Screening of mungbean for drought tolerance and transcriptome profiling between drought-tolerant and susceptible genotype in response to drought stress

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.

A robust in-vitro and ex-vitro Agrobacterium rhizogenes-mediated hairy root transformation system in mungbean for efficient visual screening of transformants using the RUBY reporter

BACKGROUND

Mungbean is one of the most economically important grain legume crops in Asia. Functional genomics studies in mungbean are necessary to understand the molecular mechanisms behind agronomic traits, to advance the crop improvement. However, this progress is significantly impeded by the absence of effective and extensive genetic analysis tools. Agrobacterium rhizogenes-mediated hairy root transformation has become a powerful tool for studying gene function and an efficient alternative for investigating root-specific interactions and processes in different species, due to its quick and simple methodology. Agrobacterium-mediated plant transformation, however, is known to be difficult in legumes, especially in mungbean.

RESULTS

In this report, we developed an Agrobacterium rhizogenes-mediated mungbean transformation system using both in-vitro and ex-vitro approaches, with RUBY employed as a reporter gene. We optimized various parameters, including mungbean genotypes, explant age, optical density of the bacterial culture, co-cultivation medium, and acetosyringone concentration. Our findings indicated that in-vitro transformation was more efficient than ex-vitro in terms of hairy root induction percentage and the proportion of transformed hairy roots expressing the RUBY reporter gene. However, the ex-vitro transformation technique was faster and less complex than the in-vitro method. The highest transformation efficiency for RUBY expression was achieved using 5-day-old cotyledonary nodal explants of cv. K-851, inoculated for 30 min with A4 Agrobacterium cells resuspended in full-strength MS medium at an OD₆₀₀ of 0.5 and supplemented with 100 µM acetosyringone. A total of 60 composite plants were generated and evaluated through PCR, resulting in a transformation efficiency of 6.13%. These optimized parameters also led to the highest percentage of RUBY expression using the two-step ex-vitro hairy root transformation method.

CONCLUSION

We have developed a simple, rapid, low-cost, and labor-efficient Agrobacterium rhizogenes-mediated mungbean transformation protocol using both in-vitro and ex-vitro approaches, with RUBY as a reporter gene. This method enables the generation of composite mungbean plants that are easier to handle, exhibit higher transformation efficiency, and can be effectively used for root specific functional genomics studies. We expect this technology to be widely adopted for investigating root-related processes in mungbean and other plant species.

Streptomyces improves sugarcane drought tolerance by enhancing phenylalanine biosynthesis and optimizing the rhizosphere environment

Drought stress is a common hazard faced by sugarcane growth, and utilizing microorganisms to enhance plant tolerance to abiotic stress has become an important method for sustainable agricultural development. Several studies have demonstrated that Streptomyces chartreuses WZS021 improves sugarcane tolerance to drought stress. However, the molecular mechanisms underlying tolerance at the transcriptional and metabolomic levels remain unclear. We comprehensively evaluated the physiological and molecular mechanisms by which WZS021 enhances drought tolerance in sugarcane, by performing transcriptome sequencing and non-targeted metabolomics; and examining rhizosphere soil properties and plant tissue antioxidant capacity. WZS021 inoculation improved the rhizosphere nutritional environment (AP, ammonia, OM) of sugarcane and enhanced the antioxidant capacity of plant roots, stems, and leaves (POD, SOD, CAT). Comprehensive analyses of the transcriptome and metabolome revealed that WZS021 mainly affects plant drought tolerance through phenylalanine metabolism, plant hormone signal transduction, and flavonoid biosynthesis pathways. The drought tolerance signaling molecules mediated by WZS021 include petunidin, salicylic acid, α-Linoleic acid, auxin, geranylgeraniol and phenylalanine, as well as key genes related to plant hormone signaling transduction (YUCCA, amiE, AUX, CYPs, PAL, etc.). Interestingly, inoculation with WZS021 during regular watering induces a transcriptome-level response to biological stress in sugarcane plants. This study further elucidates a WZS021-dependent rhizosphere-mediated regulatory mechanism for improving sugarcane drought tolerance, providing a theoretical basis for increasing sugarcane production capacity.

Effect of exogenous selenium on physicochemical, structural, functional, thermal, and gel rheological properties of mung bean (Vigna radiate L.) protein

Selenium (Se) biofortification during the growth process of mung bean is an effective method to improve the Se content and quality. However, the effect of Se biofortification on the physicochemical properties of mung bean protein is unclear. The objective of this study was to clarify the changes in the composition, Se forms, particle structure, functional properties, thermal stability, and gel properties of mung bean protein at four Se application levels. The results showed that the Se content of mung bean protein increased in a dose-dependent manner, with 7.96-fold (P1) and 8.52-fold (P2) enhancement at the highest concentration. Exogenous Se application promotes the conversion of inorganic Se to organic Se. Among them, selenomethionine (SeMet) and methyl selenocysteine (MeSeCys) replaced Met and Cys through the S metabolic pathway and became the dominant organic Se forms in Se-enriched mung bean protein, accounting for more than 80 % of the total Se content. Exogenous Se at 30 g/hm2 significantly up-regulated protein content and promoted the synthesis of sulfur-containing protein components and hydrophobic amino acids in the presence of increased levels of SeMet and MeSeCys. Meanwhile, Cys and Met substitution altered the sulfhydryl groups (SH), β-sheets, and β-turns of protein. The particle size and microstructural characteristics depend on the protein itself and were not affected by exogenous Se. The Se-induced increase in the content of hydrophobic amino acids and β-sheets synergistically increases the thermal stability of the protein. Moderate Se application altered the functional properties of mung bean protein, which was mainly reflected in the significant increase in oil holding capacity (OHC) and foaming capacity (FC). In addition, the increase in SH and β-sheets induced by exogenous Se could alter the protein intermolecular network, contributing to the increase in storage modulus (G') and loss modulus (G″), which resulted in the formation of more highly elastic gels. This study further promotes the application of mung bean protein in the field of food processing and provides a theoretical basis for the extensive development of Se-enriched mung bean protein.

Identification of Drought-Resistant Response in Proso Millet (Panicum miliaceum L.) Root through Physiological and Transcriptomic Analysis

Proso millet (Panicum miliaceum L.) is resilient to abiotic stress, especially to drought. However, the mechanisms by which its roots adapt and tolerate salt stress are obscure. In this study, to clarify the molecular mechanism of proso millet in response to drought stress, the physiological indexes and transcriptome in the root of seedlings of the proso millet cultivar 'Yumi 2' were analyzed at 0, 0.5, 1.0, 1.5, and 3.0 h of stimulated drought stress by using 20% PEG-6000 and after 24 h of rehydration. The results showed that the SOD activity, POD activity, soluble protein content, MDA, and O2-· content of 'Yumi 2' increased with the time of drought stress, but rapidly decreased after rehydration. Here, 130.46 Gb of clean data from 18 samples were obtained, and the Q30 value of each sample exceeded 92%. Compared with 0 h, the number of differentially expressed genes (DEGs) reached the maximum of 16,105 after 3 h of drought, including 9153 upregulated DEGs and 6952 downregulated DEGs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that upregulated DEGs were mainly involved in ATP binding, nucleus, protein serine/threonine phosphatase activity, MAPK signaling pathway-plant, plant-pathogen interactions, and plant hormone signal transduction under drought stress, while downregulated DEGs were mainly involved in metal ion binding, transmembrane transporter activity, and phenylpropanoid biosynthesis. Additionally, 1441 TFs screened from DEGs were clustered into 64 TF families, such as AP2/ERF-ERF, bHLH, WRKY, NAC, MYB, and bZIP TF families. Genes related to physiological traits were closely related to starch and sucrose metabolism, phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction. In conclusion, the active oxygen metabolism system and the soluble protein of proso millet root could be regulated by the activity of protein serine/threonine phosphatase. AP2/ERF-ERF, bHLH, WRKY, NAC, MYB, and bZIP TF families were found to be closely associated with drought tolerance in proso millet root. This study will provide data to support a subsequent study on the function of the drought tolerance gene in proso millet.

Environmental conditions affect the nutritive value and alkaloid profiles of Lupinus forage: Opportunities and threats for sustainable ruminant systems

The identification of crops that simultaneously contribute to the global protein supply and mitigate the effects of climate change is an urgent matter. Lupins are well adapted to nutrient-poor or contaminated soils, tolerate various abiotic stresses, and present relevant traits for acting as ecosystem engineers. Lupins are best studied for their seeds, but their full foraging potential needs further evaluation. This study evaluated the effects of location and sowing date on forage production, proximate composition, and the detailed mineral and alkaloid profiles of three species of Lupinus (L. albus cv. Estoril, L. angustifolius cv. Tango, and L. luteus cv. Cardiga). Sowing date and location and their interaction with the plant species significantly affected the vast majority of measured parameters, emphasizing the effects of climate and soil conditions on these crops. The relatively high crude protein and in vitro digestibility support the potential of the lupin species studied as sustainable forage protein sources in diets for ruminant animals. The content of individual essential macro and trace elements was below the maximum tolerable levels for cattle and sheep. Lupanine, smipine, and sparteine were the most abundant quinolizidine alkaloids in L. albus cv. Estoril, lupanine, and sparteine in L. angustifolius cv. Tango, and lupinine, gramine, ammodendrine, and sparteine in L. luteus cv. Cardiga. Based on the maximum tolerable levels of total quinolizidine alkaloid intake, the dietary inclusion of forages of L. albus cv. Estoril and L. angustifolius cv. Tango does not pose a risk to the animals, but the high alkaloid content of L. luteus cv. Cardiga may compromise its utilization at high levels in the diet. Overall, the results reveal a high potential for lupins as protein forage sources well adapted to temperate regions and soils with lower fertility, with a relevant impact on livestock sustainability in a climate change era.

Comparative transcriptome analysis of two contrasting genotypes provides new insights into the drought response mechanism in pigeon pea (Cajanus cajan L. Millsp.)

BACKGROUND

Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon pea is already quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity.

OBJECTIVE

Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea.

METHODS

The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performed to identify the orthologs of the DEGs.

RESULTS

1102 potential drought-responsive genes were found to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) and were highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response.

CONCLUSION

In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand and improve susceptibility to drought.

Genome-wise association study identified genomic regions associated with drought tolerance in mungbean (Vigna radiata (L.) R. Wilczek)

A total of 282 mungbean accessions were resequenced to identify genome-wide variants and construct a highly precise variant map, and drought tolerance-related loci and superior alleles were identified by GWAS. Mungbean (Vigna radiata (L.) R. Wilczek) is an important food legume crop that is highly adapted to drought environments, but severe drought significantly curtails mungbean production. Here, we resequenced 282 mungbean accessions to identify genome-wide variants and constructed a highly precise map of mungbean variants. A genome-wide association study was performed to identify genomic regions for 14 drought tolerance-related traits in plants grown under stress and well-watered conditions over three years. One hundred forty-six SNPs associated with drought tolerance were detected, and 26 candidate loci associated with more than two traits were subsequently selected. Two hundred fifteen candidate genes were identified at these loci, including eleven transcription factor genes, seven protein kinase genes and other protein coding genes that may respond to drought stress. Furthermore, we identified superior alleles that were associated with drought tolerance and positively selected during the breeding process. These results provide valuable genomic resources for molecular breeding and will accelerate future efforts aimed at mungbean improvement.

Biofortification of mungbean (Vigna radiata L. (Wilczek)) with boron, zinc and iron alters its grain yield and nutrition

Mungbean [Vigna radiata L. (Wilczek)] is considered as an extremely nutritious crop possessing a high level of micronutrients, but their low bioavailability in the crop leads to micronutrient malnutrition in humans. Therefore, the present study was conducted to investigate the potential of nutrients viz. boron (B), zinc (Zn) and iron (Fe) biofortification on productivity, nutrient concentration and uptake as well as the economics of mungbean cultivation. In the experiment, the various combinations of RDF with ZnSO₄.7H₂O (0.5%), FeSO₄.7H₂O (0.5%) and borax (0.1%) were applied to mungbean variety ML 2056. The combined foliar application of Zn, Fe and B was highly efficient in increasing the yield of grain as well as straw in mungbean exhibiting maximum values i.e. 944 kg ha^-1 and 6133 kg ha^-1, respectively. Similar results for B, Zn and Fe concentration in grain (27.3 mg kg^-1, 35.7 mg kg^-1 and 187.1 mg kg^-1, respectively) and straw (21.1 mg kg^-1, 18.6 mg kg^-1 and 376.1 mg kg^-1, respectively) of mungbean were observed. Also, uptake of Zn and Fe by grain (31.3 g ha^-1 and 164.4 g ha^-1, respectively), as well as straw (113.7 g ha^-1 and 2295.0 g ha^-1, respectively), was maximum for the above treatment. Whereas, the B uptake was found to enhance significantly through the combined application of B, Zn and Fe, where the values 24.0 g ha^-1 and 128.7 g ha^-1 corresponded to grain and straw, respectively. Thus, combined use of ZnSO₄.7H₂O (0.5%) + FeSO₄.7H₂O (0.5%) and borax (0.1%) significantly improved the yield outcomes, the concentration of B, Zn and Fe, uptake and economic returns of mungbean cultivation to alleviate the B, Zn and Fe deficiency.

Effects of exogenous auxin on yield in foxtail millet (Setaria italica L.) when applied at the grain-filling stage

Foxtail millet (Setaria italica L.) is of high nutritious value, which is an important crop in arid and semi-arid regions. The objective of this experiment was to explore the effects of the synthetic auxin naphthalene acetic acid (NAA) on the physiological processes of foxtail millet, and to provide a theoretical basis and technical approaches for its efficient use in millet cultivation. Two foxtail millet varieties ('Jingu 21' and 'Zhangzagu 5') were treated with six concentrations of NAA from 0-144 mg L^-1 at the grain-filling stage in field experiments. The photosynthetic pigment contents, gas exchange parameters, chlorophyll fluorescence parameters, and grain yield were measured in foxtail millet. The results showed that low concentrations of NAA (18-36 mg L^-1) increased the contents of photosynthetic pigments, and increased the activities of antioxidant enzymes, the photosynthetic rate, and the activity of photosystem system II (PS II). At higher NAA concentrations, the facilitation effect of the treatments diminished, showing a clear concentration effect. In this study, yield was significantly and positively correlated with PS II effective quantum yield (Y(II)) and the PSII electron transport rate (ETR), and the net photosynthetic rate (Pn) was significantly and positively correlated with chlorophyll content, stomatal conductance (Gs), Y(II), and ETR. These results also indicated that exogenous NAA application promotes the production of ATP and NADPH by increasing the efficiency of electron transfer within the photosystems and also improved photochemical utilization, which facilitates the fixation and reduction of carbon, ultimately leading to an increase in Pn and increasing grain yield in foxtail millet.

Metabolomic and transcriptomic changes in mungbean (Vigna radiata (L.) R. Wilczek) sprouts under salinity stress

Mungbean (Vigna radiata) sprouts are consumed globally as a healthy food with high nutritional values, having antioxidant and anticancer capacity. Under mild salinity stress, plants accumulate more secondary metabolites to alleviate oxidative stress. In this study, metabolomic and transcriptomic changes in mungbean sprouts were identified using a reference cultivar, sunhwa, to understand the regulatory mechanisms of secondary metabolites in response to salinity stress. Under salinity conditions, the contents of phenylpropanoid-derived metabolites, including catechin, chlorogenic acid, isovitexin, p-coumaric acid, syringic acid, ferulic acid, and vitexin, significantly increased. Through RNA sequencing, 728 differentially expressed genes (DEGs) were identified and 20 DEGs were detected in phenylpropanoid and flavonoid biosynthetic pathways. Among them, 11 DEGs encoding key enzymes involved in the biosynthesis of the secondary metabolites that increased after NaCl treatment were significantly upregulated, including dihydroflavonol 4-reductase (log₂FC 1.46), caffeoyl-CoA O-methyltransferase (1.38), chalcone synthase (1.15), and chalcone isomerase (1.19). Transcription factor families, such as MYB, WRKY, and bHLH, were also identified as upregulated DEGs, which play a crucial role in stress responses in plants. Furthermore, this study showed that mild salinity stress can increase the contents of phenylpropanoids and flavonoids in mungbean sprouts through transcriptional regulation of the key enzymes involved in the biosynthetic pathways. Overall, these findings will provide valuable information for molecular breeders and scientists interested in improving the nutritional quality of sprout vegetables.

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.

Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.)

Drought is among the most serious environmental issue globally, and seriously affects the development, growth, and yield of crops. Maize (Zea mays L.), an important crop and industrial raw material, is planted on a large scale worldwide and drought can lead to large-scale reductions in maize corn production; however, few studies have focused on the maize root system mechanisms underlying drought resistance. In this study, miRNA-mRNA analysis was performed to deeply analyze the molecular mechanisms involved in drought response in the maize root system under drought stress. Furthermore, preliminary investigation of the biological function of miR408a in the maize root system was also conducted. The morphological, physiological, and transcriptomic changes in the maize variety "M8186" at the seedling stage under 12% PEG 6000 drought treatment (0, 7, and 24 h) were analyzed. With prolonged drought stress, seedlings gradually withered, the root system grew significantly, and abscisic acid, brassinolide, lignin, glutathione, and trehalose content in the root system gradually increased. Furthermore, peroxidase activity increased, while gibberellic acid and jasmonic acid gradually decreased. Moreover, 32 differentially expressed miRNAs (DEMIRs), namely, 25 known miRNAs and 7 new miRNAs, and 3,765 differentially expressed mRNAs (DEMRs), were identified in maize root under drought stress by miRNA-seq and mRNA-seq analysis, respectively. Through combined miRNA-mRNA analysis, 16 miRNA-target gene pairs, comprising 9 DEMIRs and 15 DEMRs, were obtained. In addition, four metabolic pathways, namely, "plant hormone signal transduction", "phenylpropane biosynthesis", "glutathione metabolism", and "starch and sucrose metabolism", were predicted to have important roles in the response of the maize root system to drought. MiRNA and mRNA expression results were verified by real-time quantitative PCR. Finally, miR408a was selected for functional analysis and demonstrated to be a negative regulator of drought response, mainly through regulation of reactive oxygen species accumulation in the maize root system. This study helps to elaborate the regulatory response mechanisms of the maize root system under drought stress and predicts the biological functions of candidate miRNAs and mRNAs, providing strategies for subsequent mining for, and biological breeding to select for, drought-responsive genes in the maize root system.

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.

Thirty Years of Mungbean Genome Research: Where Do We Stand and What Have We Learned?

Mungbean is a socioeconomically important legume crop in Asia that is currently in high demand by consumers and industries both as dried beans and in plant-based protein foods. Marker-assisted and genomics-assisted breeding are promising approaches to efficiently and rapidly develop new cultivars with improved yield, quality, and resistance to biotic and abiotic stresses. Although mungbean was at the forefront of research at the dawn of the plant genomics era 30 years ago, the crop is a "slow runner" in genome research due to limited genomic resources, especially DNA markers. Significant progress in mungbean genome research was achieved only within the last 10 years, notably after the release of the VC1973A draft reference genome constructed using next-generation sequencing technology, which enabled fast and efficient DNA marker development, gene mapping, and identification of candidate genes for complex traits. Resistance to biotic stresses has dominated mungbean genome research to date; however, research is on the rise. In this study, we provide an overview of the past progress and current status of mungbean genomics research. We also discuss and evaluate some research results to provide a better understanding of mungbean genomics.

Distinctive Physio-Biochemical Properties and Transcriptional Changes Unfold the Mungbean Cultivars Differing by Their Response to Drought Stress at Flowering Stage

Mungbean is a nutritionally and economically important pulse crop cultivated around Asia, mainly in India. The crop is sensitive to drought at various developmental stages of its growing period. However, there is limited or almost no research on a comparative evaluation of mung-bean plants at the flowering stage under drought conditions. Hence, the aim of this research was to impose the drought stress on two mungbean cultivars VRM (Gg) 1 and CO6 at the flowering stage and assess the physio-biochemical and transcriptional changes. After imposing the drought stress, we found that VRM (Gg) 1 exhibited a low reduction in physiological traits (Chlorophyll, relative water content, and plant dry mass) and high proline content than CO6. Additionally, VRM (Gg) 1 has a low level of H2O2 and MDA contents and higher antioxidant enzymes (SOD, POD, and CAT) activity than CO6 during drought stress. The transcriptional analysis of photosynthesis (PS II-PsbP, PS II-LHC, PS I-PsaG/PsaK, and PEPC 3), antioxidant (SOD 2, POD, CAT 2), and drought-responsive genes (HSP-90, DREB2C, NAC 3 and AREB 2) show that VRM (Gg) 1 had increased transcripts more than CO6 under drought stress. Taken together, VRM (Gg) 1 had a better photosynthetic performance which resulted in fewer reductions in chlorophyll, relative water content, and plant dry mass during drought stress. In addition, higher antioxidative enzyme activities led to lower H2O2 and MDA levels, limiting oxidative damage in VRM (Gg) 1. This was positively correlated with increased transcripts of photosynthesis and antioxidant-related genes in VRM (Gg) 1. Further, the increased transcripts of drought-responsive genes indicate that VRM (Gg) 1 has a better genetic basis against drought stress than CO6. These findings help to understand the mungbean response to drought stress and will aid in the development of genotypes with greater drought tolerance by utilizing natural genetic variants.

De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal

BACKGROUND

The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers.

RESULTS

We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis.

CONCLUSIONS

The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement.

Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean

Background

Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes.

Methods

Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of -1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed.

Results

Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.

Transcriptome Characterization of the Roles of Abscisic Acid and Calcium Signaling during Water Deficit in Garlic

Garlic (Allium sativum L.) is one of the most important vegetable crops, and breeding drought-tolerant varieties is a vital research goal. However, the underlying molecular mechanisms in response to drought stress in garlic are still limited. In this study, garlic seedlings were subjected to 15% PEG6000 for 0, 1, 4, and 12 h, respectively, to simulate drought stress. Changes of transcriptomes as a result of drought stress in garlic leaves were determined by de novo assembly using the Illumina platform. In total, 96,712 unigenes and 11,936 differentially expressed genes (DEGs) were identified in the presence of drought conditions. Transcriptome profiling revealed that the DEGs were mainly enriched in the biosynthesis of secondary metabolites, MAPK signaling pathway, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction. Genes involved in abscisic acid and calcium signaling were further investigated and discussed. Our results indicated that a coordinated interplay between abscisic acid and calcium is required for drought-induced response in garlic.

Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root

Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R² = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.

Transcriptome and methylome changes in two contrasting mungbean genotypes in response to drought stress

Background

Due to drought stress, the growth, distribution, and production of mungbean is severely restricted. Previous study combining physiological and transcriptomic data indicated different genotypes of mungbean exhibited variable responses when exposed to drought stress. Aside from the genetic variation, the modifications of environmentally induced epigenetics alterations on mungbean drought-stress responses were still elusive.

Results

In this study, firstly, we compared the drought tolerance capacity at seedling stage by detecting physiological parameters in two contrasting genotypes wild mungbean 61 and cultivar 70 in response to drought stress. We found that wild mungbean 61 showed lower level of MDA and higher levels of POD and CAT, suggesting wild mungbean 61 exhibited stronger drought resistance. Transcriptomic analysis indicated totally 2859 differentially expressed genes (DEGs) were detected when 70 compared with 61 (C70 vs C61), and the number increased to 3121 in the comparison of drought-treated 70 compared with drought-treated 61 (D70 vs D61). In addition, when drought-treated 61 and 70 were compared with their controls, the DEGs were 1117 and 185 respectively, with more down-regulated DEGs than up-regulated in D61 vs C61, which was opposite in D70 vs C70. Interestingly, corresponding to this, after drought stress, more hypermethylated differentially methylated regions (DMRs) in 61 were detected and more hypomethylated DMRs in 70 were detected. Further analysis suggested that the main variations between 61 and 70 existed in CHH methylation in promoter. Moreover, the preference of methylation status alterations in D61 vs C61 and D70 vs C70 also fell in CHH sequence context. Further analysis of the correlation between DMRs and DEGs indicated in both D61 vs C61 and D70 vs C70, the DMRs in gene body was significantly negatively correlated with DEGs.

Conclusions

The physiological parameters in this research suggested that wild mungbean 61 was more resistant to drought stress, with more hypermethylated DMRs and less hypomethylated DMRs after drought stress, corresponding to more down-regulated DEGs than up-regulated DEGs. Among the three DNA methylation contexts CG, CHG, and CHH, asymmetric CHH contexts were more dynamic and prone to be altered by drought stress and genotypic variations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08315-z.

Comparative analysis of alfalfa (Medicago sativa L.) seedling transcriptomes reveals genotype-specific drought tolerance mechanisms

Drought is one of the main abiotic factors that affect alfalfa yield. The identification of genes that control this complex trait can provide important insights for alfalfa breeding. However, little is known about how alfalfa responds and adapts to drought stress, particularly in cultivars of differing drought tolerance. In this study, the drought-tolerant cultivar Dryland 'DT' and the drought-sensitive cultivar WL343HQ 'DS' were used to characterize leaf and root physiological responses and transcriptional changes in response to water deficit. Under drought stress, Dryland roots (DTR) showed more differentially expressed genes than WL343HQ roots (DSR), whereas WL343HQ leaves (DSL) showed more differentially expressed genes than Dryland leaves (DTL). Many of these genes were involved in stress-related pathways, carbohydrate metabolism, and lignin and wax biosynthesis, which may have improved the drought tolerance of alfalfa. We also observed that several genes related to ABA metabolism, root elongation, peroxidase activity, cell membrane stability, ubiquitination, and genetic processing responded to drought stress in alfalfa. We highlighted several candidate genes, including sucrose synthase, xylan 1,4-beta-xylosidase, primary-amine oxidase, and alcohol-forming fatty acyl-CoA reductase, for future studies on drought stress resistance in alfalfa and other plant species. In summary, our results reveal the unique drought adaptation and resistance characteristics of two alfalfa genotypes. These findings, which may be valuable for drought resistance breeding, warrant further gene functional analysis to augment currently available information and to clarify the drought stress regulatory mechanisms of alfalfa and other plants.

Micronutrient fertilization enhances ROS scavenging system for alleviation of abiotic stresses in plants

Reactive oxygen species (ROS) such as hydrogen peroxide at low concentrations act as signaling of several abiotic stresses. Overproduction of hydrogen peroxide causes the oxidation of plant cell lipid phosphate layer promoting senescence and cell death. To mitigate the effect of ROS, plants develop antioxidant defense mechanisms (superoxide dismutase, catalase, guaiacol peroxidase), ascorbate-glutathione cycle enzymes (ASA-GSH) (ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase and glutathione reductase), which have the function of removing and transforming ROS into non-toxic substances to maintain cellular homeostasis. Foliar or soil application of fertilizers containing B, Cu, Fe, Mn, Mo, Ni, Se and Zn at low concentrations has the ability to elicit and activate antioxidative enzymes, non-oxidizing metabolism, as well as sugar metabolism to mitigate damage by oxidative stress. Plants treated with micronutrients show higher tolerance to abiotic stress and better nutritional status. In this review, we summarized results indicating micronutrient actions in order to reduce ROS resulting the increase of photosynthetic capacity of plants for greater crop yield. This meta-analysis provides information on the mechanism of action of micronutrients in combating ROS, which can make plants more tolerant to several types of abiotic stress such as extreme temperatures, salinity, heavy metals and excess light.