Differential Physio-Biochemical and Metabolic Responses of Peanut (Arachis hypogaea L.) under Multiple Abiotic Stress Conditions

Mechanisms of plant acclimation to multiple abiotic stresses

Plants frequently encounter a range of abiotic stresses and their combinations. Even though stresses rarely occur in isolation, research on plant stress resilience typically focuses on single environmental stressors. Plant responses to abiotic stress combinations are often distinct from corresponding individual stresses. Factors determining the outcomes of combined stresses are complex and multifaceted. In this review, we summarize advancements in our understanding of the mechanisms underlying plant responses to co-occurring (combined and sequential) abiotic stresses, focusing on morphological, physiological, developmental, and molecular aspects. Comprehensive understanding of plant acclimation, including the signaling and response mechanisms to combined and individual stresses, can contribute to the development of strategies for enhancing plant resilience in dynamic environments.

Comparative physiological and co-expression network analysis reveals potential hub genes and adaptive mechanisms responsive to NaCl stress in peanut (Arachis hypogaea L.)

BACKGROUND

Salt stress has become a major threat to peanut yield and quality, and salt stress is particularly detrimental to seedling growth. Combined analysis of the physiology and transcriptomics of salt-tolerant variety (NH5) and salt-sensitive variety (FH23) under 200 mM NaCl stress was conducted to identify the key factors influencing the differences in salt tolerance and to investigate the potential regulatory mechanisms and hub genes associated with salt tolerance in peanuts.

RESULTS

Malondialdehyde (MDA) content and electrolyte leakage rate were significantly increased under prolonged NaCl stress, with the increase in FH23 being even more pronounced. NH5 maintained intracellular osmotic homeostasis by accumulating free proline and soluble protein content. In addition, NH5 exhibited higher antioxidant enzyme activity. The net photosynthetic rate (Pn) of NH5 and FH23 decreased by 64.24% and 94.49% after 96 h of stress. The intercellular CO2 concentration (Ci) of NH5 significantly decreased by 7.82%, while that of FH23 increased by 42.74%. This suggests that non-stomatal limiting factors were the primary cause of the decline in photosynthesis observed in FH23. Transcriptome analysis revealed the presence of 12,612 differentially expressed genes (DEGs) in response to salt stress, with FH23 exhibiting a greater number than NH5. The number of upregulated genes was significantly higher than that of downregulated genes at 24 h of salt stress, whereas the number of downregulated genes exceeded that of upregulated genes at 48 h. Subsequently, Weighted Gene Co-expression Network Analysis (WGCNA) was performed in conjunction with physiological data. Twenty-four hub genes of salt response were identified, which encoded delta-1-pyrroline-5-carboxylate synthase, aldehyde dehydrogenase, SNF1-related protein kinase, magnesium transporter, temperature-induced lipocalin-1, and ERF transcription factors.

CONCLUSION

A regulatory network for potential salt tolerance in peanuts has been constructed. The findings revealed distinct mechanisms of response to salt tolerance and identified candidate genes for further investigation.

Intragenic cytosine methylation modification regulates the response of SUCLα1 to lower temperature in Solanaceae

The tricarboxylic acid cycle (TCAC) is a fundamental metabolic process governing matter and energy in plant cells, playing an indispensable role. However, its involvement in responding to low temperature stress in potato remains poorly understood. Previous studies have identified succinyl-CoA ligase (SUCL), which catalyzes the phosphorylation of TCAC substrates, as a gene associated with lower temperatures. Nevertheless, its function in potato's response to lower temperatures remains unclear. Phylogenetic analysis has revealed that Solanum tuberosum possesses α and β subunits of SUCL, which cluster with those of Solanum lycopersicum, Nicotiana tabacum and Nicotiana benthamiana. Further investigation has shown that StSUCLα1 is predominantly located within mitochondria. Low temperatures induce methylation modification alterations at 11 intragenic cytosine sites and lead to changes in StSUCLα1 expression levels. Correlation analysis suggests that alterations in intragenic cytosine methylation sites of SUCLα1 may be associated with MET1. Knocking down NbSUCLα1, the homologous gene of StSUCLα1 in N. benthamiana, results in increased susceptibility to low temperature stress in plants. In summary, we have confirmed that SUCLα1 is a key gene modulated by intragenic cytosine methylation in response to lower temperatures, providing a novel target for genetic breeding aimed at enhancing potato tolerance to low temperature stress.

Metabolomic insights into the multiple stress responses of metabolites in major oilseed crops

The multidimensional significance of metabolomics has gained increasing attention in oilseeds research and development. Sesame, peanut, soybean, sunflower, rapeseed, and perilla are the most important oilseed crops consumed as vegetable oils worldwide. However, multiple biotic and abiotic stressors affect metabolites essential for plant growth, development, and ecological adaptation, resulting in reduced productivity and quality. Stressors can result in dynamic changes in oilseed crops' overall performance, leading to changes in primary (ex: saccharides, lipids, organic acids, amino acids, vitamins, phytohormones, and nucleotides) and secondary (ex: flavonoids, alkaloids, phenolic acids, terpenoids, coumarins, and lignans) major metabolite classes. Those metabolites indicate plant physiological conditions and adaptation strategies to diverse biotic and abiotic stressors. Advancements in targeted and untargeted detection and quantification approaches and technologies aided metabolomics and crop improvement. This review seeks to clarify the metabolomics advancements, significant contributions of metabolites, and specific metabolites that accumulate in reaction to various stressors in oilseed crops. Considering the response of metabolites to multiple stress effects, we compiled comprehensive and combined metabolic biosynthesis pathways for six major classes. Understanding these essential metabolites and pathways can inform molecular breeding strategies to develop resilient oilseed cultivars. Hence, this review highlights metabolomics advancements and metabolites' potential roles in major oilseed crops' biotic and abiotic stress responses.

Integrated Metabolomic and Transcriptomic Analysis of Nitraria Berries Indicate the Role of Flavonoids in Adaptation to High Altitude

Background: Plants of Nitraria, belonging to the Zygophyllaceae family, are not only widely distributed at an altitude of about 1000 m but also at an altitude of about 3000 m, which is a rare phenomenon. However, little is known about the effect of altitude on the accumulation of metabolites in plants of Nitraria. Furthermore, the mechanism of the high-altitude adaptation of Nitraria has yet to be fully elucidated. Methods: In this study, metabolomics and transcriptomics were used to investigate the differential accumulation of metabolites of Nitraria berries and the regulatory mechanisms in different altitudes. Results: As a result, the biosynthesis of flavonoids is the most significant metabolic pathway in the process of adaptation to high altitude, and 5 Cyanidins, 1 Pelargonidin, 3 Petunidins, 1 Peonidin, and 4 Delphinidins are highly accumulated in high-altitude Nitraria. The results of transcriptomics showed that the structural genes C4H (2), F3H, 4CL (2), DFR (2), UFGT (2), and FLS (2) were highly expressed in high-altitude Nitraria. A network metabolism map of flavonoids was constructed, and the accumulation of differential metabolites and the expression of structural genes were analyzed for correlation. Conclusions: In summary, this study preliminarily offers a new understanding of metabolic differences and regulation mechanisms in plants of Nitraria from different altitudes.

SmJAZ3/4 positively and SmJAZ8 negatively regulates salt tolerance in transgenic Arabidopsis thaliana

Salvia miltiorrhiza Bunge, a model plant for medicinal research, is extensively utilized for its dried roots and rhizomes for treatment of various diseases. Soil salinization hinders the large-scale cultivation and industrial production of S. miltiorrhiza by affecting its active compounds. Methyl jasmonate (MeJA) is a crucial plant hormone that regulates plant responses under salt stress. Jasmonate zim domain (JAZ) proteins function as transcriptional repressors in jasmonic acid (JA) signaling pathways. This study explores the interaction between JA and salt stress by using transgenic Arabidopsis thaliana to elucidate the roles of SmJAZ3, SmJAZ4, and SmJAZ8. We found that 2.5 μM MeJA reduced the inhibitory effect of 150 mM NaCl on wild-type seed germination, and this effect was reversed by 15 μM dihydroxyindole-2-carboxylic acid (DIECA). Similar results were observed in transgenic A. thaliana lines overexpressing SmJAZ3/4/8. Inclusion of SmJAZ3/4 enhanced salt resistance by increasing antioxidant enzyme activity, chlorophyll content, proline content, and Na+/K+ content, while SmJAZ8 had the opposite effect. These findings suggest that appropriate concentrations of MeJA can alleviate the negative effect of salt stress on plant growth and development. Investigating the salt tolerance of SmJAZ3/4/8 is significant for cultivating high-quality salt-tolerant S. miltiorrhiza.

Integrated stress responses in okra plants (cv. ''Meya']: unravelling the mechanisms underlying drought and nematode co-occurrence

BACKGROUND

Climate change threatens sub-Saharan Africa's agricultural production, causing abiotic and biotic stressors. The study of plant responses to joint stressors is crucial for understanding molecular processes and identifying resilient crops for global food security. This study aimed to explore the shared and tailored responses of okra plants (cv. ''Meya'), at the biochemical and molecular levels, subjected to combined stresses of drought and Meloidogyne incognita infection.

DESIGN

The study involved 240 okra plants in a completely randomized design, with six treatments replicated 20 times. Okra plants were adequately irrigated at the end of every 10-days water deficit that lasted for 66 days (D). Also, the plants were infected with M. incognita for 66 days and irrigated at 2-days intervals (R). The stresses were done independently, in sequential combination (D before R and R before D) and concurrently (R and D). All biochemical and antioxidant enzyme assays were carried out following standard procedures.

RESULTS

Significant reductions in leaf relative water content were recorded in all stressed plants, especially in leaves of plants under individual drought stress (D) (41.6%) and plants stressed with root-knot nematode infection before drought stress (RBD) (41.4%). Malondialdehyde contents in leaf tissues from plants in D, nematode-only stress (RKN), drought stress before root-knot nematode infection (DBR), RBD, and concurrent drought-nematode stress (RAD) significantly increased by 320.2%, 152.9%, 186.5%, 283.7%, and 109.6%, respectively. Plants in D exhibited the highest superoxide dismutase activities in leaf (147.1% increase) and root (105.8% increase) tissues. Catalase (CAT) activities were significantly increased only in leaves of plants in D (90.8%) and RBD (88.9%), while only roots of plants in D exhibited a substantially higher CAT activity (139.3% increase) in comparison to controlled plants. Okra plants over-expressed NCED3 and under-expressed Me3 genes in leaf tissues. The NCED3 gene was overexpressed in roots from all treatments, while CYP707A3 was under-expressed only in roots of plants in RBD and RKN. CYP707A3 and NCED3 were grouped as closely related genes, while members of the Me3 genes were clustered into a separate group.

CONCLUSION

The biochemical and molecular responses observed in okra plants (cv. ''Meya') subjected to combined stresses of drought and Meloidogyne incognita infection provide valuable insights into enhancing crop resilience under multifaceted stress conditions, particularly relevant for agricultural practices in sub-Saharan Africa facing increasing climatic challenges.

Diethyl aminoethyl hexanoate reprogramed accumulations of organic metabolites associated with water balance and metabolic homeostasis in white clover under drought stress

Diethyl aminoethyl hexanoate (DA-6) serving as a non-toxic and low-cost plant growth regulator is used for improving plant growth and stress tolerance, but the DA-6-mediated organic metabolites remodeling in relation to drought tolerance is not well documented in crops. The aims of the present study were to evaluate impacts of DA-6 on physiological functions including osmotic adjustment, photochemical efficiency, oxidative damage, and cell membrane stability as well as organic metabolites remodeling in white clover (Trifolium repens) leaves based on the analysis of metabolomics. Plants were foliarly treated with or without DA-6 and subsequently exposed to drought stress for 8 days. Results demonstrated that foliar application of DA-6 (1.5 mM) could significantly ameliorate drought tolerance, which was linked with better leaf water status, photosynthetic performance, and cell membrane stability as well as lower oxidative injury in leaves. Metabolic profiling of organic metabolites identified a total of 59 metabolites including 17 organic acids, 20 sugars, 12 alcohols, and 10 other metabolites. In response to drought stress, the DA-6 induced accumulations of many sugars and sugar alcohols (erythrulose, arabinose, xylose, inosose, galactose, talopyranose, fucose, erythritol, and ribitol), organic acids (propanoic acid, 2,3-dihydroxybutanoic acid, palmitic acid, linolenic acid, and galacturonic acid), and other metabolites (2-oxazoline, silane, and glycine) in white clover. These altered metabolites induced by the DA-6 could perform critical functions in maintenances of osmo-protection, osmotic adjustment, redox homeostasis, cell wall structure and membrane stability when white clover suffered from water deficit. In addition, the campesterol and stigmasterol significantly accumulated in all plants in spite of the DA-6 pretreatment under drought stress, which could be an important adaptive response to water deficit due to beneficial roles of those two metabolites in regulating cell membrane stability and antioxidant defense. Present findings provide new evidence of DA-6-regulated metabolic homeostasis contributing to drought tolerance in leguminous plants.

Multi-Omics Approaches in Oil Palm Research: A Comprehensive Review of Metabolomics, Proteomics, and Transcriptomics Based on Low-Temperature Stress

Oil palm (Elaeis guineensis Jacq.) is a typical tropical oil crop with a temperature of 26-28 °C, providing approximately 35% of the total world's vegetable oil. Growth and productivity are significantly affected by low-temperature stress, resulting in inhibited growth and substantial yield losses. To comprehend the intricate molecular mechanisms underlying the response and acclimation of oil palm under low-temperature stress, multi-omics approaches, including metabolomics, proteomics, and transcriptomics, have emerged as powerful tools. This comprehensive review aims to provide an in-depth analysis of recent advancements in multi-omics studies on oil palm under low-temperature stress, including the key findings from omics-based research, highlighting changes in metabolite profiles, protein expression, and gene transcription, as well as including the potential of integrating multi-omics data to reveal novel insights into the molecular networks and regulatory pathways involved in the response to low-temperature stress. This review also emphasizes the challenges and prospects of multi-omics approaches in oil palm research, providing a roadmap for future investigations. Overall, a better understanding of the molecular basis of the response of oil palm to low-temperature stress will facilitate the development of effective breeding and biotechnological strategies to improve the crop's resilience and productivity in changing climate scenarios.

Lipid remodelling and the conversion of lipids into sugars associated with tolerance to cadmium toxicity during white clover seed germination

Cadmium (Cd) is a leading environmental issue worldwide. The current study was conducted to investigate Cd tolerance of 10 commercial white clover (Trifolium repens) cultivars during seed germination and to further explore differences in lipid remodelling, glycometabolism, and the conversion of lipids into sugars contributing to Cd tolerance in the early phase of seedling establishment as well as the accumulation of Cd in seedlings and mature plants. The results show that Cd stress significantly reduced seed germination of 10 cultivars. Compared to Cd-sensitive Sulky, Cd-tolerant Pixie accelerated amylolysis to produce more glucose, fructose, and sucrose by maintaining higher amylase and sucrase activities under Cd stress. Pixie maintained higher contents of various lipids, higher DGDG/MGDG ratio, and lower unsaturation levels of lipids, which could be beneficial to membrane stability and integrity as well as signal transduction in cells after being subjected to Cd stress. In addition, Pixie upregulated expression levels of key genes (TrACX1, TrACX4, TrSDP6, and TrPCK1) involved in the conversion of lipids into sugars for early seedling establishment under Cd stress. These findings indicate that lipid remodelling, enhanced glycometabolism, and accelerated conversion of lipids into sugars are important adaptive strategies for white clover seed germination and subsequent seedling establishment under Cd stress. In addition, Pixie not only accumulated more Cd in seedlings and mature plants than Sulky but also had significantly better growth and phytoremediation efficiency under Cd stress. Pixie could be used as a suitable and critical germplasm for the rehabilitation and re-establishment of Cd-contaminated areas.

Modulation of physio-biochemical and photosynthesis parameters by overexpressing SbPIP2 gene improved abiotic stress tolerance of transgenic tobacco

The present study aims to explore the potential of a plasma-membrane localized PIP2-type aquaporin protein sourced from the halophyte Salicornia brachiata to alleviate salinity and water deficit stress tolerance in a model plant through transgenic intervention. Transgenic plants overexpressing SbPIP2 gene showed improved physio-biochemical parameters like increased osmolytes (proline, total sugar, and amino acids), antioxidants (polyphenols), pigments and membrane stability under salinity and drought stresses compared to control plants [wild type (WT) and vector control (VC) plants]. Multivariate statistical analysis showed that, under water and salinity stresses, osmolytes, antioxidants and pigments were correlated with SbPIP2-overexpressing (SbPIP2-OE) plants treated with salinity and water deficit stress, suggesting their involvement in stress tolerance. As aquaporins are also involved in CO2 transport, SbPIP2-OE plants showed enhanced photosynthesis performance than wild type upon salinity and drought stresses. Photosynthetic gas exchange (net CO2 assimilation rate, PSII efficiency, ETR, and non-photochemical quenching) were significantly higher in SbPIP2-OE plants compared to control plants (wild type and vector control plants) under both unstressed and stressed conditions. The higher quantum yield for reduction of end electron acceptors at the PSI acceptor side [Φ( R0 )] in SbPIP2-OE plants compared to control plants under abiotic stresses indicates a continued PSI functioning, leading to retained electron transport rate, higher carbon assimilation, and less ROS-mediated injuries. In conclusion, the SbPIP2 gene functionally validated in the present study could be a potential candidate for engineering abiotic stress resilience in important crops.

Evaluation of zinc tolerance and accumulation in eight cultivars of bermudagrass (Cynodon spp.): implications for zinc phytoremediation

Zinc (Zn) is a vital element for plant growth and development, however, excessive Zn is toxic to plants. Common bermudagrass (Cynodon dactylon (L.) Pers.) and hybrid bermudagrass (C. dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) are widely used turfgrass species with strong tolerance to diverse abiotic stresses, including excessive Zn2+ stress. However, the variation of zinc tolerance and accumulation in different bermudagrass cultivars remain unclear. In this study, we systematically analyzed the growth performance, physiological index and ion concentration in eight commercial cultivars of common and hybrid bermudagrass under different concentration of Zn2+ treatments using pot experiments. The results indicated that four cultivars of common bermudagrass could tolerate 20 mM Zn2+, whereas four cultivars of hybrid bermudagrass could only tolerate 10 mM Zn2+. Among the four common bermudagrass cultivars, cultivar Guanzhong and Common showed stronger Zn tolerance and accumulation abilities than other two cultivars. Further analyses of the expression of selected Zn homeostasis-related genes indicated that bermudagrass cultivars with stronger tolerance to excessive Zn have at least one expression-elevated gene involved in Zn homeostasis. These results not only expanded our understanding of Zn tolerance and accumulation in bermudagrass but also facilitated the application of commercial bermudagrass cultivars in phytoremediation of Zn pollution.

Overexpressing plant ferredoxin-like protein enhances photosynthetic efficiency and carbohydrates accumulation in Phalaenopsis

Crassulacean acid metabolism (CAM) is one of three major models of carbon dioxide assimilation pathway with better water-use efficiency and slower photosynthetic efficiency in photosynthesis. Previous studies indicated that the gene of sweet pepper plant ferredoxin-like protein (PFLP) shows high homology to the ferredoxin-1(Fd-1) family that belongs to photosynthetic type Fd and involves in photosystem I. It is speculated that overexpressing pflp in the transgenic plant may enhance photosynthetic efficiency through the electron transport chain (ETC). To reveal the function of PFLP in photosynthetic efficiency, pflp transgenic Phalaenopsis, a CAM plant, was generated to analyze photosynthetic markers. Transgenic plants exhibited 1.2-folds of electron transport rate than that of wild type (WT), and higher CO2 assimilation rates up to 1.6 and 1.5-folds samples at 4 pm and 10 pm respectively. Enzyme activity of phosphoenolpyruvate carboxylase (PEPC) was increased to 5.9-folds in Phase III, and NAD+-linked malic enzyme (NAD+-ME) activity increased 1.4-folds in Phase IV in transgenic plants. The photosynthesis products were analyzed between transgenic plants and WT. Soluble sugars contents such as glucose, fructose, and sucrose were found to significantly increase to 1.2, 1.8, and 1.3-folds higher in transgenic plants. The starch grains were also accumulated up to 1.4-folds in transgenic plants than that of WT. These results indicated that overexpressing pflp in transgenic plants increases carbohydrates accumulation by enhancing electron transport flow during photosynthesis. This is the first evidence for the PFLP function in CAM plants. Taken altogether, we suggest that pflp is an applicable gene for agriculture application that enhances electron transport chain efficiency during photosynthesis.

Widely targeted metabolic profiling provides insights into variations in bioactive compounds and antioxidant activity of sesame, soybean, peanut, and perilla

Oilseeds are important sources of diversified nutraceuticals with marked health attributes. Thus, a better understanding of metabolome differences between common oilseeds will be conducive to the food pharmacy. This study aimed to compare the metabolite profiles and antioxidant activity of sesame, soybean, peanut, and perilla seeds and reveal the variation in bioactive compounds. LC-MS-based widely targeted metabolic profiling identified a total of 975 metabolites, of which 753 were common to the four crops. Multivariate analyses unveiled a crop-specific accumulation of metabolites, with 298-388 DAMs (differentially accumulated metabolites) identified. Amino acid metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and lipid metabolism were the most differentially regulated pathways. Furthermore, we revealed the variation in the relative content of 48, 20, 18, 9, 18, 11, and 6 differentially accumulated bioactive flavonoids, phenolic acids, amino acids, vitamins, terpenoids, alkaloids, and coumarins, respectively. Most of the flavonoids accumulated highly in soybean, followed by perilla. Sesame exhibited a better amino acid profile than other oilseeds. DPPH and FRAP assays showed that the antioxidant activity of perilla seed extracts was the highest, followed by soybean, peanut, and sesame. Our results provide data support for the comprehensive use of sesame, perilla, soybean, and peanut seeds in food, and pharmaceutical industries.

Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut (Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency

This study identified 45 calcium-dependent protein kinase (CDPK) genes in cultivated peanut (Arachis hypogaea L.), which are integral in plant growth, development, and stress responses. These genes, classified into four subgroups based on phylogenetic relationships, are unevenly distributed across all twenty peanut chromosomes. The analysis of the genetic structure of AhCDPKs revealed significant similarity within subgroups, with their expansion primarily driven by whole-genome duplications. The upstream promoter sequences of AhCDPK genes contained 46 cis-acting regulatory elements, associated with various plant responses. Additionally, 13 microRNAs were identified that target 21 AhCDPK genes, suggesting potential post-transcriptional regulation. AhCDPK proteins interacted with respiratory burst oxidase homologs, suggesting their involvement in redox signaling. Gene ontology and KEGG enrichment analyses affirmed AhCDPK genes' roles in calcium ion binding, protein kinase activity, and environmental adaptation. RNA-seq data revealed diverse expression patterns under different stress conditions. Importantly, 26 AhCDPK genes were significantly induced when exposed to Ca deficiency during the pod stage. During the seedling stage, four AhCDPKs (AhCDPK2/-25/-28/-45) in roots peaked after three hours, suggesting early signaling roles in pod Ca nutrition. These findings provide insights into the roles of CDPK genes in plant development and stress responses, offering potential candidates for predicting calcium levels in peanut seeds.

Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp. revealed their role in multiple stresses

Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.

The physio-biochemical characterization reflected different calcium utilization efficiency between the sensitive and tolerant peanut accessions under calcium deficiency

Peanut yield in southern China is usually limited by calcium deficiency in soil. Most previous studies have found that small-seed varieties showed higher tolerance than large-seed varieties (e.g. Virginia type) under calcium deficiency, however, our preliminary research found that sensitive varieties also existed in small-seed counterparts. Few studies have been conducted to characterize low-calcium tolerance among small-seed germplasms with genetic diversity, and the differences in physiological characteristics between sensitive and tolerant varieties has not been reported yet. Thus, in order to better understand such differences, the current study firstly collected and characterized a diversity germplasm panel consisting of 50 small-seed peanut genotypes via a 2-year field trial, followed by the physiological characterization in sensitive (HN032) and tolerant (HN035) peanut genotypes under calcium deficiency. As a result, the adverse effects brought by calcium deficiency on calcium uptake and distribution in HN032 was much larger than HN035. In details, calcium uptake in the aboveground part (leaves and stems) was reduced by 16.17% and 33.66%, while in the underground part (roots and pods), it was reduced by 13.69% and 68.09% under calcium deficiency for HN035 and HN032, respectively; The calcium distribution rate in the pods of HN035 was 2.74 times higher than HN032. The utilization efficiency of calcium in the pods of HN035 was 1.68 and 1.37 times than that of HN032 under calcium deficiency and sufficiency, respectively. In addition, under calcium deficiency conditions, the activities of antioxidant enzymes SOD, POD, and CAT, as well as the MDA content, were significantly increased in the leaves of HN032, peanut yield was significantly reduced by 22.75%. However, there were no significant changes in the activities of antioxidant enzymes, MDA content, and peanut yield in HN035. Therefore, higher calcium absorption and utilization efficiency may be the key factors maintaining peanut yield in calcium-deficient conditions for tolerant genotypes. This study lays a solid foundation for selecting low-calcium tolerant varieties in future peanut breeding.

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses

The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing

Low temperatures significantly affect the growth and yield of peanuts. Temperatures lower than 12 °C are generally detrimental for the germination of peanuts. To date, there has been no report on precise information on the quantitative trait loci (QTL) for cold tolerance during the germination in peanuts. In this study, we developed a recombinant inbred line (RIL) population comprising 807 RILs by tolerant and sensitive parents. Phenotypic frequencies of germination rate low-temperature conditions among RIL population showed normally distributed in five environments. Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. The cold tolerance-related QTLs were repeatedly detected in all five environments, and the genetic distance was 6.01 cM (46.74 cM - 61.75 cM) after taking a union set. To further confirm that qRGRB09 was located on chromosome B09, we developed Kompetitive Allele Specific PCR (KASP) markers for the corresponding QTL regions. A regional QTL mapping analysis, which was conducted after taking the intersection of QTL intervals of all environments into account, confirmed that qRGRB09 was between the KASP markers, G22096 and G220967 (chrB09:155637831-155854093), and this region was 216.26 kb in size, wherein a total of 15 annotated genes were detected. This study illustrates the relevance of WGRS-based genetic maps for QTL mapping and KASP genotyping that facilitated QTL fine mapping of peanuts. The results of our study also provided useful information on the genetic architecture underlying cold tolerance during germination in peanuts, which in turn may be useful for those engaged in molecular studies as well as crop improvement in the cold-stressed environment.

Comparative Analysis of Antioxidant System and Salt-Stress Tolerance in Two Hibiscus Cultivars Exposed to NaCl Toxicity

Hibiscus (Hibiscus syriacus L.) is known as a horticultural plant of great ornamental and medicinal value. However, the effect of NaCl stress on hibiscus seedlings is unclear. Little is known about H. syriacus 'Duede Brabaul' (DB) and H. syriacus 'Blueberry Smoothie' (BS). Here, the effects of solutions with different concentrations of NaCl on the organic osmolytes, ion accumulation, and antioxidant enzyme activity of hibiscus seedling leaves were determined. The results showed that the Na⁺/K⁺ ratio was imbalanced with increasing NaCl concentration, especially in BS (range 34% to 121%), which was more sensitive than DB (range 32% to 187%) under NaCl concentrations of 50 to 200 mM. To cope with the osmotic stress, the content of organic osmolytes increased significantly. Additionally, NaCl stress caused a large increase in O₂·^- and H₂O₂, and other reactive oxygen species (ROS), and antioxidant enzyme activity was significantly increased to remove excess ROS. The expression level of genes related to salt tolerance was significantly higher in DB than that in BS under different NaCl concentrations. Taken together, DB possessed a stronger tolerance to salt stress and the results suggest membrane stability, Na⁺/K⁺, H₂O₂, catalase and ascorbate peroxidase as salt tolerance biomarkers that can be used for gene transformation and breeding in future hibiscus research.

Plant Metabolomics: An Overview of the Role of Primary and Secondary Metabolites against Different Environmental Stress Factors

Several environmental stresses, including biotic and abiotic factors, adversely affect the growth and development of crops, thereby lowering their yield. However, abiotic factors, e.g., drought, salinity, cold, heat, ultraviolet radiations (UVr), reactive oxygen species (ROS), trace metals (TM), and soil pH, are extremely destructive and decrease crop yield worldwide. It is expected that more than 50% of crop production losses are due to abiotic stresses. Moreover, these factors are responsible for physiological and biochemical changes in plants. The response of different plant species to such stresses is a complex phenomenon with individual features for several species. In addition, it has been shown that abiotic factors stimulate multi-gene responses by making modifications in the accumulation of the primary and secondary metabolites. Metabolomics is a promising way to interpret biotic and abiotic stress tolerance in plants. The study of metabolic profiling revealed different types of metabolites, e.g., amino acids, carbohydrates, phenols, polyamines, terpenes, etc, which are accumulated in plants. Among all, primary metabolites, such as amino acids, carbohydrates, lipids polyamines, and glycine betaine, are considered the major contributing factors that work as osmolytes and osmoprotectants for plants from various environmental stress factors. In contrast, plant-derived secondary metabolites, e.g., phenolics, terpenoids, and nitrogen-containing compounds (alkaloids), have no direct role in the growth and development of plants. Nevertheless, such metabolites could play a significant role as a defense by protecting plants from biotic factors such as herbivores, insects, and pathogens. In addition, they can enhance the resistance against abiotic factors. Therefore, metabolomics practices are becoming essential and influential in plants by identifying different phytochemicals that are part of the acclimation responses to various stimuli. Hence, an accurate metabolome analysis is important to understand the basics of stress physiology and biochemistry. This review provides insight into the current information related to the impact of biotic and abiotic factors on variations of various sets of metabolite levels and explores how primary and secondary metabolites help plants in response to these stresses.

Developing drought-smart, ready-to-grow future crops

Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS-associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought-smart future crops. In short, we recommend incorporating several approaches, such as multi-omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought-smart cultivars to achieve the 'zero hunger' goal.

Overexpression of SmMYC2 enhances salt resistance in Arabidopsis thaliana and Salvia miltiorrhiza hairy roots

Soil salinity significantly affects both Salvia miltiorrhiza growth and development as well as seed germination throughout field cultivation and production. The basic helix-loop-helix (bHLH) transcription factor (TF) MYC2 contributes significantly to plant stress resistance as a key regulator of the jasmonic acid signaling pathway. In transgenic S. miltiorrhiza hairy roots, SmMYC2 has been shown to promote the accumulation of tanshinone and salvianolic acid, but its role in S. miltiorrhiza of resistance to abiotic stress is unclear. Herein, we found methyl jasmonate (MeJA), NaCl, and PEG treatment all significantly increased SmMYC2 expression. In response to salt stress, SmMYC2 overexpression in yeast increased its rate of growth. Additionally, overexpression of SmMYC2 transgenic Arabidopsis thaliana and S. miltiorrhiza hairy root showed that it might improve salt resistance in transgenic plant. In particular, compared to WT, overexpression of SmMYC2 transgenic Arabidopsis had higher levels of three antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), proline (Pro) content, and ABA-dependent and ABA-independent genes expression. They also had lower levels of malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. What's more, overexpression of SmMYC2 increases the expression of flavonoid synthesis genes and the accumulation of related components in Arabidopsis. These findings imply that SmMYC2 functions as a positive regulator that regulates plant tolerance to salt through ABA-dependent and independent signaling pathways.

Comparative Multi-Omics Analysis Reveals Lignin Accumulation Affects Peanut Pod Size

Pod size is one of the important factors affecting peanut yield. However, the metabolites relating to pod size and their biosynthesis regulatory mechanisms are still unclear. In the present study, two peanut varieties (Tif and Lps) with contrasting pod sizes were used for a comparative metabolome and transcriptome analysis. Developing peanut pods were sampled at 10, 20 and 30 days after pegging (DAP). A total of 720 metabolites were detected, most of which were lipids (20.3%), followed by phenolic acids (17.8%). There were 43, 64 and 99 metabolites identified as differentially accumulated metabolites (DAMs) at 10, 20 and 30 DAP, respectively, and flavonoids were the major DAMs between Tif and Lps at all three growth stages. Multi-omics analysis revealed that DAMs and DEGs (differentially expressed genes) were significantly enriched in the phenylpropanoid biosynthesis (ko00940) pathway, the main pathway of lignin biosynthesis, in each comparison group. The comparisons of the metabolites in the phenylpropanoid biosynthesis pathway accumulating in Tif and Lps at different growth stages revealed that the accumulation of p-coumaryl alcohol (H-monolignol) in Tif was significantly greater than that in Lps at 30 DAP. The differential expression of gene-LOC112771695, which is highly correlated with p-coumaryl alcohol and involved in the biosynthesis of monolignols, between Tif and Lps might explain the differential accumulation of p-coumaryl alcohol. The content of H-lignin in genetically diverse peanut varieties demonstrated that H-lignin content affected peanut pod size. Our findings would provide insights into the metabolic factors influencing peanut pod size and guidance for the genetic improvement of the peanut.

Introgression of a novel gene AhBINR differentially expressed during PGPR Brachybacterium saurashtrense-Arachis hypogaea interaction enhances plant performance under nitrogen starvation and salt stress in tobacco

Plant growth-promoting rhizobacteria provide endurance during environmental stress conditions. Previously, we have shown that the interaction of the halotolerant diazotrophic bacteria Brachybacterium saurashtrense JG06 induces physio-biochemical and molecular changes in Arachis hypogaea under nitrogen starvation conditions. Here we deciphered the role of a novel gene AhBINR that was differentially overexpressed in A. hypogaea after interaction with B. saurashtrense JG06 under nitrogen deficit conditions. Overexpression of the AhBINR gene in the model plant (tobacco) showed higher growth parameters (root length, shoot length, fresh weight, and dry weight) under nitrogen starvation and salt stress in comparison to the wild type and vector control. Transgenic plants were enabled with a higher photosynthesis rate, which provides the support for better performance under N₂ starvation and salt stress. Results showed that the transgenic plants overexpressing the AhBINR gene had better physiological status and lower ROS accumulation under adverse conditions. Microarray transcriptome analysis showed that the transcription factors, biotic and abiotic stress, photosynthesis, and metabolism-related genes were differentially expressed (total 736 and 6530 genes were expressed under nitrogen deficit and salt stress conditions, respectively at a 5-fold change level) in comparison to wild type plants. Overall results showed the involvement of the AhBINR gene in the activation of the abiotic stress (nitrogen starvation and salt stress) related pathways, which can be overexpressed after legume-rhizobacterial interaction.

Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut (Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance

Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.

Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops

The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.