Can omics deliver temperature resilient ready-to-grow crops?

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

Millets, comprising a diverse group of small-seeded grains, have emerged as vital crops with immense nutritional, environmental, and economic significance. The comprehension of complex traits in millets, influenced by multifaceted genetic determinants, presents a compelling challenge and opportunity in agricultural research. This review delves into the transformative roles of phenomics and genomics in deciphering these intricate genetic architectures. On the phenomics front, high-throughput platforms generate rich datasets on plant morphology, physiology, and performance in diverse environments. This data, coupled with field trials and controlled conditions, helps to interpret how the environment interacts with genetics. Genomics provides the underlying blueprint for these complex traits. Genome sequencing and genotyping technologies have illuminated the millet genome landscape, revealing diverse gene pools and evolutionary relationships. Additionally, different omics approaches unveil the intricate information of gene expression, protein function, and metabolite accumulation driving phenotypic expression. This multi-omics approach is crucial for identifying candidate genes and unfolding the intricate pathways governing complex traits. The review highlights the synergy between phenomics and genomics. Genomically informed phenotyping targets specific traits, reducing the breeding size and cost. Conversely, phenomics identifies promising germplasm for genomic analysis, prioritizing variants with superior performance. This dynamic interplay accelerates breeding programs and facilitates the development of climate-smart, nutrient-rich millet varieties and hybrids. In conclusion, this review emphasizes the crucial roles of phenomics and genomics in unlocking the genetic enigma of millets.

Designing future peanut: the power of genomics-assisted breeding

KEY MESSAGE

Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.

Maize and heat stress: Physiological, genetic, and molecular insights

Global mean temperature is increasing at a rapid pace due to the rapid emission of greenhouse gases majorly from anthropogenic practices and predicted to rise up to 1.5°C above the pre-industrial level by the year 2050. The warming climate is affecting global crop production by altering biochemical, physiological, and metabolic processes resulting in poor growth, development, and reduced yield. Maize is susceptible to heat stress, particularly at the reproductive and early grain filling stages. Interestingly, heat stress impact on crops is closely regulated by associated environmental covariables such as humidity, vapor pressure deficit, soil moisture content, and solar radiation. Therefore, heat stress tolerance is considered as a complex trait, which requires multiple levels of regulations in plants. Exploring genetic diversity from landraces and wild accessions of maize is a promising approach to identify novel donors, traits, quantitative trait loci (QTLs), and genes, which can be introgressed into the elite cultivars. Indeed, genome wide association studies (GWAS) for mining of potential QTL(s) and dominant gene(s) is a major route of crop improvement. Conversely, mutation breeding is being utilized for generating variation in existing populations with narrow genetic background. Besides breeding approaches, augmented production of heat shock factors (HSFs) and heat shock proteins (HSPs) have been reported in transgenic maize to provide heat stress tolerance. Recent advancements in molecular techniques including clustered regularly interspaced short palindromic repeats (CRISPR) would expedite the process for developing thermotolerant maize genotypes.

2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice (Oryza sativa L.)

Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.

Plant responses to climate change, how global warming may impact on food security: a critical review

Global agricultural production must double by 2050 to meet the demands of an increasing world human population but this challenge is further exacerbated by climate change. Environmental stress, heat, and drought are key drivers in food security and strongly impacts on crop productivity. Moreover, global warming is threatening the survival of many species including those which we rely on for food production, forcing migration of cultivation areas with further impoverishing of the environment and of the genetic variability of crop species with fall out effects on food security. This review considers the relationship of climatic changes and their bearing on sustainability of natural and agricultural ecosystems, as well as the role of omics-technologies, genomics, proteomics, metabolomics, phenomics and ionomics. The use of resource saving technologies such as precision agriculture and new fertilization technologies are discussed with a focus on their use in breeding plants with higher tolerance and adaptability and as mitigation tools for global warming and climate changes. Nevertheless, plants are exposed to multiple stresses. This study lays the basis for the proposition of a novel research paradigm which is referred to a holistic approach and that went beyond the exclusive concept of crop yield, but that included sustainability, socio-economic impacts of production, commercialization, and agroecosystem management.

Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system

Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.

Smart reprograming of plants against salinity stress using modern biotechnological tools

Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.

Morphological and physio-biochemical responses under heat stress in cotton: Overview

Cotton is an important cash crop in addition to being a fiber commodity, and it plays an essential part in the economies of numerous nations. High temperature is the most critical element affecting its yield from fertilization to harvest. The optimal temperature for root formation is 30 C -35 °C; however, root development ends around 40 °C. Increased temperature, in particular, influences different biochemical and physiological processes associated with cotton plant, resulting in low seed cotton production. Many studies in various agroecological zones used various agronomic strategies and contemporary breeding techniques to reduce heat stress and improve cotton productivity. To attain desired traits, cotton breeders should investigate all potential possibilities, such as generating superior cultivars by traditional breeding, employing molecular techniques and transgenic methods, such as using genome editing techniques. The main objective of this review is to provide the recent information on the environmental factors, such as temperature, heat and drought, influence the growth and development, morphology and physio-chemical alteration associated with cotton. Furthermore, recent advancement in cotton breeding to combat the serious threat of drought and heat stress.

Enhancing cold and drought tolerance in cotton: a protective role of SikCOR413PM1

The present study explored the potential role of cold-regulated plasma membrane protein COR413PM1 isolated from Saussurea involucrata (Matsum. & Koidz)(SikCOR413PM1), in enhancing cotton (Gossypium hirsutum) tolerance to cold and drought stresses through transgenic methods. Under cold and drought stresses, the survival rate and the fresh and dry weights of the SikCOR413PM1-overexpressing lines were higher than those of the wild-type plants, and the degree of leaf withering was much lower. Besides, overexpressing SikCOR413PM1 overexpression increased the relative water content, reduced malondialdehyde content and relative conductivity, and elevated proline and soluble sugar levels in cotton seedlings. These findings suggest that SikCOR413PM1 minimizes cell membrane damage and boosts plant stability under challenging conditions. Additionally, overexpression of this gene upregulated antioxidant enzyme-related genes in cotton seedlings, resulting in enhanced antioxidant enzyme activity, lowered peroxide content, and reduced oxidative stress. SikCOR413PM1 overexpression also modulated the expression of stress-related genes (GhDREB1A, GhDREB1B, GhDREB1C, GhERF2, GhNAC3, and GhRD22). In field trials, the transgenic cotton plants overexpressing SikCOR413PM1 displayed high yields and increased environmental tolerance. Our study thus demonstrates the role of SikCOR413PM1 in regulating stress-related genes, osmotic adjustment factors, and peroxide content while preserving cell membrane stability and improving cold and drought tolerance in cotton.

Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants

The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.

Physiological Control and Genetic Basis of Leaf Curvature and Heading in Brassica rapa L

BACKGROUND

Heading is an important agronomic feature for Chinese cabbage, cabbage, and lettuce. The heading leaves function as nutrition storage organs, which contribute to the high quality and economic worth of leafy heads. Leaf development is crucial during the heading stage, most genes previously predicted to be involved in the heading process are based on Arabidopsis leaf development studies.

AIM OF REVIEW

Till date, there is no published review article that demonstrated a complete layout of all the identified regulators of leaf curvature and heading. In this review, we have summarized all the identified physiological and genetic regulators that are directly or indirectly involved in leaf curvature and heading in Brassica crops. By integrating all identified regulators that provide a coherent logic of leaf incurvature and heading, we proposed a molecular mechanism in Brassica crops with graphical illustrations. This review adds value to future breeding of distinct heading kinds of cabbage and Chinese cabbage by providing unique insights into leaf development.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Leaf curvature and heading are established by synergistic interactions among genes, transcription factors, microRNAs, phytohormones, and environmental stimuli that regulate primary and secondary morphogenesis. Various genes have been identified using transformation and genome editing that are responsible for the formation of leaf curvature and heading in Brassica crops. A range of leaf morphologies have been observed in Brassica, which are established because of the mutated determinants that are responsible for cell division and leaf polarity.

Photosynthesis regulation, cell membrane stabilization and methylglyoxal detoxification seems major altered pathways under cold stress as revealed by integrated multi-omics meta-analysis

Climate change has altered cold weather patterns, resulting in irregular cold weather conditions, and changing the global plant distribution pattern affecting plant development processes resulting in severe yield losses. Although molecular mechanisms and interconnections are quite well studied, a cumulative understanding of plant responses to cold stress (CS) is still lacking. Through meta-analysis, integration of data at the multi-omics level and its correlation with known physiological changes to map and understand the global changes in response to CS was made. Meta-analysis was conducted using the metafor R package program based on physiological parameters like relative electrolytic leakage, malondialdehyde, soluble sugar, proline and antioxidant enzymes activity. Proline and soluble sugars showed the highest (> 1.5 mean fold) change over control thus qualifying as global markers for studying CS. Surprisingly most up-regulated (> 15-fold) DEGs corresponded with the dehydrin family and glyoxalase superfamily proteins. Functional annotations of DEGs corresponded with photosynthesis and glycolysis pathway. Proteins responsible for cell signalling and increased soluble sugars were common in all the datasets studied thus correlating with the transcriptome and proteomic data. Proline and soluble sugars were positively regulated in all the metabolomics datasets. This study supported the earlier known players like proline and soluble sugars. Surprisingly, a new player glyoxalase seems to be contributing in CS.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01367-9.

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

Study on the impact of exogenously applied methyl jasmonate concentrations on Solanum lycopersicum under low temperature stress

BACKGROUND

To decipher the capability of Methyl Jasmonate (MeJA) in resisting cold stress in Solanum lycopersicum assessment regarding various physiological parameters in response to diverse doses of MeJA was done. Low temperature (LT) were given to the plants with MeJA (J1C, J2C, J3C) or without MeJA (LT) application. MeJA in the form of foliar spray was given before stress, during stress and after stress. Three concentrations of MeJA were used under normal and LT stress conditions that includes of J1 (0.5 µM), J2 (10 µM), and J3 (15 µM).

RESULTS

Oxidative stress, growth characteristics, stress tolerance parameters, antioxidant response and photosynthetic parameters were investigated. In our current study we observed that oxidative stress markers declined by MeJA supplementation under cold stress conditions. MeJA boosted antioxidant enzyme activity along with photosynthetic parameters. The best concentration of MeJA was J2 based on results obtained. This is the first study related to MeJA best dose screening in Solanum lycopersicum under LT stress conditions.

CONCLUSION

The LT stress in the Solanum lycopersicum plant was reduced by MeJA. The adverse consequences of LT stress can be significantly attenuated by the J2 concentration of MeJA. So, the optimal concentration of MeJA supplied exogenously to LT stressed Solanum lycopersicum can be a smart strategy to mitigate harmful impact of LT stress on detox system and overall growth of plant.

miRNAs for crop improvement

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.

Silicate solubilizing and plant growth promoting bacteria interact with biogenic silica to impart heat stress tolerance in rice by modulating physiology and gene expression

Heat stress caused due to increasing warming climate has become a severe threat to global food production including rice. Silicon plays a major role in improving growth and productivity of rice by aiding in alleviating heat stress in rice. Soil silicon is only sparingly available to the crops can be made available by silicate solubilizing and plant-growth-promoting bacteria that possess the capacity to solubilize insoluble silicates can increase the availability of soluble silicates in the soil. In addition, plant growth promoting bacteria are known to enhance the tolerance to abiotic stresses of plants, by affecting the biochemical and physiological characteristics of plants. The present study is intended to understand the role of beneficial bacteria viz. Rhizobium sp. IIRR N1 a silicate solublizer and Gluconacetobacter diazotrophicus, a plant growth promoting bacteria and their interaction with insoluble silicate sources on morpho-physiological and molecular attributes of rice (Oryza sativa L.) seedlings after exposure to heat stress in a controlled hydroponic system. Joint inoculation of silicates and both the bacteria increased silicon content in rice tissue, root and shoot biomass, significantly increased the antioxidant enzyme activities (viz. superoxidase dismutase, catalase and ascorbate peroxidase) compared to other treatments with sole application of either silicon or bacteria. The physiological traits (viz. chlorophyll content, relative water content) were also found to be significantly enhanced in presence of silicates and both the bacteria after exposure to heat stress conditions. Expression profiling of shoot and root tissues of rice seedlings revealed that seedlings grown in the presence of silicates and both the bacteria exhibited higher expression of heat shock proteins (HSPs viz., OsHsp90, OsHsp100 and 60 kDa chaperonin), hormone-related genes (OsIAA6) and silicon transporters (OsLsi1 and OsLsi2) as compared to seedlings treated with either silicates or with the bacteria alone. The results thus reveal the interactive effect of combined application of silicates along with bacteria Rhizobium sp. IIRR N1, G. diazotrophicus inoculation not only led to augmented silicon uptake by rice seedlings but also influenced the plant biomass and elicited higher expression of HSPs, hormone-related and silicon transporter genes leading to improved tolerance of seedling to heat stress.

The role of γ-aminobutyric acid and salicylic acid in heat stress tolerance under salinity conditions in Origanum vulgare L

Origanum vulgare L., a medicinal and aromatic herb, has been used for hundreds of years. This plant contains valuable chemical compounds that can be used as medicine for treatment. On the other hand, a gradual increase in the planet's average temperature could negatively affect the growth and the composition of the O. vulgare. For this reason, in this study, the effect of two protective compounds, namely salicylic acid (SA) and gamma-aminobutyric acid (GABA), on temperature and salinity stress conditions was investigated. Oregano plants were grown at 23/12°C temperature as control and 27/16°C heat stress in the greenhouse (16/8 h photoperiod) for one months. The plants were treated with GABA and SA and subjected to salt stress for 30 days. Subsequently, the plant's physiological, biochemical, and phytochemical characteristics were examined. The results showed that all studied traits (in control and treated samples) were significantly different at 27°C, from 23°C. In addition, the highest amount of thymol and carvacrol were detected from plants grown at 27°C. In regards to salinity, stressed- plants had less damage to membrane stability and H2O2 level, when treated with GABA or SA. This study revealed that both SA and GABA compounds had an exellent protective effect on temperature and salt stress on O. vulgare. Based on enzyme-pigment evaluations and secondary metabolites, SA showed a better protective effect on temperature effects and GABA in a saline environment. In general, using these compounds can provide better conditions for the growth and preservation of O. vulgare chemical compounds. However, it certainly requires more experiments to find the signal pathways involved in these processes.

Metabolomic and transcriptomic analyses reveal the effects of grafting on blood orange quality

Introduction

Blood orange (Citrus sinensis L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored.

Methods

In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (Citrus sinensis L. Osbeck cv. Lido) grafted onto two rootstocks.

Results and discussion

The Trifoliate orange rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (C2H2, GANT, MYB-related, AP2/ERF, NAC, bZIP, and MYB) and five genes associated with anthocyanin synthesis pathway (CHS, F3H, UFGT, and ANS) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.

Cloning and Functional Characterization of Cold-Inducible MYB-like 17 Transcription Factor in Rapeseed (Brassica napus L.)

Rapeseed (Brassica napus L.) is an important crop for edible oil, vegetables, and biofuel. Rapeseed growth and development require a minimum temperature of ~1-3 °C. Notably, frost damage occurs during overwintering, posing a serious threat to the productivity and yield of rapeseed. MYB proteins are important transcription factors (TFs) in plants, and have been proven to be involved in the regulation of stress responses. However, the roles of the MYB TFs in rapeseed under cold stress conditions are yet to be fully elucidated. To better understand the molecular mechanisms of one MYB-like 17 gene, BnaMYBL17, in response to low temperature, the present study found that the transcript level of BnaMYBL17 is induced by cold stress. To characterize the gene's function, the 591 bp coding sequence (CDS) from rapeseed was isolated and stably transformed into rapeseed. The further functional analysis revealed significant sensitivity in BnaMYBL17 overexpression lines (BnaMYBL17-OE) after freezing stress, suggesting its involvement in freezing response. A total of 14,298 differentially expressed genes relative to freezing response were found based on transcriptomic analysis of BnaMYBL17-OE. Overall, 1321 candidate target genes were identified based on differential expression, including Phospholipases C1 (PLC1), FCS-like zinc finger 8 (FLZ8), and Kinase on the inside (KOIN). The qPCR results confirmed that the expression levels of certain genes showed fold changes ranging from two to six when compared between BnaMYBL17-OE and WT lines after exposure to freezing stress. Furthermore, verification indicated that BnaMYBL17 affects the promoter of BnaPLC1, BnaFLZ8, and BnaKOIN genes. In summary, the results suggest that BnaMYBL17 acts as a transcriptional repressor in regulating certain genes related to growth and development during freezing stress. These findings provide valuable genetic and theoretical targets for molecular breeding to enhance freezing tolerance in rapeseed.

Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea

Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.

Assessment of proline function in higher plants under extreme temperatures

Climate change and abiotic stress factors are key players in crop losses worldwide. Among which, extreme temperatures (heat and cold) disturb plant growth and development, reduce productivity and, in severe cases, lead to plant death. Plants have developed numerous strategies to mitigate the detrimental impact of temperature stress. Exposure to stress leads to the accumulation of various metabolites, e.g. sugars, sugar alcohols, organic acids and amino acids. Plants accumulate the amino acid 'proline' in response to several abiotic stresses, including temperature stress. Proline abundance may result from de novo synthesis, hydrolysis of proteins, reduced utilization or degradation. Proline also leads to stress tolerance by maintaining the osmotic balance (still controversial), cell turgidity and indirectly modulating metabolism of reactive oxygen species. Furthermore, the crosstalk of proline with other osmoprotectants and signalling molecules, e.g. glycine betaine, abscisic acid, nitric oxide, hydrogen sulfide, soluble sugars, helps to strengthen protective mechanisms in stressful environments. Development of less temperature-responsive cultivars can be achieved by manipulating the biosynthesis of proline through genetic engineering. This review presents an overview of plant responses to extreme temperatures and an outline of proline metabolism under such temperatures. The exogenous application of proline as a protective molecule under extreme temperatures is also presented. Proline crosstalk and interaction with other molecules is also discussed. Finally, the potential of genetic engineering of proline-related genes is explained to develop 'temperature-smart' plants. In short, exogenous application of proline and genetic engineering of proline genes promise ways forward for developing 'temperature-smart' future crop plants.

Brassinosteroids mediate moderate soil-drying to alleviate spikelet degeneration under high temperature during meiosis of rice

This study tested the hypothesis that brassinosteroids (BRs) mediate moderate soil-drying (MD) to alleviate spikelet degeneration under high temperature (HT) stress during meiosis of rice (Oryza sativa L.). A rice cultivar was pot-grown and subjected to normal temperature (NT) and HT treatments during meiosis, and two irrigation regimes including well-watered (WW) and MD were imposed to the plants simultaneously. The MD effectively alleviated the spikelet degeneration and yield loss under HT stress mainly via improving root activity and canopy and panicle traits including higher photosynthetic capacity, tricarboxylic acid cycle activity, and antioxidant capacity than WW. These parameters were regulated by BRs levels in plants. The decrease in BRs levels at HT was due mainly to the enhanced BRs decomposition, and the MD could rescue the BRs deficiency at HT via enhancing BRs biosynthesis and impeding decomposition. The connection between BRs and HT was verified by using rice BRs-deficient mutants, transgenic rice lines, and chemical regulators. Similar results were obtained in the open-air field experiment. The results suggest that BRs can mediate the MD to alleviate spikelet degeneration under HT stress during meiosis mainly via enhancing root activity, canopy traits, and young panicle traits of rice.

In-silico identification and characterization of O-methyltransferase gene family in peanut (Arachis hypogaea L.) reveals their putative roles in development and stress tolerance

Cultivated peanut (Arachis hypogaea) is a leading protein and oil-providing crop and food source in many countries. At the same time, it is affected by a number of biotic and abiotic stresses. O-methyltransferases (OMTs) play important roles in secondary metabolism, biotic and abiotic stress tolerance. However, the OMT genes have not been comprehensively analyzed in peanut. In this study, we performed a genome-wide investigation of A. hypogaea OMT genes (AhOMTs). Gene structure, motifs distribution, phylogenetic history, genome collinearity and duplication of AhOMTs were studied in detail. Promoter cis-elements, protein-protein interactions, and micro-RNAs targeting AhOMTs were also predicted. We also comprehensively studied their expression in different tissues and under different stresses. We identified 116 OMT genes in the genome of cultivated peanut. Phylogenetically, AhOMTs were divided into three groups. Tandem and segmental duplication events played a role in the evolution of AhOMTs, and purifying selection pressure drove the duplication process. AhOMT promoters were enriched in several key cis-elements involved in growth and development, hormones, light, and defense-related activities. Micro-RNAs from 12 different families targeted 35 AhOMTs. GO enrichment analysis indicated that AhOMTs are highly enriched in transferase and catalytic activities, cellular metabolic and biosynthesis processes. Transcriptome datasets revealed that AhOMTs possessed varying expression levels in different tissues and under hormones, water, and temperature stress. Expression profiling based on qRT-PCR results also supported the transcriptome results. This study provides the theoretical basis for further work on the biological roles of AhOMT genes for developmental and stress responses.

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.

Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants

Crop plants are vulnerable to various biotic and abiotic stresses, whereas plants tend to retain their physiological mechanisms by evolving cellular regulation. To mitigate the adverse effects of abiotic stresses, many defense mechanisms are induced in plants. One of these mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signaling pathway used in the transduction of extracellular stimuli into intercellular responses. This stress signaling pathway is activated by a series of responses involving MAPKKKs→MAPKKs→MAPKs, consisting of interacting proteins, and their functions depend on the collaboration and activation of one another by phosphorylation. These proteins are key regulators of MAPK in various crop plants under abiotic stress conditions and also related to hormonal responses. It is revealed that in response to stress signaling, MAPKs are characterized as multigenic families and elaborate the specific stimuli transformation as well as the antioxidant regulation system. This pathway is directed by the framework of proteins and stopping domains confer the related associates with unique structure and functions. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in plants, such as Arbodiposis, tomato, potato, alfalfa, poplar, rice, wheat, maize, and apple. In this review, we summarized the recent work on MAPK response to abiotic stress and the classification of MAPK cascade in crop plants. Moreover, we highlighted the modern research methodologies such as transcriptomics, proteomics, CRISPR/Cas technology, and epigenetic studies, which proposed, identified, and characterized the novel genes associated with MAPKs and their role in plants under abiotic stress conditions. In-silico-based identification of novel MAPK genes also facilitates future research on MAPK cascade identification and function in crop plants under various stress conditions.

Alternative Splicing in the Regulatory Circuit of Plant Temperature Response

As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled.

Integrated transcriptome and metabolome analysis reveals that flavonoids function in wheat resistance to powdery mildew

Powdery mildew is a fungal disease devastating to wheat, causing significant quality and yield loss. Flavonoids are important secondary plant metabolites that confer resistance to biotic and abiotic stress. However, whether they play a role in powdery mildew resistance in wheat has yet to be explored. In the present study, we combined transcriptome and metabolome analyses to compare differentially expressed genes (DEGs) and differentially accumulated flavonoids identified in plants with and without powdery mildew inoculation. Transcriptome analysis identified 4,329 DEGs in susceptible wheat cv. Jimai229, and 8,493 in resistant cv. HHG46. The DEGs were functionally enriched using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, revealing the flavonoid synthesis pathway as the most significant in both cultivars. This was consistent with the upregulation of flavonoid synthesis pathway genes observed by quantitative PCR. Metabolome analysis indicated flavone and flavonol biosynthesis pathways as the most significantly enriched following powdery mildew inoculation. An accumulation of total flavonoids content was also found to be induced by powdery mildew infection. Exogenous flavonoids treatment of inoculated plants led to less severe infection, with fewer and smaller powdery mildew spots on the wheat leaves. This reduction is speculated to be regulated through malondialdehyde content and the activities of peroxidase and catalase. Our study provides a fundamental theory for further exploration of the potential of flavonoids as biological prevention and control agents against powdery mildew in wheat.

Developing future heat-resilient vegetable crops

Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.

Characterization and expression analysis of basic leucine zipper (bZIP) transcription factors responsive to chilling injury in peach fruit

BACKGROUND

Peach (Prunus persica L.) is prone to chilling injury as exhibited by inhibition of the ethylene production, failure in softening, and the manifestation of internal browning. The basic leucine zipper (bZIP) transcription factors play an essential role in regulatory networks that control many processes associated with physiological, abiotic and biotic stress responses in fruits. Formerly, the underlying molecular and regulatory mechanism of (bZIP) transcription factors responsive to chilling injury in peach fruit is still elusive.

METHODS AND RESULTS

In the current experiment, the solute peach 'Zhongyou Peach No. 13' was used as the test material and cold storage at low temperature (4 °C). It was found that long-term low-temperature storage induced the production of ethylene, the hardness of the pulp decreased, and the low temperature also induced ABA accumulation. The changes of ABA and ethylene in peach fruits during low-temperature storage were clarified. Since the bZIP transcription factor is involved in the regulation of downstream pathways of ABA signals, 47 peach bZIP transcription factor family genes were identified through bioinformatics analysis. Further based on RT-qPCR analysis, 18 PpbZIP genes were discovered to be expressed in refrigerated peach fruits. Among them, the expression of PpbZIP23 and PpbZIP25 was significantly reduced during the refrigeration process, the promoter analysis of these genes found that this region contains the MYC/MYB/ABRES binding element, but not the DRES/CBFS element, indicating that the expression may be regulated by the ABA-dependent cold induction pathway, thereby responding to chilling injury in peach fruit.

CONCLUSIONS

Over investigation will provide new insights for further postharvest protocols related to molecular changes during cold storage and will prove a better cope for chilling injury.

Exogenous melatonin confers cold tolerance in rapeseed (Brassica napus L.) seedlings by improving antioxidants and genes expression

Rapeseed (Brassica napus L.) is an important oilseed crop globally. However, its growth and production are significantly influenced by cold stress. To reveal the protective role of exogenous melatonin (MEL) in cold tolerance, rapeseed seedlings were pretreated with different concentrations of MEL before cold stress. The results indicated that the survival rate was increased significantly by the MEL pretreatment under cold stress. Seedlings pretreated with 0.01 g L^-1 MEL were all survived and were used to analyze the physiological characteristics and the expression level of various genes related to cold tolerance. Under cold stress, exogenous MEL significantly increased the contents of proline, soluble sugar, and soluble protein; while the malondialdehyde content was decreased by exogenous MEL under cold stress. On the other hand, the activities of antioxidant defense enzymes such as catalase, peroxidase, and superoxide dismutase were also significantly enhanced. The results also showed that MEL treatment significantly upregulated the expression of Cu-SOD, COR6.6 (cold-regulated), COR15, and CBFs (C-repeat binding factor) genes under cold stress. It was suggested exogenous MEL improved the content of osmotic regulatory substances to maintain the balance of cellular osmotic potential under cold stress and improved the scavenging capacity of reactive oxygen species by strengthening the activity of antioxidant enzymes and the cold-related genes expression.

Melatonin-mediated temperature stress tolerance in plants

Global climate changes cause extreme temperatures and a significant reduction in crop production, leading to food insecurity worldwide. Temperature extremes (including both heat and cold stresses) is one of the most limiting factors in plant growth and development and severely affect plant physiology, biochemical, and molecular processes. Biostimulants like melatonin (MET) have a multifunctional role that acts as a "defense molecule" to safeguard plants against the noxious effects of temperature stress. MET treatment improves plant growth and temperature tolerance by improving several defense mechanisms. Current research also suggests that MET interacts with other molecules, like phytohormones and gaseous molecules, which greatly supports plant adaptation to temperature stress. Genetic engineering via overexpression or CRISPR/Cas system of MET biosynthetic genes uplifts the MET levels in transgenic plants and enhances temperature stress tolerance. This review highlights the critical role of MET in plant production and tolerance against temperature stress. We have documented how MET interacts with other molecules to alleviate temperature stress. MET-mediated molecular breeding would be great potential in helping the adverse effects of temperature stress by creating transgenic plants.

Salicylic Acid Improves the Constitutive Freezing Tolerance of Potato as Revealed by Transcriptomics and Metabolomics Analyses

Freezing severely impacts potato production. Deciphering the pathways and metabolites that regulate the freezing tolerance of potato is useful in cultivation and breeding for hardiness. In the present study, Solanum acaule was identified to be more freezing tolerant than S. tuberosum. Furthermore, the two genotypes before/after exposure to 4 °C for 7 d with additional -1 °C for 12 h were analysed by RNA-seq and metabolomics, and the results were compared with the previous -1 °C for 12 h. The results showed that S. acaule activated numerous genes that differed from those of S. tuberosum. Among the genes, five pathways, such as the hormone signalling pathway, which includes salicylic acid, were enriched. Further metabolomics analysis showed that the content of salicylic acid was improved in S. acaule in response to -1 °C for 12 h. Moreover, exogenous application of 0.1 mM salicylic acid to potato was shown to improve constitutive freezing tolerance and increase the expression of HSFC1. Following transcriptome and metabolome analyses, it was documented that the content of SA that increased in freezing-tolerant S. acaule after exposure to cold condition, associated with the SA signalling pathway, enhanced potato freezing tolerance, probably through HSFC1.

Multi-omics revolution to promote plant breeding efficiency

Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

Molecular insights into mechanisms underlying thermo-tolerance in tomato

Plant productivity is being seriously compromised by climate-change-induced temperature extremities. Agriculture and food safety are threatened due to global warming, and in many cases the negative impacts have already begun. Heat stress leads to significant losses in yield due to changes in growth pattern, plant phonologies, sensitivity to pests, flowering, grain filling, maturity period shrinkage, and senescence. Tomato is the second most important vegetable crop. It is very sensitive to heat stress and thus, yield losses in tomato due to heat stress could affect food and nutritional security. Tomato plants respond to heat stress with a variety of cellular, physiological, and molecular responses, beginning with the early heat sensing, followed by signal transduction, antioxidant defense, osmolyte synthesis and regulated gene expression. Recent findings suggest that specific plant organs are extremely sensitive to heat compared to the entire plant, redirecting the research more towards generative tissues. This is because, during sexual reproduction, developing pollens are the most sensitive to heat. Often, just a few degrees of temperature elevation during pollen development can have a negative effect on crop production. Furthermore, recent research has discovered certain genetic and epigenetic mechanisms playing key role in thermo-tolerance and have defined new directions for tomato heat stress response (HSR). Present challenges are to increase the understanding of molecular mechanisms underlying HS, and to identify superior genotypes with more tolerance to extreme temperatures. Several metabolites, genes, heat shock factors (HSFs) and microRNAs work together to regulate the plant HSR. The present review provides an insight into molecular mechanisms of heat tolerance and current knowledge of genetic and epigenetic control of heat-tolerance in tomato for sustainable agriculture in the future. The information will significantly contribute to improve breeding programs for development of heat tolerant cultivars.

Smart breeding approaches in post-genomics era for developing climate-resilient food crops

Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.

Plant hormones and neurotransmitter interactions mediate antioxidant defenses under induced oxidative stress in plants

Due to global climate change, abiotic stresses are affecting plant growth, productivity, and the quality of cultivated crops. Stressful conditions disrupt physiological activities and suppress defensive mechanisms, resulting in stress-sensitive plants. Consequently, plants implement various endogenous strategies, including plant hormone biosynthesis (e.g., abscisic acid, jasmonic acid, salicylic acid, brassinosteroids, indole-3-acetic acid, cytokinins, ethylene, gibberellic acid, and strigolactones) to withstand stress conditions. Combined or single abiotic stress disrupts the normal transportation of solutes, causes electron leakage, and triggers reactive oxygen species (ROS) production, creating oxidative stress in plants. Several enzymatic and non-enzymatic defense systems marshal a plant's antioxidant defenses. While stress responses and the protective role of the antioxidant defense system have been well-documented in recent investigations, the interrelationships among plant hormones, plant neurotransmitters (NTs, such as serotonin, melatonin, dopamine, acetylcholine, and γ-aminobutyric acid), and antioxidant defenses are not well explained. Thus, this review discusses recent advances in plant hormones, transgenic and metabolic developments, and the potential interaction of plant hormones with NTs in plant stress response and tolerance mechanisms. Furthermore, we discuss current challenges and future directions (transgenic breeding and genome editing) for metabolic improvement in plants using modern molecular tools. The interaction of plant hormones and NTs involved in regulating antioxidant defense systems, molecular hormone networks, and abiotic-induced oxidative stress tolerance in plants are also discussed.

Tolerant mechanism of model legume plant Medicago truncatula to drought, salt, and cold stresses

Legume plants produce one-third of the total yield of primary crops and are important food sources for both humans and animals worldwide. Frequent exposure to abiotic stresses, such as drought, salt, and cold, greatly limits the production of legume crops. Several morphological, physiological, and molecular studies have been conducted to characterize the response and adaptation mechanism to abiotic stresses. The tolerant mechanisms of the model legume plant Medicago truncatula to abiotic stresses have been extensively studied. Although many potential genes and integrated networks underlying the M. truncatula in responding to abiotic stresses have been identified and described, a comprehensive summary of the tolerant mechanism is lacking. In this review, we provide a comprehensive summary of the adaptive mechanism by which M. truncatula responds to drought, salt, and cold stress. We also discuss future research that need to be explored to improve the abiotic tolerance of legume plants.

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L

Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

Mainstreaming orphan millets for advancing climate smart agriculture to secure nutrition and health

The ever-changing climate and the current COVID-19 pandemic compound the problems and seriously impact agriculture production, resulting in socio-economic insecurities and imposing health implications globally. Most of the poor and malnourished population in the developing countries depends on agriculture for food, income, and employment. Impact of climate change together with the COVID-19 outbreak revealed immense problems highlighting the importance of mainstreaming climate-resilient and low input crops with more contemporary agriculture practices. Orphan millets play a vital role in the poor and malnourished population's livelihood, food and nutrition security. Recognizing their unique potential, the United Nations-Food and Agriculture Organization has announced the year 2023 as the "International Year of Millets". However, despite the unique properties for present and future agriculture of orphan millets, their cultivation is declining in many countries. As a result, millets have gained attention from researchers which eventually decelerated "multi-omics" resource generation. This review summarizes the benefits of millets and major barriers/ bottlenecks in their improvement. We also discuss the pre- and post-harvest technologies; policies required to introduce and establish millets in mainstream agriculture. To improve and ensure the livelihood of the poor/malnourished population, intensive efforts are urgently needed in advancing the research and development, implementing pre- and post-harvest technological intervention strategies, and making favorable policies for orphan crops to accomplish food and nutrition security. National and international collaborations are also indispensable to address the uncertain effects of climate change and COVID-19.

Uncovering the Research Gaps to Alleviate the Negative Impacts of Climate Change on Food Security: A Review

Climatic variability has been acquiring an extensive consideration due to its widespread ability to impact food production and livelihoods. Climate change has the potential to intersperse global approaches in alleviating hunger and undernutrition. It is hypothesized that climate shifts bring substantial negative impacts on food production systems, thereby intimidating food security. Vast developments have been made addressing the global climate change, undernourishment, and hunger for the last few decades, partly due to the increase in food productivity through augmented agricultural managements. However, the growing population has increased the demand for food, putting pressure on food systems. Moreover, the potential climate change impacts are still unclear more obviously at the regional scales. Climate change is expected to boost food insecurity challenges in areas already vulnerable to climate change. Human-induced climate change is expected to impact food quality, quantity, and potentiality to dispense it equitably. Global capabilities to ascertain the food security and nutritional reasonableness facing expeditious shifts in biophysical conditions are likely to be the main factors determining the level of global disease incidence. It can be apprehended that all food security components (mainly food access and utilization) likely be under indirect effect via pledged impacts on ménage, incomes, and damages to health. The corroboration supports the dire need for huge focused investments in mitigation and adaptation measures to have sustainable, climate-smart, eco-friendly, and climate stress resilient food production systems. In this paper, we discussed the foremost pathways of how climate change impacts our food production systems as well as the social, and economic factors that in the mastery of unbiased food distribution. Likewise, we analyze the research gaps and biases about climate change and food security. Climate change is often responsible for food insecurity issues, not focusing on the fact that food production systems have magnified the climate change process. Provided the critical threats to food security, the focus needs to be shifted to an implementation oriented-agenda to potentially cope with current challenges. Therefore, this review seeks to have a more unprejudiced view and thus interpret the fusion association between climate change and food security by imperatively scrutinizing all factors.

Hydrogen sulfide: an emerging component against abiotic stress in plants

As a result of climate change, abiotic stresses are the most common cause of crop losses worldwide. Abiotic stresses significantly impair plants' physiological, biochemical, molecular and cellular mechanisms, limiting crop productivity under adverse climate conditions. However, plants can implement essential mechanisms against abiotic stressors to maintain their growth and persistence under such stressful environments. In nature, plants have developed several adaptations and defence mechanisms to mitigate abiotic stress. Moreover, recent research has revealed that signalling molecules like hydrogen sulfide (H₂ S) play a crucial role in mitigating the adverse effects of environmental stresses in plants by implementing several physiological and biochemical mechanisms. Mainly, H₂ S helps to implement antioxidant defence systems, and interacts with other molecules like nitric oxide (NO), reactive oxygen species (ROS), phytohormones, etc. These molecules are well-known as the key players that moderate the adverse effects of abiotic stresses. Currently, little progress has been made in understanding the molecular basis of the protective role of H₂ S; however, it is imperative to understand the molecular basis using the state-of-the-art CRISPR-Cas gene-editing tool. Subsequently, genetic engineering could provide a promising approach to unravelling the molecular basis of stress tolerance mediated by exogenous/endogenous H₂ S. Here, we review recent advances in understanding the beneficial roles of H₂ S in conferring multiple abiotic stress tolerance in plants. Further, we also discuss the interaction and crosstalk between H₂ S and other signal molecules; as well as highlighting some genetic engineering-based current and future directions.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.

Multidimensional Role of Silicon to Activate Resilient Plant Growth and to Mitigate Abiotic Stress

Sustainable agricultural production is critically antagonistic by fluctuating unfavorable environmental conditions. The introduction of mineral elements emerged as the most exciting and magical aspect, apart from the novel intervention of traditional and applied strategies to defend the abiotic stress conditions. The silicon (Si) has ameliorating impacts by regulating diverse functionalities on enhancing the growth and development of crop plants. Si is categorized as a non-essential element since crop plants accumulate less during normal environmental conditions. Studies on the application of Si in plants highlight the beneficial role of Si during extreme stressful conditions through modulation of several metabolites during abiotic stress conditions. Phytohormones are primary plant metabolites positively regulated by Si during abiotic stress conditions. Phytohormones play a pivotal role in crop plants' broad-spectrum biochemical and physiological aspects during normal and extreme environmental conditions. Frontline phytohormones include auxin, cytokinin, ethylene, gibberellin, salicylic acid, abscisic acid, brassinosteroids, and jasmonic acid. These phytohormones are internally correlated with Si in regulating abiotic stress tolerance mechanisms. This review explores insights into the role of Si in enhancing the phytohormone metabolism and its role in maintaining the physiological and biochemical well-being of crop plants during diverse abiotic stresses. Moreover, in-depth information about Si's pivotal role in inducing abiotic stress tolerance in crop plants through metabolic and molecular modulations is elaborated. Furthermore, the potential of various high throughput technologies has also been discussed in improving Si-induced multiple stress tolerance. In addition, a special emphasis is engrossed in the role of Si in achieving sustainable agricultural growth and global food security.

Mechanistic Insights Into Trehalose-Mediated Cold Stress Tolerance in Rapeseed (Brassica napus L.) Seedlings

Cold stress (CS) severely affects several physiological, biochemical, and molecular mechanisms and limits the growth and production of rapeseed (Brassica napus L.). Trehalose (Tre) acts as a growth modulator, which is extensively used to improve the tolerance to multiple plant stresses. Further, Tre also serves as an external force in inducing plant signaling molecules, regulating the expression of stress-responsive genes, and enhancing the CS tolerance in plants. Nevertheless, the importance of exogenous Tre in improving the CS tolerance in rapeseed is still unclear. Therefore, the current study was designed to get mechanistic insights into Tre-mediated CS tolerance in rapeseed seedlings. To explore the Tre role, we designed four treatments [control (CK), CK + 20 mM L^-1 Tre, Cold, and Cold + 20 mM L^-1 Tre] and three CS conditions (4, 0, and -4°C). The results showed that Tre treatments significantly mitigated the adverse effects of CS on the seedlings and increased the survival rate of Tre-treated seedlings under CS conditions. The exogenous Tre dramatically increased the contents of osmoprotectants, including the soluble sugar (SS), soluble protein (SP), and proline (Pro), and the activities of antioxidant enzymes, such as catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX) were also increased under CS conditions. Additionally, Tre decreased the malondialdehyde (MDA) contents to protect the rapeseed seedlings. Moreover, Tre also remarkably augmented the expression levels of antioxidant genes (CAT12, POD34, and FSD7), CS-responsive marker genes (CBF1, CBF2, CBF4, COR6.6, COR15, COR25, COL1, and KIN1), and Tre-biosynthesis genes (TPS4, TPS8, and TPS9). Briefly, exogenous Tre not only regulates the antioxidant and osmotic balance, but it also significantly participates in Tre metabolism and signaling network to improve the CS tolerance in rapeseed. Thus, Tre-induced supervisory connections between physiological or/and biochemical attributes provide information to dissect the mechanisms of Tre-mediated CS tolerance.

Unfolding molecular switches in plant heat stress resistance: A comprehensive review

Plant heat stress response is a multi-factorial trait that is precisely regulated by the complex web of transcription factors from various families that modulate heat stress responsive gene expression. Global warming due to climate change affects plant growth and development throughout its life cycle. Adds to this, the frequent occurrence of heat waves is drastically reducing the global crop yield. Molecular plant scientists can help crop breeders by providing genetic markers associated with stress resistance. Plant heat stress response (HSR), however, is a multi-factorial trait and using a single stress resistance trait might not be ideal to develop thermotolerant crops. Transcription factors participate in regulation of plant biological processes and environmental stress responses. Recent studies have revealed that plant HSR is precisely regulated by the complex web of transcription factors from various families. These transcription factors enhance plant heat stress tolerance by regulating the expression level of several stress-responsive genes independently or in cross talk with different other transcription factors. This review explores how signaling pathways triggered by heat stress are regulated by multiple transcription factor families. To our knowledge, we for the first time analyze the role of major transcription factor families in plant HSR along with their regulatory mechanisms. In the end, we will also discuss the potential of emerging technologies to improve thermotolerance in plants.

Analyzing the regulatory role of heat shock transcription factors in plant heat stress tolerance: a brief appraisal

An increase in ambient temperature throughout the twenty-first century has been described as a "worldwide threat" for crop production. Due to their sessile lifestyles, plants have evolved highly sophisticated and complex heat stress response (HSR) mechanisms to respond to higher temperatures. The HSR allows plants to minimize the damages caused by heat stress (HS), thus enabling cellular protection. HSR is crucial for their lifecycle and yield, particularly for plants grown in the field. At the cellular level, HSR involves the production of heat shock proteins (HSPs) and other stress-responsive proteins to counter the negative effects of HS. The expression of most HSPs is transcriptionally regulated by heat shock transcription factors (HSFs). HSFs are a group of evolutionary conserved regulatory proteins present in all eukaryotes and regulate various stress responses and biological processes in plants. In recent years, significant progress has been made in deciphering the complex regulatory network of HSFs, and several HSFs not only from model plants but also from major crops have been functionally characterized. Therefore, this review explores the progress made in this fascinating research area and debates the further potential to breed thermotolerant crop cultivars through the modulation of HSF networks. Furthermore, we discussed the role of HSFs in plant HS tolerance in a class-specific manner and shed light on their functional diversity, which is evident from their mode of action. Additionally, some research gaps have been highlighted concerning class-specific manners.

Response and tolerance mechanism of food crops under high temperature stress: a review

High temperature stress events are critical factors inhibiting crop yield. Meanwhile, world population is growing very rapidly and will be reached up to 9 billion by 2050. To feed increasing world population, it is challenging task to increase about 70% global food productions. Food crops have significant contribution toward global food demand and food security. However, consequences from increasing heat stress events are demolishing their abilities to survive and sustain yield when subjected to extreme high temperature stress. Therefore, there is dire need to better understand response and tolerance mechanism of food crops following exposure to heat stress. Here, we aimed to provide recent update on impact of high temperature stress on crop yield of food crops, pollination, pollinators, and novel strategies for improving tolerance of food crop under high temperature stress. Importantly, development of heat-resistant transgenic food crops can grant food security through transformation of superior genes into current germplasm, which are associated with various signaling pathways as well as epigenetic regulation in response to extreme high temperature stress.

Genome-Wide Identification and Expression Profiling of DUF221 Gene Family Provides New Insights Into Abiotic Stress Responses in Potato

The domain of the unknown function 221 proteins regulate several processes in plants, including development, growth, hormone transduction mechanism, and abiotic stress response. Therefore, a comprehensive analysis of the potato genome was conducted to identify the deafness-dystonia peptide (DDP) proteins' role in potatoes. In the present study, we performed a genome-wide analysis of the potato domain of the unknown function 221 (DUF221) genes, including phylogenetic inferences, chromosomal locations, gene duplications, gene structures, and expression analysis. In our results, we identified 10 DDP genes in the potato genome. The phylogenetic analysis results indicated that StDDPs genes were distributed in all four clades, and clade IV was the largest clade. The gene duplication under selection pressure analysis indicated various positive and purifying selections in StDDP genes. The putative stu-miRNAs from different families targeting StDDPs were also predicted in the present study. Promoter regions of StDDP genes contain different cis-acting components involved in multiple stress responses, such as phytohormones and abiotic stress-responsive factors. The analysis of the tissue-specific expression profiling indicated the StDDPs gene expression in stem, root, and leaf tissues. We subsequently observed that StDDP4, StDDP5, and StDDP8 showed higher expressions in roots, stems, and leaves. StDDP5 exhibited high expression against heat stress response, and StDDP7 showed high transcript abundance against salt stress in potatoes. Under abscisic acid (ABA) and indole acetic acid (IAA) treatments, seven StDDP genes' expressions indicated that ABA and IAA performed important roles in immunity response. The expression profiling and real-time qPCR of stems, roots, and leaves revealed StDDPs' significant role in growth and development. These expression results of DDPs are primary functional analysis and present basic information for other economically important crops.