Transcriptomic and physiological responses of contrasting maize genotypes to drought stress

Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves

Drought poses a significant threat to global crop productivity and food security. In this study, we aimed to elucidate the impact of drought on transcriptional regulation and alternative splicing in barley (Hordeum vulgare), and to determine whether these transcriptomic alterations correlate with changes in hormonal profiles. We hypothesized that drought stress induces extensive reprogramming of gene expression, including alternative splicing events, and that these molecular responses are accompanied by tissue-specific shifts in hormone levels, ultimately underpinning adaptive responses in both leaves and roots. To test this, we performed RNA-seq and comprehensive hormone profiling on leaves and roots sampled at 25 days after planting under both optimal and drought conditions. Our analysis identified over 6,655 differentially expressed genes, with a substantial subset exhibiting differential alternative splicing. In leaves, drought primarily downregulated photosynthesis-related genes while upregulating pathways involved in water stress and abscisic acid (ABA) signaling. In contrast, roots displayed broader metabolic adjustments and significant isoform switching. Hormone analysis revealed marked ABA accumulation, particularly in roots, alongside organ-specific modulation of jasmonates and auxins. A limited assessment of the rhizosphere microbial community revealed low transcript abundance, underscoring the primacy of intrinsic plant responses. Collectively, these findings provide valuable insights into the multilayered adaptive strategies of barley under drought stress.

Transcriptomics-proteomics analysis reveals StCOMT1 regulates drought, alkali and combined stresses in potato

KEY MESSAGE

Transcriptome proteome association analysis screened candidate DEGs, DEPs, and DEGs/DEPs associated with potato response to drought, alkali, and combined stresses. Overexpression of StCOMT1 enhances potato drought and alkali tolerance. Drought and salinity have severely impeded potato (Solanum tuberosum L.) growth and development, significantly reducing global potato production. However, the molecular mechanisms regulating the combined drought and alkali stress process are not fully understood. This study compared the mRNA and protein expression profiles of potato under drought (PEG-6000), alkali (NaHCO3), and combined (PEG-6000 + NaHCO3) stresses by transcriptome and TMT proteomics sequencing to investigate the common or specific responses of 'Atlantic' potato to single and combined stresses of drought and alkali were preliminarily explored. It was found that 2215 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were jointly identified under drought, alkali, and combined stresses. Under drought, alkali, and combined stresses, 234, 185, and 246 DEGs/DEPs were identified, respectively. These DEGs, DEPs, and DEGs/DEPs identified revealed the potential roles of several signaling and metabolic pathways in mediating drought and alkali stress tolerance, including plant hormone signaling, MAPK signaling pathway, phenylpropanoid biosynthesis, and glutathione metabolism. Caffeic acid-O-methyltransferase (COMT) is an essential methylating enzyme in the phenylpropane biosynthetic pathway, which is involved in lignin synthesis and plays an important role in protecting plants from abiotic stresses. In this study, we investigated the changes in physiologic characteristics, such as growth, antioxidant defense, osmotic regulation and lignin accumulation, in overexpressing StCOMT1 (PT0001512/M0ZIL7) transgenic potato after stress. It proved that the gene has the function of adapting to drought and alkali stress, and provided a theoretical basis for further research on the resistance mechanism of the gene in drought and alkali tolerance in potato.

Drought stress memory in maize: understanding and harnessing the past for future resilience

Maize (Zea mays L.), a cornerstone of global food security, faces significant challenges due to drought stress, which disrupts its growth, development, and productivity. This review synthesizes advances in our understanding of drought stress memory, a mechanism that enables maize to "remember" prior drought exposure through transcriptional, epigenetic, and physiological pathways. Key regulators, including transcription factors (ZmEREB24 and ZmNF-YC12) and epigenetic modifications (DNA methylation and histone acetylation), orchestrate stress-responsive pathways that ensure rapid adaptation to recurrent drought events. Complementing these molecular mechanisms, physiological adaptations, such as optimized root and leaf architecture, enhanced water-use efficiency, and antioxidant defenses, further strengthen drought tolerance. Practical applications, including molecular priming techniques (e.g., osmopriming, hydropriming, nanoparticles) and advanced genetic tools (CRISPR/Cas9, GWAS), promise scalable solutions for breeding drought-resilient maize varieties. Despite this progress, challenges remain, including genotype-specific variability, scalability, and trade-offs between resilience and yield. This review provides a roadmap for integrating laboratory discoveries with field-level practices, bridging molecular and agronomic innovations to address climate variability and ensure sustainable maize production and global food security.

Genome-wide association mapping and genomic prediction analyses reveal the genetic architecture of grain yield and agronomic traits under drought and optimum conditions in maize

BACKGROUND

Drought is a major abiotic stress in sub-Saharan Africa, impacting maize growth and development leading to severe yield loss. Drought tolerance is a complex trait regulated by multiple genes, making direct grain yield selection ineffective. To dissect the genetic architecture of grain yield and flowering traits under drought stress, a genome-wide association study (GWAS) was conducted on a panel of 236 maize lines testcrossed and evaluated under managed drought and optimal growing conditions in multiple environments using seven multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO, and FARMCPU) from mrMLM and GAPIT R packages. Genomic prediction with RR-BLUP model was applied on BLUEs across locations under optimum and drought conditions.

RESULTS

A total of 172 stable and reliable quantitative trait nucleotides (QTNs) were identified, of which 77 are associated with GY, AD, SD, ASI, PH, EH, EPO and EPP under drought and 95 are linked to GY, AD, SD, ASI, PH, EH, EPO and EPP under optimal conditions. Among these QTNs, 17 QTNs explained over 10% of the phenotypic variation (R2 ≥ 10%). Furthermore, 43 candidate genes were discovered and annotated. Two major candidate genes, Zm00001eb041070 closely associated with grain yield near peak QTN, qGY_DS1.1 (S1_216149215) and Zm00001eb364110 closely related to anthesis-silking interval near peak QTN, qASI_DS8.2 (S8_167256316) were identified, encoding AP2-EREBP transcription factor 60 and TCP-transcription factor 20, respectively under drought stress. Haplo-pheno analysis identified superior haplotypes for qGY_DS1.1 (S1_216149215) associated with the higher grain yield under drought stress. Genomic prediction revealed moderate to high prediction accuracies under optimum and drought conditions.

CONCLUSION

The lines carrying superior haplotypes can be used as potential donors in improving grain yield under drought stress. Integration of genomic selection with GWAS results leads not only to an increase in the prediction accuracy but also to validate the function of the identified candidate genes as well increase in the accumulation of favorable alleles with minor and major effects in elite breeding lines. This study provides valuable insight into the genetic architecture of grain yield and secondary traits under drought stress.

Comparative physiological and transcriptomic analyses reveal genotype specific response to drought stress in Siberian wildrye (Elymus sibiricus)

Siberian wildrye (Elymus sibiricus) is a xero-mesophytic forage grass with high nutritional quality and stress tolerance. Among its numerous germplasm resources, some possess superior drought resistance. In this study, we firstly investigated the physiological differences between the leaves of drought-tolerant (DT) and drought-sensitive (DS) genotypes under different field water contents (FWC) in soil culture. The results showed that, under drought stress, DT maintained a lower leaf water potential for water absorption, sustained higher photosynthetic efficiency, and reduced oxidative damage in leaves by efficiently maintaining the ascorbic acid-glutathione (ASA-GSH) cycle to scavenge reactive oxygen species (ROS) compared to DS. Secondly, using RNA sequencing (RNA-seq), we analyzed the gene expression profiles of DT and DS leaves under osmotic stress of hydroponics induced by PEG-6000. Through differential analysis, we identified 1226 candidate unigenes, from which we subsequently screened out 115/212 differentially expressed genes (DEGs) that were more quickly induced/reduced in DT than in DS under osmotic stress. Among them, Unigene0005863 (EsSnRK2), Unigene0053902 (EsLRK10) and Unigene0031985 (EsCIPK5) may be involved in stomatal closure induced by abscisic acid (ABA) signaling pathway. Unigene0047636 (EsCER1) may positively regulates the synthesis of very-long-chain (VLC) alkanes in cuticular wax biosynthesis, influencing plant responses to abiotic stresses. Finally, the contents of wax and cutin were measured by GC-MS under osmotic stress of hydroponics induced by PEG-6000. Corresponding to RNA-seq, contents of wax monomers, especially alkanes and alcohols, showed significant induction by osmotic stress in DT but not in DS. It is suggested that limiting stomatal and cuticle transpiration under drought stress to maintain higher photosynthetic efficiency and water use efficiency (WUE) is one of the critical mechanisms that confer stronger drought resistance to DT. This study provides some insights into the molecular mechanisms underlying drought tolerance in E. sibiricus. The identified genes may provide a foundation for the selection and breeding of drought-tolerant 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.

Transcriptomic and Metabolomic Insights into ABA-Related Genes in Cerasus humilis under Drought Stress

Cerasus humilis, a small shrub of the Cerasus genus within the Rosaceae family, is native to China and renowned for its highly nutritious and medicinal fruits, robust root system, and remarkable drought resistance. This study primarily employed association transcriptome and metabolome analyses to assess changes in abscisic acid (ABA) levels and identify key regulatory genes in C. humilis subjected to varying degrees of drought stress. Notably, we observed distinct alterations in transcription factors across different drought intensities. Specifically, our transcriptome data indicated noteworthy shifts in GATA, MYB, MYC, WRKY, C2H2, and bHLH transcription factor families. Furthermore, combined transcriptomic and metabolomic investigations demonstrated significant enrichment of metabolic pathways, such as 'Carbon metabolism', 'Biosynthesis of amino acids', 'Biosynthesis of cofactors', 'Phenylpropanoid biosynthesis', 'Starch and sucrose metabolism', and 'Plant hormone signal transduction' under moderate (Mod) or severe (Sev) drought conditions. A total of 11 candidate genes involved in ABA biosynthesis and signaling pathways were identified. The down-regulated genes included secoisolariciresinol dehydrogenase-like and PYL2. Conversely, genes including FAD-dependent urate hydroxylase-like, cytochrome P450 97B2, carotenoid cleavage dioxygenase 4 (CCD4), SnRK2.2, ABI 5-like protein 5, PP2C 51, and SnRK2.3, were up-regulated under Mod or Sev drought stress. This study lays the genetic foundation for ABA biosynthesis to enhance drought tolerance and provides genetic resources for plant genetic engineering and breeding efforts.

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.

The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress

Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO₂ fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.