Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis

A panomics-driven framework for the improvement of major food legume crops: advances, challenges, and future prospects

Food legume crops, including common bean, faba bean, mungbean, cowpea, chickpea, and pea, have long served as vital sources of energy, protein, and minerals worldwide, both as grains and vegetables. Advancements in high-throughput phenotyping, next-generation sequencing, transcriptomics, proteomics, and metabolomics have significantly expanded genomic resources for food legumes, ushering research into the panomics era. Despite their nutritional and agronomic importance, food legumes still face constraints in yield potential and genetic improvement due to limited genomic resources, complex inheritance patterns, and insufficient exploration of key traits, such as quality and stress resistance. This highlights the need for continued efforts to comprehensively dissect the phenome, genome, and regulome of these crops. This review summarizes recent advances in technological innovations and multi-omics applications in food legumes research and improvement. Given the critical role of germplasm resources and the challenges in applying phenomics to food legumes-such as complex trait architecture and limited standardized methodologies-we first address these foundational areas. We then discuss recent gene discoveries associated with yield stability, seed composition, and stress tolerance and their potential as breeding targets. Considering the growing role of genetic engineering, we provide an update on gene-editing applications in legumes, particularly CRISPR-based approaches for trait enhancement. We advocate for integrating chemical and biochemical signatures of cells ('molecular phenomics') with genetic mapping to accelerate gene discovery. We anticipate that combining panomics approaches with advanced breeding technologies will accelerate genetic gains in food legumes, enhancing their productivity, resilience, and contribution to sustainable global food security.

The full-length transcriptome analysis of blueberry under different pH conditions

The breeding of high soil pH tolerant blueberry cultivars is conducive to their cultivation and can reduce fertility costs. However, the molecular mechanisms of high soil pH tolerance of blueberry cultivars remain unclear. To understand the adaptive response of blueberry varieties to high pH, the full-length transcriptome analysis was performed with Spartan (high pH-soil-sensitive variety) and Reka (high pH-soil-tolerant variety) treated with low and high pH by hydroponics. The nutrient content analysis showed that significant changes in the content of Al, Fe, K, N and P were detected between low and high pH treatments in roots and leaves between two cultivars. Full-length transcriptome analysis found the total 131,143 transcripts were identified through sequencing, in which 18,193 were novel transcripts and 887 lncRNAs were predicted. We identified 1508 up-regulated and 944 down-regulated genes in leaves of Reka under high pH, and 3910 up-regulated and 3853 down-regulated DETs were identified in the root of Reka under high pH. Specifically, we identified 11 Al-responsive genes, seven Fe-responsive genes, 10 P-responsive genes, and two K-responsive genes that displayed differential expression between low and high pH treatments in roots between two cultivars. Meanwhile, weighted gene co-expression network analysis (WGCNA) was used to identify hub gene in each group. The top 30 hub genes were identified in the root and leaves of Reka under high pH, which include two glycosyl hydrolases family, one membrane transport protein, one Polysaccharide biosynthesis, two lipid-transfer protein, one Glycosyl hydrolases family, one Copper binding protein and one AUX/IAA family. These provide a theoretical basis for the mechanism of high pH tolerance in blueberries and varieties developed.

Comparative metabolomics of two nettle species unveils distinct high-altitude adaptation mechanisms on the Tibetan Plateau

BACKGROUND

The extreme high-altitude conditions of the Tibetan Plateau, characterized by intense solar radiation, low temperatures, and reduced oxygen levels, poses significant challenges to plant survival. Plants inhabiting this region have evolved specialized mechanisms to adapt to high-altitude environments. While most studies have focused on genomic and ecological perspectives, few have explored adaptive mechanisms in a metabolic context. In particular, comparative studies examining similarities and differences in the metabolomes of closely related species are exceedingly rare. As sister species, the nettle species Urtica hyperborea and U. dioica are distributed above 4000 m above sea level, with a sympatric distribution on the Tibetan Plateau, they provide an ideal system to investigate the aforementioned question.

RESULTS

In this study, we conducted non-targeted metabolic profiling of the leaves from U. hyperborea and U. dioica collected at three sympatric sites on the Tibetan Plateau. A total of 2906 annotated metabolites were detected. Differential metabolites at Sites 1 (4697 m) and 3 (4465 m) were enriched in pathways for flavonoid, flavone and flavonol, and phenylpropanoid biosynthesis. In contrast, Site 2, located at the highest altitude (5007 m), primarily exhibited enrichment in carbon metabolism pathways. Regarding the altitudinal variation of the same species, common metabolic pathways between the two groups included fructose and mannose metabolism, α-linolenic acid metabolism, and glycerophospholipid metabolism. The metabolic pathways enriched only inU. hyperboreaincluded starch and sucrose metabolism, galactose metabolism, and phenylpropanoid biosynthesis. The metabolically enriched pathways specific toU. dioicaincluded pantothenate and coenzyme A biosynthesis, as well as glutathione metabolism.

CONCLUSIONS

We found that the metabolic differences between the two sympatric species are primarily in carbohydrate and phenylpropanoid contents. The differential metabolites of the same species across different altitudes were enriched mainly in carbon metabolism pathways and lipid metabolism pathways. Thus, our study revealed that the high-altitude adaptation mechanisms of sympatric species are not identical. Moreover, adaptation strategies within the same species were generally consistent across altitudes, exhibiting only slight variations. This study provide novel insights into the adaptive metabolic strategies of U. hyperborea and U. dioica, contributing to a deeper understanding of the mechanisms underlying plant adaptation to extreme high-altitude conditions.

Exploring physiological and molecular dynamics of drought stress responses in plants: challenges and future directions

Plants face multifactorial environmental stressors mainly due to global warming and climate change which affect their growth, metabolism, and productivity. Among them, is drought stress which alters intracellular water relations, photosynthesis, ion homeostasis and elevates reactive oxygen species which eventually reduce their growth and yields. In addition, drought alters soil physicochemical properties and beneficial microbiota which are critical for plant survival. Recent reports have shown that climate change is increasing the occurrence and intensity of drought in many regions of the world, which has become a primary concern in crop productivity, ecophysiology and food security. To develop ideas and strategies for protecting plants against the harmful effects of drought stress and meeting the future food demand under climatic calamities an in-depth understanding of molecular regulatory pathways governing plant stress responses is imperative. In parallel, more research is needed to understand how drought changes the features of soil, particularly microbiomes, as microorganisms can withstand drought stress faster than plants, which could assist them to recover. In this review we first discuss the effect of drought stress on plants, soil physicochemical properties and microbiomes. How drought stress affects plant microbe interactions and other microbe-driven beneficial traits was also highlighted. Next, we focused on how plants sense drought and undergo biochemical reprogramming from root to shoot to regulate diverse adaptive traits. For instance, the role of calcium (Ca2+), reactive oxygen species (ROS) and abscisic acid (ABA) in modulating different cellular responses like stomata functioning, osmotic adjustment, and other adaptive traits. We also provide an update on the role of different hormones in drought signaling and their crosstalk which allows plants to fine tune their responses during drought stress. Further, we discussed how recurrent drought exposure leads to the development of short-term memory in plants that allows them to survive future drought stresses. Lastly, we discussed the application of omics and biotechnological-based mitigating approaches to combat drought stress in sustainable agriculture. This review offers a deeper understanding of multiple factors that are related to drought stress in plants which can be useful for drought improvement programs.

MicroRNAs in Plant Genetic Regulation of Drought Tolerance and Their Function in Enhancing Stress Adaptation

Adverse environmental conditions, including drought stress, pose a significant threat to plant survival and agricultural productivity, necessitating innovative and efficient approaches to enhance their resilience. MicroRNAs (miRNAs) are recognized as key elements in regulating plant adaptation to drought stress, with a notable ability to modulate various physiological and molecular mechanisms. This review provides an in-depth analysis of the role of miRNAs in drought response mechanisms, including abscisic acid (ABA) signaling, reactive oxygen species (ROS) detoxification, and the optimization of root system architecture. Additionally, it examines the effectiveness of bioinformatics tools, such as those employed in in silico analyses, for studying miRNA-mRNA interactions, as well as the potential for their integration with experimental methods. Advanced methods such as microarray analysis, high-throughput sequencing (HTS), and RACE-PCR are discussed for their contributions to miRNA target identification and validation. Moreover, new data and perspectives are presented on the role of miRNAs in plant responses to abiotic stresses, particularly drought adaptation. This review aims to deepen the understanding of genetic regulatory mechanisms in plants and to establish a robust scientific foundation for the development of drought-tolerant crop varieties.

Integrated transcriptomic, proteomic and metabolomic analyses revealing the roles of amino acid and sucrose metabolism in augmenting drought tolerance in Agropyron mongolicum

Drought, a major consequence of climate change, initiates molecular interactions among genes, proteins, and metabolites. Agropyron mongolicum a high-quality perennial grass species, exhibits robust drought resistance. However, the molecular mechanism underlying this resistance remaining largely unexplored. In this study, we performed an integrated analysis of the transcriptome, proteome, and metabolome of A. mongolicum under optimal and drought stress conditions. This combined analysis highlighted the pivotal role of transporters in responding to drought stress. Moreover, metabolite profiling indicated that arginine and proline metabolism, as well as the pentose phosphate pathway, are significantly involved in the drought response of A. mongolicum. Additionally, the integrated analysis suggested that proline metabolism and the pentose phosphate pathway are key elements of the drought resistance strategy in A. mongolicum plants. In summary, our research elucidates the drought adaptation mechanisms of A. mongolicum and identifies potential candidate genes for further study.

SaTDT enhanced plant tolerance to NaCl stress by modulating the levels of malic acid and citric acid in cells

The issue of soil salinization is a global concern that significantly impairs crop productivity, quality, and distribution. Tonoplast Dicarboxylate Transporter (TDT) is a pivotal malic acid transporter localized on the vacuolar membrane, involving in maintaining intracellular pH homeostasis in plants. However, the molecular mechanisms and regulatory pathways underlying plant salt tolerance through TDT remain elusive. In this study, we cloned a gene encoding vacuolar membrane dicarboxylic acid transporter designated as SaTDT from the halophyte Spartina alterniflora. Subsequently, its role in regulating salt stress was investigated. The heterologous expression of SaTDT in Arabidopsis thaliana was observed to enhance the transgenic plants' tolerance to salt stress and alleviate the growth damage caused by this stress. The overexpression of SaTDT can simultaneously enhance plant photosynthetic efficiency by regulating the cellular contents of malic acid and citric acid, or by increasing the activity of MDH and PEPC enzymes. It also regulates and balances energy utilization during carbon assimilation under salt-stressed conditions, thereby establishing an energetic foundation for enhancing plant tolerance to stress. SaTDT also has the capacity to enhance the plant cells' ability in regulating antioxidant enzyme activity or osmotic accumulation, thereby playing a crucial role in maintaining intracellular redox homeostasis. In conclusion, our findings establish a foundation basis for elucidating the regulatory role of the SaTDT gene in S.alterniflora's adaptation to high-salinity habitats.

Gene regulatory networks in abiotic stress responses via single-cell sequencing and spatial technologies: Advances and opportunities

Understanding intricate gene regulatory networks (GRNs) orchestrating responses to abiotic stresses is crucial for enhancing climate resilience in crop plants. Recent advancements in single-cell and spatial technologies have revolutionized our ability to dissect the GRNs at unprecedented resolution. Here, we explore the progress, challenges, and opportunities these state-of-the-art technologies offer in delineating the cellular intricacies of plant responses to abiotic stress. Using scRNA-seq, the transcriptome landscape of individual plant cells along with their lineages and regulatory interactions can be unraveled. Moreover, coupling scRNA-seq with spatial transcriptomics provides spatially resolved gene expression and insights into cell-to-cell interactions. In addition, the chromatin accessibility assays can discover the regulatory regions governing abiotic stress responses. An integrated multi-omics approach can facilitate discovery of cell-type-specific GRNs to reveal the key components that coordinate adaptive responses to different stresses. These potential regulatory factors can be harnessed for genetic engineering to enhance stress resilience in crop plants.

Natural variation in the chickpea metabolome under drought stress

Chickpea is the world's fourth largest grown legume crop, which significantly contributes to food security by providing calories and dietary protein globally. However, the increased frequency of drought stress has significantly reduced chickpea production in recent years. Here, we have performed a field experiment with 36 diverse chickpea genotypes to evaluate grain yield, photosynthetic activities and molecular traits related to drought stress. For metabolomics analysis, leaf tissue was collected at three time points representing different pod-filling stages. We identified L-threonic acid, fructose and sugar alcohols involved in chickpea adaptive drought response within the mid-pod-filling stage. A stress susceptibility index for each genotype was calculated to identify tolerance capacity under drought, distributing the 36 genotypes into four categories from best to worst performance. To understand how biochemical mechanisms control different traits for genetic improvement, we performed a differential Jacobian analysis, which unveiled the interplay between various metabolic pathways across three time points, including higher flux towards inositol interconversions, glycolysis for high-performing genotypes, fumarate to malate conversion, and carbon and nitrogen metabolism perturbations. Metabolic GWAS (mGWAS) analysis uncovered gene candidates involved in glycolysis and MEP pathway corroborating with the differential biochemical Jacobian results. Accordingly, this proposed data analysis strategy bridges the gap from pure statistical association to causal biochemical relations by exploiting natural variation. Our study offers new perspectives on the genetic and metabolic understanding of drought tolerance-associated diversity in the chickpea metabolome and led to the identification of metabolic control points that can be also tested in other legume crops.

Codonopsis pilosula seedling drought- responsive key genes and pathways revealed by comparative transcriptome

Background

Codonopsis pilosula (Campanulaceae) is a traditional herbal plant that is widely used in China, and the drought stress during the seedling stage directly affects the quality, ultimately impacting its yield. However, the molecular mechanisms underlying the drought resistance of C. pilosula seedlings remain unclear.

Method

Herein, we conducted extensive comparative transcriptome and physiological studies on two distinct C. pilosula cultivar (G1 and W1) seedlings subjected to a 4-day drought treatment.

Results

Our findings revealed that cultivar G1 exhibited enhanced retention of proline and chlorophyll, alongside a marked elevation in peroxidase activity, coupled with diminished levels of malondialdehyde and reduced leaf relative electrolyte leakage compared with cultivar W1. This suggested that cultivar G1 had relatively higher protective enzyme activity and ROS quenching capacity. We discerned a total of 21,535 expressed genes and identified 4,192 differentially expressed genes (DEGs) by RNA sequencing (RNA-seq). Our analysis revealed that 1,764 DEGs unique to G1 underwent thorough annotation and functional categorization utilizing diverse databases. Under drought conditions, the DEGs in G1 were predominantly linked to starch and sucrose metabolic pathways, plant hormone signaling, and glutathione metabolism. Notably, the drought-responsive genes in G1 were heavily implicated in hormonal modulation, such as ABA receptor3-like gene (PYL9), regulation by transcription factors (KAN4, BHLH80, ERF1B), and orchestration of drought-responsive gene expression. These results suggest that cultivar G1 possesses stronger stress tolerance and can better adapt to drought growing conditions. The congruence between qRT-PCR validation and RNA-seq data for 15 DEGs further substantiated our findings.

Conclusion

Our research provides novel insights into the physiological adaptations of C. pilosula to arid conditions and lays the groundwork for the development of new, drought-tolerant C. pilosula cultivars.

Identification of Drought Stress-Responsive Genes in Rice by Random Walk with Multi-Restart Probability on MultiPlex Biological Networks

Exploring drought stress-responsive genes in rice is essential for breeding drought-resistant varieties. Rice drought resistance is controlled by multiple genes, and mining drought stress-responsive genes solely based on single omics data lacks stability and accuracy. Multi-omics correlation analysis and biological molecular network analysis provide robust solutions. This study proposed a random walk with a multi-restart probability (RWMRP) algorithm, based on the Restarted Random Walk (RWR) algorithm, to operate on rice MultiPlex biological networks. It explores the interactions between biological molecules across various levels and ranks potential genes. RWMRP uses eigenvector centrality to evaluate node importance in the network and adjusts the restart probabilities accordingly, diverging from the uniform restart probability employed in RWR. In the random walk process, it can be better to consider the global relationships in the network. Firstly, we constructed a MultiPlex biological network by integrating the rice protein-protein interaction, gene pathway, and gene co-expression network. Then, we employed RWMRP to predict the potential genes associated with rice tolerance to drought stress. Enrichment and correlation analyses resulted in the identification of 12 drought-related genes. We further conducted quantitative real-time polymerase chain reaction (qRT-PCR) analysis on these 12 genes, ultimately identifying 10 genes responsive to drought stress.

Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice

Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.