together could influence the expression of several maize's miRNAs. The miRNA's probable targets were identified, and some of them were observed to be differentially expressed. Dcl4, myb122, myb22, and morf3 mRNAs were probably regulated by their respective miRNAs. Other probable targets were observed responding to the IAA level, the bacterium, or all of them. A. brasilense was able to influence the expression of some maize's miRNA, for example, miR159f, miR164a, miR169j, miR396c, and miR399c. The results allow us to conclude that the bacterium can influence directly or indirectly the expression of some of the identified mRNA targets, probably due to an IAA-independent pathway, and that they are somehow involved in the previously observed physiological effects.

Physiological Characteristic Changes and Transcriptome Analysis of Maize (Zea mays L.) Roots under Drought Stress

Water deficit is a key limiting factor for limiting yield in maize (Zea mays L.). It is crucial to elucidate the molecular regulatory networks of stress tolerance for genetic enhancement of drought tolerance. The mechanism of drought tolerance of maize was explored by comparing physiological and transcriptomic data under normal conditions and drought treatment at polyethylene glycol- (PEG-) induced drought stress (5%, 10%, 15%, and 20%) in the root during the seedling stage. The content of saccharide, SOD, CAT, and MDA showed an upward trend, proteins showed a downward trend, and the levels of POD first showed an upward trend and then decreased. Compared with the control group, a total of 597, 2748, 6588, and 5410 differentially expressed genes were found at 5%, 10%, 15%, and 20% PEG, respectively, and 354 common DEGs were identified in these comparisons. Some differentially expressed genes were remarkably enriched in the MAPK signaling pathway and plant hormone signal transduction. The 50 transcription factors (TFs) divided into 15 categories were screened from the 354 common DEGs during drought stress. Auxin response factor 10 (ARF10), auxin-responsive protein IAA9 (IAA9), auxin response factor 14 (ARF14), auxin-responsive protein IAA1 (IAA1), auxin-responsive protein IAA27 (IAA27), and 1 ethylene response sensor 2 (ERS2) were upregulated. The two TFs, including bHLH 35 and bHLH 96, involved in the MAPK signal pathway and plant hormones pathway, are significantly upregulated in 5%, 10%, 15%, and 20% PEG stress groups. The present study provides greater insight into the fundamental transcriptome reprogramming of grain crops under drought.

Whole-Transcriptome Sequencing Reveals the Global Molecular Responses and NAC Transcription Factors Involved in Drought Stress in Dendrobium catenatum

Dendrobium catenatum is a highly drought-tolerant herb, which usually grows on cliffs or in the branches of trees, yet the underlying molecular mechanisms for its tolerance remain poorly understood. We conducted a comprehensive study utilizing whole-transcriptome sequencing approaches to investigate the molecular response to extreme drought stress in D. catenatum. A large number of differentially expressed mRNAs, lncRNAs, and circRNAs have been identified, and the NAC transcription factor family was highly enriched. Meanwhile, 46 genes were significantly up-regulated in the ABA-activated signaling pathway. In addition to the 89 NAC family members accurately identified in this study, 32 members were found to have different expressions between the CK and extreme drought treatment. They may regulate drought stress through both ABA-dependent and ABA-independent pathways. Moreover, the 32 analyzed differentially expressed DcNACs were found to be predominantly expressed in the floral organs and roots. The ceRNA regulatory network showed that DcNAC87 is at the core of the ceRNA network and is regulated by miR169, miR393, and four lncRNAs. These investigations provided valuable information on the role of NAC transcription factors in D. catenatum's response to drought stress.

Current perspectives of lncRNAs in abiotic and biotic stress tolerance in plants

Abiotic/biotic stresses pose a major threat to agriculture and food security by impacting plant growth, productivity and quality. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long non-coding RNAs (lncRNAs) with sizes larger than 200 nucleotides in length, provides an important new perspective on the centrality of RNA in gene regulation. In plants, lncRNAs are widespread and fulfill multiple biological functions in stress response. In this paper, the research advances on the biological function of lncRNA in plant stress response were summarized, like as Natural Antisense Transcripts (NATs), Competing Endogenous RNAs (ceRNAs) and Chromatin Modification etc. And in plants, lncRNAs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid (ABA), jasmonate (JA), salicylic acid (SA) and redox signaling in response to many abiotic/biotic stresses. Moreover, conserved sequence motifs and structural motifs enriched within stress-responsive lncRNAs may also be responsible for the stress-responsive functions of lncRNAs, it will provide a new focus and strategy for lncRNA research. Taken together, we highlight the unique role of lncRNAs in integrating plant response to adverse environmental conditions with different aspects of plant growth and development. We envisage that an improved understanding of the mechanisms by which lncRNAs regulate plant stress response may further promote the development of unconventional approaches for breeding stress-resistant crops.

Functions of arbuscular mycorrhizal fungi in regulating endangered species Heptacodium miconioides growth and drought stress tolerance

KEY MESSAGE

The important values of AMF in regulating endangered species Heptacodium miconioides growth and drought stress tolerance. The wild endangered tree Heptacodium miconioides is distributed sporadically in mountainous areas and often subjected to various abiotic stresses, such as drought. The mutualistic association between plants and arbuscular mycorrhizal fungi (AMF) is known to have a significant impact on plant growth and their ability to withstand drought conditions. However, the role of AMF in H. miconioides seedlings in regulating drought tolerance remains unknown. This study investigated the ability of AMF symbionts to mitigate drought and their underlying mechanism on H. miconioides leaves. The results showed that drought stress dramatically decreased the leaf biomass and damaged the chloroplast structure in seedlings. Conversely, inoculation with AMF noticeably alleviated the deleterious effects of drought stress by restoring leaf morphology and improving the photosynthetic capacity. Moreover, plants inoculated with AMF enhanced the proportion of palisade tissue to spongy tissue in the leaves and the size of starch grains and number of plastoglobules in the chloroplast ultrastructure. A transcriptomic analysis showed that 2157 genes (691 upregulated and 1466 downregulated) were differentially expressed between drought stress with AMF inoculation and drought treatment. Further examination demonstrated that the genes exhibiting differential expression were predominantly associated with the advancement of photosynthesis, sucrose and starch metabolism, nitrogen metabolism, chloroplast development, and phenylpropanoid biosynthetic pathways, and the key potential genes were screened. These findings conclusively provided the physiological and molecular mechanisms that underlie improved drought resistance in H. miconioides in the presence of AMF, which could contribute to improving the survival and species conservation of H. miconioides.

Comparative Transcriptome Analysis Reveals the Underlying Response Mechanism to Salt Stress in Maize Seedling Roots

Crop growth and development can be impeded by salt stress, leading to a significant decline in crop yield and quality. This investigation performed a comparative analysis of the physiological responses of two maize inbred lines, namely L318 (CML115) and L323 (GEMS58), under salt-stress conditions. The results elucidated that CML115 exhibited higher salt tolerance compared with GEMS58. Transcriptome analysis of the root system revealed that DEGs shared by the two inbred lines were significantly enriched in the MAPK signaling pathway-plant and plant hormone signal transduction, which wield an instrumental role in orchestrating the maize response to salt-induced stress. Furthermore, the DEGs' exclusivity to salt-tolerant genotypes was associated with sugar metabolism pathways, and these unique DEGs may account for the disparities in salt tolerance between the two genotypes. Meanwhile, we investigated the dynamic global transcriptome in the root systems of seedlings at five time points after salt treatment and compared transcriptome data from different genotypes to examine the similarities and differences in salt tolerance mechanisms of different germplasms.

Continuous Cropping Inhibits Photosynthesis of Polygonatum odoratum

Polygonatum odoratum (Mill.) Druce possesses widespread medicinal properties; however, the continuous cropping (CC) often leads to a severe consecutive monoculture problem (CMP), ultimately causing a decline in yield and quality. Photosynthesis is the fundamental process for plant growth development. Improving photosynthesis is one of the most promising approaches to increase plant yields. To better understand how P. odoratum leaves undergo photosynthesis in response to CC, this study analyzed the physiochemical indexes and RNA-seq. The physiochemical indexes, such as the content of chlorophyll (chlorophyll a, b, and total chlorophyll), light response curves (LRCs), and photosynthetic parameters (Fv/Fm, Fv/F0, Fm/F0, Piabs, ABS/RC, TRo/RC, ETo/RC, and DIo/RC) were all changed in P. odoratum under the CC system. Furthermore, 13,798 genes that exhibited differential expression genes (DEGs) were identified in the P. odoratum leaves of CC and first cropping (FC) plants. Among them, 7932 unigenes were upregulated, while 5860 unigenes were downregulated. Here, the DEGs encoding proteins associated with photosynthesis and carbon assimilation showed a significant decrease in expression under the CC system, such as the PSII protein complex, PSI protein complex, Cytochorome b6/f complex, the photosynthetic electron transport chain, light-harvesting chlorophyll protein complex, and Calvin cycle, etc., -related gene. This study demonstrates that CC can suppress photosynthesis and carbon mechanism in P. odoratum, pinpointing potential ways to enhance photosynthetic efficiency in the CC of plants.

Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye (Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress

Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.

Transcriptomic Analysis of Three Differentially Senescing Maize (Zea mays L.) Inbred Lines upon Heat Stress

Maize, one of the world's major food crops, is facing the challenge of rising temperature. Leaf senescence is the most significant phenotypic change of maize under heat stress at the seedling stage, but the underlying molecular mechanism is still unknown. Here, we screened for three inbred lines (PH4CV, B73, and SH19B) that showed differentially senescing phenotypes under heat stress. Among them, PH4CV showed no obviously senescing phenotype under heat stress, while SH19B demonstrated a severely senescing phenotype, with B73 being between the two extremes. Subsequently, transcriptome sequencing showed that differentially expressed genes (DEGs) were generally enriched in response to heat stress, reactive oxygen species (ROS), and photosynthesis in the three inbred lines under heat treatment. Notably, ATP synthesis and oxidative phosphorylation pathway genes were only significantly enriched in SH19B. Then, the expression differences of oxidative phosphorylation pathways, antioxidant enzymes, and senescence-related genes in response to heat stress were analyzed in the three inbred lines. In addition, we demonstrated that silencing ZmbHLH51 by virus-induced gene silencing (VIGS) inhibits the heat-stress-induced senescence of maize leaves. This study helps to further elucidate the molecular mechanisms of heat-stress-induced leaf senescence at the seedling stage of maize.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

Transcriptome studies on cadmium tolerance and biochar mitigating cadmium stress in muskmelon

Cadmium pollution in agricultural soil is a great threat to crop growth and human health. In this research, with 1%, 3% and 5% biochar applied to control soil cadmium pollution, melon was selected to be the experimental object for physiological detection and transcriptome analysis, through which we explored the mechanism of cadmium tolerance and biochar mitigating cadmium stress in muskmelon. Three set concentrations of biochar have a mitigative effect on muskmelon cadmium stress, and 5% biochar and 3% biochar respectively have the best and the worst alleviative effect. The alleviation of biochar to cadmium stress on muskmelon is primarily in the manner of inhibiting cadmium transfer, while the resistance of muskmelon to cadmium stress is through activating phenylpropanoid pathway and overexpressing stress related genes. Under cadmium treatment, 11 genes of the phenylpropane pathway and 19 stress-related genes including cytochrome P450 family protein genes and WRKY transcription factor genes were up-regulated, while 1%, 3%, 5% biochar addition significantly downregulated 3, 0, 7 phenylpropane pathway genes and 17, 5, 16 stress-related genes, respectively. Genes such as cytochrome P450 protein family genes, WRKY transcription factor genes, and annexin genes may play a key role in muskmelon's resistance to cadmium stress. The results show the key pathways and genes of cadmium stress resistance and the effect of different concentrations of biochar in alleviating cadmium stress, which provide a reference for the research of cadmium stress resistance in crops and the application of biochar in cadmium pollution in agricultural soil.

CiXTH29 and CiLEA4 Role in Water Stress Tolerance in Cichorium intybus Varieties

Drought causes massive crop quality and yield losses. Limiting the adverse effects of water deficits on crop yield is an urgent goal for a more sustainable agriculture. With this aim, six chicory varieties were subjected to drought conditions during seed germination and at the six week-old plant growth stage, in order to identify some morphological and/or molecular markers of drought resistance. Selvatica, Zuccherina di Trieste and Galatina varieties, with a high vegetative development, showed a major germination index, greater seedling development (6 days of growth) and a greater dehydration resistance (6 weeks of growth plus 10 days without water) than the other ones (Brindisina, Esportazione and Rossa Italiana). Due to the reported involvement, in the abiotic stress response, of xyloglucan endotransglucosylase/hydrolases (XTHs) and late embryogenesis abundant (LEA) multigene families, XTH29 and LEA4 expression profiles were investigated under stress conditions for all analyzed chicory varieties. We showed evidence that chicory varieties with high CiXTH29 and CiLEA4 basal expression and vegetative development levels better tolerate drought stress conditions than varieties that show overexpression of the two genes only in response to drought. Other specific morphological traits characterized almost all chicory varieties during dehydration, i.e., the appearance of lysigen cavities and a general increase of the amount of xyloglucans in the cell walls of bundle xylem vessels. Our results highlighted that high CiXTH29 and CiLEA4 basal expression, associated with a high level of vegetative growth, is a potential marker for drought stress tolerance.

Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress

Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.

Global Responses of Autopolyploid Sugarcane Badila (Saccharum officinarum L.) to Drought Stress Based on Comparative Transcriptome and Metabolome Profiling

Sugarcane (Saccharum spp. hybrid) is frequently affected by seasonal drought, which causes substantial declines in quality and yield. To understand the drought resistance mechanisms of S. officinarum, the main species of modern sugarcane, at a molecular level, we carried out a comparative analysis of transcriptome and metabolome profiling of the sugarcane variety Badila under drought stress (DS). Compared with control group (CG) plants, plants exposed to DS had 13,744 (6663 up-regulated and 7081 down-regulated) differentially expressed genes (DEGs). GO and KEGG analysis showed that the DEGs were enriched in photosynthesis-related pathways and most DEGs had down-regulated expression. Moreover, the chlorophyll content, photosynthesis (Photo), stomatal conductance (Cond), intercellular carbon dioxide concentration (Ci) and transpiration rate (Trmmol) were sharply decreased under DS. These results indicate that DS has a significant negative influence on photosynthesis in sugarcane. Metabolome analysis identified 166 (37 down-regulated and 129 up-regulated) significantly regulated metabolites (SRMs). Over 50% of SRMs were alkaloids, amino acids and their derivatives, and lipids. The five most significantly enriched KEGG pathways among SRMs were Aminoacyl-tRNA biosynthesis, 2-Oxocarboxylic acid metabolism, Biosynthesis of amino acids, Phenylalanine metabolism, and Arginine and proline metabolism (p < 0.05). Comparing CG with DS for transcriptome and metabolome profiling (T_CG/DS and M_CG/DS, respectively), we found three of the same KEGG-enriched pathways, namely Biosynthesis of amino acids, Phenylalanine metabolism and Arginine and proline metabolism. The potential importance of Phenylalanine metabolism and Arginine and proline metabolism was further analyzed for response to DS in sugarcane. Seven SRMs (five up-regulated and two down-regulated) and 60 DEGs (17 up-regulated and 43 down-regulated) were enriched in Phenylalanine metabolism under DS, of which novel.31261, Sspon.04G0008060-1A, Sspon.04G0008060-2B and Sspon.04G0008060-3C were significantly correlated with 7 SRMs. In Arginine and proline metabolism, eight SRMs (seven up-regulated and one down-regulated) and 63 DEGs (32 up-regulated and 31 down-regulated) were enriched, of which Sspon.01G0026110-1A (OAT) and Sspon.03G0002750-3D (P5CS) were strongly associated with proline (r > 0.99). These findings present the dynamic changes and possible molecular mechanisms of Phenylalanine metabolism as well as Arginine and proline metabolism under DS and provide a foundation for future research and sugarcane improvement.

SNP-based bulk segregant analysis revealed disease resistance QTLs associated with northern corn leaf blight in maize

Maize (Zea mays L.) is the most important food security crop worldwide. Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, severely reduces production causing millions of dollars in losses worldwide. Therefore, this study aimed to identify significant QTLs associated with NCLB by utilizing next-generation sequencing-based bulked-segregant analysis (BSA). Parental lines GML71 (resistant) and Gui A10341 (susceptible) were used to develop segregating population F₂. Two bulks with 30 plants each were further selected from the segregating population for sequencing along with the parental lines. High throughput sequencing data was used for BSA. We identified 10 QTLs on Chr 1, Chr 2, Chr 3, and Chr 5 with 265 non-synonymous SNPs. Moreover, based on annotation information, we identified 27 candidate genes in the QTL regions. The candidate genes associated with disease resistance include AATP1, At4g24790, STICHEL-like 2, BI O 3-BIO1, ZAR1, SECA2, ABCG25, LECRK54, MKK7, MKK9, RLK902, and DEAD-box ATP-dependent RNA helicase. The annotation information suggested their involvement in disease resistance-related pathways, including protein phosphorylation, cytoplasmic vesicle, protein serine/threonine kinase activity, and ATP binding pathways. Our study provides a substantial addition to the available information regarding QTLs associated with NCLB, and further functional verification of identified candidate genes can broaden the scope of understanding the NCLB resistance mechanism in maize.

Transcriptome and functional analyses reveal ERF053 from Medicago falcata as key regulator in drought resistances

Medicago falcata L. is an important legume forage grass with strong drought resistant, which could be utilized as an important gene pool in molecular breed of forage grass. In this study, M. falcata seedlings were treated with 400 mM mannitol to simulate drought stress, and the morphological and physiological changes were investigated, as well as the transcriptome changes of M. falcata seedlings at different treatment time points (0 h, 2 h, 6 h, 12 h, 24 h, 36 h and 48 h). Transcriptome analyses revealed four modules were closely related with drought response in M. falcata by WGCNA analysis, and four ERF transcription factor genes related with drought stress were identified (MfERF053, MfERF9, MfERF034 and MfRAP2.1). Among them, MfERF053 was highly expressed in roots, and MfERF053 protein showed transcriptional activation activity by transient expression in tobacco leaves. Overexpression of MfERF053 in Arabidopsis improved root growth, number of lateral roots and fresh weight under drought, salt stress and exogenous ABA treatments. Transgenic Arabidopsis over-expressing MfERF053 gene grew significantly better than the wild type under both drought stress and salt stress when grown in soil. Taken together, our strategy with transcriptome combined WGCNA analyses identified key transcription factor genes from M. falcata, and the selected MfERF053 gene was verified to be able to enhance drought and salt resistance when over-expressed in Arabidopsis.

Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with drought tolerance in Tartary buckwheat

Drought stress is one of the major abiotic stress factors that affect plant growth and crop productivity. Tartary buckwheat is a nutritionally balanced and flavonoid-rich pseudocereal crop and also has strong adaptability to different adverse environments including drought. However, little is known about its drought tolerance mechanism. In this study, we performed comparative physiological and transcriptomic analyses of two contrasting drought-resistant Tartary buckwheat genotypes under nature drought treatment in the reproductive stage. Under drought stress, the drought-tolerant genotype XZSN had significantly higher contents of relative water, proline, and soluble sugar, as well as lower relative electrolyte leakage in the leaves than the drought-susceptible LK3. A total of 5,058 (2,165 upregulated and 2,893 downregulated) and 5,182 (2,358 upregulated and 2,824 downregulated) potential drought-responsive genes were identified in XZSN and LK3 by transcriptome sequencing analysis, respectively. Among the potential drought-responsive genes of XZSN, 1,206 and 1,274 genes were identified to be potential positive and negative contributors for XZSN having higher drought resistance ability than LK3. Furthermore, 851 out of 1,206 positive drought-resistant genes were further identified to be the core drought-resistant genes of XZSN based on WGCNA analysis, and most of them were induced earlier and quicker by drought stress than those in LK3. Functional annotation of the 851 core drought-resistant genes found that a large number of stress-responsive genes were involved in TFs, abscisic acid (ABA) biosynthesis, signal transduction and response, non-ABA signal molecule biosynthesis, water holding, oxygen species scavenging, osmotic adjustment, cell damage prevention, and so on. Transcriptional regulatory network analyses identified the potential regulators of these drought-resistant functional genes and found that the HD-ZIP and MYB TFs might be the key downstream TFs of drought resistance in Tartary buckwheat. Taken together, these results indicated that the XZSN genotype was more drought-tolerant than the LK3 genotype as evidenced by triggering the rapid and dramatic transcriptional reprogramming of drought-resistant genes to reduce water loss, prevent cell damage, and so on. This research expands our current understanding of the drought tolerance mechanisms of Tartary buckwheat and provides important information for its further drought resistance research and variety breeding.

Comparative physiological and root transcriptome analysis of two annual ryegrass cultivars under drought stress

Annual ryegrass is a widely cultivated forage grass with rapid growth and high productivity. However, drought is one of the abiotic stresses affecting ryegrass growth and quality. In this study, we compared the physiological and transcriptome responses of Chuansi No.1 (drought-tolerant, DT) and Double Barrel (drought-sensitive, DS) under drought stress simulated by PEG-6000 for 7 days. The results showed that Chuansi No. 1 had stronger physiological and biochemical parameters such as root properties, water content, osmotic adjustment ability and antioxidant ability. In addition, RNA-seq was used to elucidate the molecular mechanism of root drought resistance. We identified 8588 differentially expressed genes related to drought tolerance in root, which were mainly enriched in oxidation-reduction process, carbohydrate metabolic process, apoplast, arginine and proline metabolism, and phenylpropanoid biosynthesis pathways. The expression levels of DEGs were consistent with physiological changes of ryegrass under drought stress. We found that genes related to sucrose and starch synthesis, root development, osmotic adjustment, ABA signal regulation and specifically up-regulated transcription factors such as WRKY41, WRKY51, ERF7, ERF109, ERF110, NAC43, NAC68, bHLH162 and bHLH148 in Chuansi No. 1 may be the reason for its higher drought tolerance. This study revealed the underlying physiological and molecular mechanisms of root response to drought stress in ryegrass and provided some new candidate genes for breeding rye drought tolerant varieties.

Transcriptomic and physiological responses of contrasting maize genotypes to drought stress

Drought is a significant environmental stress factor that adversely affects maize productivity. However, many details regarding the molecular mechanisms of maize against drought are still unclear. In this study, leaf transcriptomics and physiological traits of two maize genotypes with differing drought resistance were analyzed. Transcriptome sequencing identified 8985 and 7305 differentially expressed genes (DEGs) in SD902 and SD609, respectively. Functional analysis suggested that numerous genes are highly involved in oxidative defense, protein modification, photosynthesis, phytohormone response, MAPK signaling, and transcription factors (TFs). Compared to SD902, SD609 had a higher expression of DEGs related to antioxidant enzymes, photosynthetic electron transport, heat shock proteins, and indole-3-acetic acid (IAA) signaling under drought conditions, which might contribute to its tolerance mechanisms to drought. Stress-induced TFs may play a crucial regulatory role in genotypic differences. Moreover, the physiological changes and gene expression abundance determined using quantitative reverse transcription polymerase chain reaction were consistent with the RNA sequencing data. The study results suggest that the higher drought tolerance of SD609 than SD902 can be attributed to stronger stress defense capabilities, IAA signal transduction, and more stable photosynthesis. Our findings provide new insights into the molecular mechanisms of maize against drought stress, and the candidate genes identified may be used in breeding drought-tolerant maize cultivars.

Overexpression of ZmEREBP60 enhances drought tolerance in maize

Apetala2/ethylene response factor (AP2/ERF) family of transcription factors plays important roles in plant development and stress responses. However, few members of this family have been functionally and mechanistically characterised in maize. In this study, we characterised a member of the AP2/ERF transcription factor family, ZmEREBP60 from maize. Amino acid sequence alignment and phylogenetic analysis showed that ZmEREBP60 belongs to cluster I of the AP2/ERF family. qRT-PCR analysis indicated that ZmEREBP60 expression was highly induced by drought in the roots, coleoptiles, and leaves. Subcellular localisation analysis revealed that ZmEREBP60 was localised in the nucleus. Moreover, overexpression of ZmEREBP60 enhanced tolerance to drought stress while alleviating the drought-induced increase in H₂O₂ accumulation and malondialdehyde content in transgenic lines. Transcriptome analysis showed that ZmEREBP60 regulates the expression of genes involved in H₂O₂ catabolism, water deprivation response, and abscisic acid signalling pathway. Collectively, as a new member of the AP2/ERF transcription factor family in maize, ZmEREBP60 is a positive regulator of plant drought response.

Genome-wide identification of BAM (β-amylase) gene family in jujube (Ziziphus jujuba Mill.) and expression in response to abiotic stress

BACKGROUND

Elevated temperature and drought stress have substantial impacts on fruit quality, especially in terms of sugar metabolism and content. β-Amylase (BAM) plays a critical role in regulating jujube fruit sugar levels and abiotic stress response. Nevertheless, little is known about the regulatory functions of the BAM genes in jujube fruit.

RESULTS

Nine jujube BAM genes were identified, clustered into four groups, and characterized to elucidate their structure, function, and distribution. Multiple sequence alignment and gene structure analysis showed that all ZjBAM genes contain Glu-186 and Glu-380 residues and are highly conserved. Phylogenetic and synteny analysis further indicated that the ZjBAM gene family is evolutionarily conserved and formed collinear pairs with the BAM genes of peach, apple, poplar, Arabidopsis thaliana, and cucumber. A single tandem gene pair was found within the ZjBAM gene family and is indicative of putative gene duplication events. We also explored the physicochemical properties, conserved motifs, and chromosomal and subcellular localization of ZjBAM genes as well as the interaction networks and 3D structures of ZjBAM proteins. A promoter cis-acting element analysis suggested that ZjBAM promoters comprise elements related to growth, development, phytohormones, and stress response. Furthermore, a metabolic pathways annotation analysis showed that ZjBAMs are significantly upregulated in the starch and sucrose metabolism, thereby controlling starch-maltose interconversion and hydrolyzing starch to maltose. Transcriptome and qRT-PCR analyses revealed that ZjBAMs respond positively to elevated temperature and drought stress. Specifically, ZjBAM1, ZjBAM2, ZjBAM5, and ZjBAM6 are significantly upregulated in response to severe drought. Bimolecular fluorescence complementation analysis demonstrated ZjBAM1-ZjAMY3, ZjBAM8-ZjDPE1, and ZjBAM7-ZjDPE1 protein interactions that were mainly present in the plasma membrane and nucleus.

CONCLUSION

The jujube BAM gene family exhibits high evolutionary conservation. The various expression patterns of ZjBAM gene family members indicate that they play key roles in jujube growth, development, and abiotic stress response. Additionally, ZjBAMs interact with α-amylase and glucanotransferase. Collectively, the present study provides novel insights into the structure, evolution, and functions of the jujube BAM gene family, thus laying a foundation for further exploration of ZjBAM functional mechanisms in response to elevated temperature and drought stress, while opening up avenues for the development of economic forests in arid areas.

Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks

Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.

Environmental Stress and Plants

Land plants are constantly subjected to multiple unfavorable or even adverse environmental conditions. Among them, abiotic stresses (such as salt, drought, heat, cold, heavy metals, ozone, UV radiation, and nutrient deficiencies) have detrimental effects on plant growth and productivity and are increasingly important considering the direct or indirect effects of climate change. Plants respond in many ways to abiotic stresses, from gene expression to physiology, from plant architecture to primary, and secondary metabolism. These complex changes allow plants to tolerate and/or adapt to adverse conditions. The complexity of plant response can be further influenced by the duration and intensity of stress, the plant genotype, the combination of different stresses, the exposed tissue and cell type, and the developmental stage at which plants perceive the stress. It is therefore important to understand more about how plants perceive stress conditions and how they respond and adapt (both in natural and anthropogenic environments). These concepts were the basis of the Special Issue that International Journal of Molecular Sciences expressly addressed to the relationship between environmental stresses and plants and that resulted in the publication of 5 reviews and 38 original research articles. The large participation of several authors and the good number of contributions testifies to the considerable interest that the topic currently receives in the plant science community, especially in the light of the foreseeable climate changes. Here, we briefly summarize the contributions included in the Special Issue, both original articles categorized by stress type and reviews that discuss more comprehensive responses to various stresses.

Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize

Amino acid transporters (AATs) are essential membrane proteins that transfer amino acids across cells. They are necessary for plant growth and development. The lysine histidine transporter (LHT) gene family in maize (Zea mays) has not yet been characterized. According to sequence composition and phylogenetic placement, this study found 15 LHT genes in the maize genome. The ZmLHT genes are scattered across the plasma membrane. The study also analyzed the evolutionary relationships, gene structures, conserved motifs, 3D protein structure, a transmembrane domain, and gene expression of the 15 LHT genes in maize. Comprehensive analyses of ZmLHT gene expression profiles revealed distinct expression patterns in maize LHT genes in various tissues. This study's extensive data will serve as a foundation for future ZmLHT gene family research. This study might make easier to understand how LHT genes work in maize and other crops.

Physiological and transcriptome analyses highlight multiple pathways involved in drought stress in Medicago falcata

Medicago falcata is one of the leguminous forage crops, which grows well in arid and semiarid region. To fully investigate the mechanism of drought resistance response in M. falcata, we challenged the M. falcata plants with 30% PEG-6000, and performed physiological and transcriptome analyses. It was found that, the activities of antioxidant enzymes (eg. SOD, POD, and CAT) and soluble sugar content were all increased in the PEG-treated group, as compared to the control group. Transcriptome results showed that a total of 706 genes were differentially expressed in the PEG-treated plants in comparison with the control. Gene enrichment analyses on differentially expressed genes revealed that a number of genes in various pathway were significantly enriched, including the phenylpropanoid biosynthesis (ko00940) and glycolysis/gluconeogenesis (ko00010), indicating the involvement of these key pathways in drought response. Furthermore, the expression levels of seven differentially expressed genes were verified to be involved in drought response in M. falcata by qPCR. Taken together, these results will provide valuable information related to drought response in M. falcata and lay a foundation for molecular studies and genetic breeding of legume crops in future research.

Identification and characterization of heat-responsive lncRNAs in maize inbred line CM1

BACKGROUND

Frequent occurrence of extreme high temperature is a major threat to crop production. Increasing evidence demonstrates that long non-coding RNAs (lncRNAs) have important biological functions in the regulation of the response to heat stress. However, the regulatory mechanism of lncRNAs involved in heat response requires further exploration and the regulatory network remains poorly understood in maize.

RESULTS

In this research, high-throughput sequencing was adopted to systematically identify lncRNAs in maize inbred line CM1. In total, 53,249 lncRNAs (259 known lncRNAs and 52,990 novel lncRNAs) were detected, of which 993 lncRNAs showed significantly differential expression (DElncRNAs) under heat stress. By predicting the target genes, 953 common targets shared by cis- and trans-regulation of the DElncRNAs were identified, which exhibited differential expression between the control and the heat stress treatments. Functional annotation indicated that a number of important biological processes and pathways, including photosynthesis, metabolism, translation, stress response, hormone signal transduction, and spliceosome, were enriched for the common targets, suggesting that they play important roles in heat response. A lncRNA-mediated regulatory network was constructed to visualize the molecular response mechanism in response to heat stress, which represented the direct regulatory relationships of DElncRNAs, differentially expressed miRNAs, target genes, and functional annotations.

CONCLUSIONS

This study lays a foundation for further elucidation of the regulatory mechanism for the response to heat stress in the maize inbred line CM1. The findings provide important information for identification of heat-responsive genes, which will be beneficial for the molecular breeding in the cultivation of heat-tolerant maize germplasm.

Rehydration Compensation of Winter Wheat Is Mediated by Hormone Metabolism and De-Peroxidative Activities Under Field Conditions

Water deficit and rehydration frequently occur during wheat cultivation. Previous investigations focused on the water deficit and many drought-responsive genes have been identified in winter wheat. However, the hormone-related metabolic responses and de-peroxidative activities associated with rehydration are largely unknown. In this study, leaves of two winter wheat cultivars, "Hengguan35" (HG, drought-tolerant cultivar) and "Shinong086" (SN, drought-sensitive cultivar), were used to investigate water deficit and the post-rehydration process. Rehydration significantly promoted wheat growth and postponed spike development. Quantifications of antioxidant enzymes, osmotic stress-related substances, and phytohormones revealed that rehydration alleviated the peroxidation and osmotic stress caused by water deficit in both cultivars. The wheat cultivar HG showed a better rehydration-compensation phenotype than SN. Phytohormones, including abscisic acid, gibberellin (GA), jasmonic acid (JA), and salicylic acid (SA), were detected using high-performance liquid chromatography and shown to be responsible for the rehydration process. A transcriptome analysis showed that differentially expressed genes related to rehydration were enriched in hormone metabolism- and de-peroxidative stress-related pathways. Suppression of genes associated with abscisic acid signaling transduction were much stronger in HG than in SN upon rehydration treatment. HG also kept a more balanced expression of genes involved in reactive oxygen species pathway than SN. In conclusion, we clarified the hormonal changes and transcriptional profiles of drought-resistant and -sensitive winter wheat cultivars in response to drought and rehydration, and we provided insights into the molecular processes involved in rehydration compensation.