New approaches to improve crop tolerance to biotic and abiotic stresses

Quantifying Genetic Parameters for Blackleg Resistance in Rapeseed: A Comparative Study

Selection is a fundamental part of the plant breeding process, enabling the identification and development of varieties with desirable traits. Thanks to advances in genetics and biotechnology, the selection process has become more precise and efficient, resulting in faster breeding progress and better adaptation of crops to environmental challenges. Genetic parameters related to gene additivity and epistasis play a key role and can influence decisions on the suitability of breeding material. In this study, 188 rapeseed doubled haploid lines were assessed in field conditions for resistance to Leptosphaeria spp. Through next-generation sequencing, a total of 133,764 molecular markers (96,121 SilicoDArT and 37,643 SNP) were obtained. The similarity of the DH lines at the phenotypic and genetic levels was calculated. The results indicate that the similarity at the phenotypic level was markedly different from the similarity at the genetic level. Genetic parameters related to additive gene action effects and epistasis (double and triple) were calculated using two methods: based on phenotypic observations only and using molecular marker observations. All evaluated genetic parameters (additive, additive-additive and additive-additive-additive) were statistically significant for both estimation methods. The parameters associated with the interaction (double and triple) had opposite signs depending on the estimation method.

Nanoparticle-mediated defense priming: A review of strategies for enhancing plant resilience against biotic and abiotic stresses

Nanotechnology has emerged as a promising field with the potential to revolutionize agriculture, particularly in enhancing plant defense mechanisms. Nanoparticles (NPs) are instrumental in plant defense priming, where plants are pre-exposed to controlled levels of stress to heighten their alertness and responsiveness to subsequent stressors. This process improves overall plant performance by enabling quicker and more effective responses to secondary stimuli. This review explores the application of NPs as priming agents, utilizing their unique physicochemical properties to bolster plants' innate defense mechanisms. It discusses key findings in NP-based plant defense priming, including various NP types such as metallic, metal oxide, and carbon-based NPs. The review also investigates the intricate mechanisms by which NPs interact with plants, including uptake, translocation, and their effects on plant physiology, morphology, and molecular processes. Additionally, the review examines how NPs can enhance plant responses to a range of stressors, from pathogen attacks and herbivore infestations to environmental stresses. It also discusses NPs' ability to improve plants' tolerance to abiotic stresses like drought, salinity, and heavy metals. Safety and regulatory aspects of NP use in agriculture are thoroughly addressed, emphasizing responsible and ethical deployment for environmental and human health safety. By harnessing the potential of NPs, this approach shows promise in reducing crop losses, increasing yields, and enhancing global food security while minimizing the environmental impact of traditional agricultural practices. The review concludes by emphasizing the importance of ongoing research to optimize NP formulations, dosages, and delivery methods for practical application in diverse agricultural settings.

Emerging Trends in Non-Protein Amino Acids as Potential Priming Agents: Implications for Stress Management Strategies and Unveiling Their Regulatory Functions

Plants endure the repercussions of environmental stress. As the advancement of global climate change continues, it is increasingly crucial to protect against abiotic and biotic stress effects. Some naturally occurring plant compounds can be used effectively to protect the plants. By externally applying priming compounds, plants can be prompted to trigger their defensive mechanisms, resulting in improved immune system effectiveness. This review article examines the possibilities of utilizing exogenous alpha-, beta-, and gamma-aminobutyric acid (AABA, BABA, and GABA), which are non-protein amino acids (NPAAs) that are produced naturally in plants during instances of stress. The article additionally presents a concise overview of the studies' discoveries on this topic, assesses the particular fields in which they might be implemented, and proposes new avenues for future investigation.

Pathogenesis related-1 proteins in plant defense: regulation and functional diversity

Climate change-related environmental stresses can negatively impact crop productivity and pose a threat to sustainable agriculture. Plants have a remarkable innate ability to detect a broad array of environmental cues, including stresses that trigger stress-induced regulatory networks and signaling pathways. Transcriptional activation of plant pathogenesis related-1 (PR-1) proteins was first identified as an integral component of systemic acquired resistance in response to stress. Consistent with their central role in immune defense, overexpression of PR-1s in diverse plant species is frequently used as a marker for salicylic acid (SA)-mediated defense responses. Recent advances demonstrated how virulence effectors, SA signaling cascades, and epigenetic modifications modulate PR-1 expression in response to environmental stresses. We and others showed that transcriptional regulatory networks involving PR-1s could be used to improve plant resilience to stress. Together, the results of these studies have re-energized the field and provided long-awaited insights into a possible function of PR-1s under extreme environmental stress.

Adenosine triphosphate alleviates high temperature-enhanced glyphosate toxicity in maize seedlings

Extracellular ATP plays a key role in regulating plants stress responses. Here, we aimed to determine whether ATP can alleviate the glyphosate toxicity in maize seedlings under high temperature by regulating antioxidant responses. Foliar spraying with 100 μM glyphosate inhibited the growth of maize seedlings at room temperature (25 °C), leading to an increase in shikimic acid accumulation and oxidative stress (evaluated via lipid peroxidation, free proline, and H2O2 content) in the leaves, all of which were further exacerbated by high temperature (35 °C). The growth inhibition and oxidative stress caused by glyphosate were both alleviated by exogenous ATP. Moreover, the glyphosate-induced antioxidant enzyme activity and antioxidant accumulation were attenuated by high temperature, while ATP treatment reversed this inhibitory effect. Similarly, qPCR data showed that the relative expression levels of antioxidant enzyme-related genes (CAT1, GR1, and γ-ECS) in maize leaves were upregulated by ATP before exposure to GLY. Moreover, high temperature-enhanced GLY residue accumulation in maize leaves was reduced by ATP. ATP-induced detoxification was attenuated through NADPH oxidase (NOX) inhibition. Higher NOX activities and O2•- production were noted in ATP-treated maize leaves compared to controls prior to GLY treatment, indicating that the extracellular ATP-induced alleviation of GLY toxicity was closely associated with NOX-dependent reactive oxygen species signalling. The current findings present a new approach for reducing herbicide toxicity in crops exposed to high temperatures.

Feedback regulation of the isoprenoid pathway by SsdTPS overexpression has the potential to enhance plant tolerance to drought stress

In order to maintain the dynamic physiological balance, plants are compelled to adjust their energy metabolism and signal transduction to cope with the abiotic stresses caused by complex and changeable environments. The diterpenoid natural compound and secondary metabolites, sclareol, derived from Salvia sclarea, has gained significant attention owing to its economic value as a spice material and diverse physiological activities. Here, we focused on the roles and regulatory mechanisms of the sclareol diterpene synthase gene SsdTPS in the resistance of S. sclarea to abiotic stresses. Our results suggested that abiotic stresses could induce the response and upregulation of SsdTPS expression and isoprenoid pathway in S. sclarea. Ectopic expression of SsdTPS conferred drought tolerance in transgenic Arabidopsis, compared with wild-type. Overexpression of SsdTPS enhanced the transcription of ABA signal transduction synthetic regulators and induced the positive feedback upregulating key regulatory genes in the MEP pathway, thereby promoting the increase of ABA content and improving drought tolerance in transgenic plants. In addition, SsdTPS-overexpressed transgenic Arabidopsis improved the responses of stomatal regulatory genes and ROS scavenging enzyme activities and gene expression to drought stress. This promoted the stomatal closure and ROS reduction, thus enhancing water retention capacity and reducing oxidative stress damage. These findings unveil the potentially positive role of SsdTPS in orchestrating multiple regulatory mechanisms and maintaining homeostasis for improved abiotic stress resistance in S. sclarea, providing a novel insight into strategies for promoting drought resistance and cultivating highly tolerant plants.

A comprehensive approach for evaluating salinity stress tolerance in brinjal (Solanum melongena L.) germplasm using membership function value

Salinity is a major stress factor affecting plant growth and development, which limits the productivity of vegetable crops. Brinjal (Solanum melongena L.), an important vegetable cultivated across the globe is susceptible to salinity stress. In the present study, the salinity tolerance response of 110 brinjal germplasm lines was evaluated at the germination stage using the membership function value (MFV). The MFV is a comprehensive index that integrates salt-tolerance indices of germination parameters. The brinjal germplasms were classified into highly salt-tolerant (>0.79), salt-tolerant (0.79-0.65), moderately salt-tolerant (0.64-0.21), salt-sensitive (0.20-0.07), and highly salt-sensitive (<0.07) based on their mean MFV. Among all the traits examined, germination percentage (0.874) and vigour index-I (0.808) were the most reliable traits for assessing salinity tolerance, showing a higher correlation with mean MFV. Furthermore, a comprehensive mathematical model was developed for evaluating the salt-tolerance of the brinjal germplasm. We validated our model by evaluating the brinjal germplasm at the seedling stage through a hydroponic experiment, and a strong positive correlation was observed between growth parameters at the germination and seedling stages. Salt-tolerant genotypes showed higher chlorophyll content, photosynthetic performance and biomass accumulation with lower canopy temperature (1.57°C) under salinity compared to susceptible genotypes (2.62°C). These findings provide valuable insights into the salinity tolerance of the brinjal germplasm, and identified potential candidates to elucidate the molecular mechanisms and develop salinity-tolerant cultivars. To our knowledge, this is the first report using a mathematical model based on MFV to evaluate the salt-tolerance of any vegetable crop.

Continuous Cropping Inhibits Photosynthesis of Polygonatum odoratum

Polygonatum odoratum (Mill.) Druce possesses widespread medicinal properties; however, the continuous cropping (CC) often leads to a severe consecutive monoculture problem (CMP), ultimately causing a decline in yield and quality. Photosynthesis is the fundamental process for plant growth development. Improving photosynthesis is one of the most promising approaches to increase plant yields. To better understand how P. odoratum leaves undergo photosynthesis in response to CC, this study analyzed the physiochemical indexes and RNA-seq. The physiochemical indexes, such as the content of chlorophyll (chlorophyll a, b, and total chlorophyll), light response curves (LRCs), and photosynthetic parameters (Fv/Fm, Fv/F0, Fm/F0, Piabs, ABS/RC, TRo/RC, ETo/RC, and DIo/RC) were all changed in P. odoratum under the CC system. Furthermore, 13,798 genes that exhibited differential expression genes (DEGs) were identified in the P. odoratum leaves of CC and first cropping (FC) plants. Among them, 7932 unigenes were upregulated, while 5860 unigenes were downregulated. Here, the DEGs encoding proteins associated with photosynthesis and carbon assimilation showed a significant decrease in expression under the CC system, such as the PSII protein complex, PSI protein complex, Cytochorome b6/f complex, the photosynthetic electron transport chain, light-harvesting chlorophyll protein complex, and Calvin cycle, etc., -related gene. This study demonstrates that CC can suppress photosynthesis and carbon mechanism in P. odoratum, pinpointing potential ways to enhance photosynthetic efficiency in the CC of plants.

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.

Temporal expression analysis of microRNAs and their target GRAS genes induced by osmotic stress in two contrasting wheat genotypes

BACKGROUND

MicroRNAs (miRNAs) are important nonprotein-coding genes in plants which participate in almost all biological processes during abiotic and biotic stresses. Understanding how plants respond to various environmental conditions requires the identification of stress-related miRNAs. In recent years, there has been an increased interest in studying miRNA genes and gene expression. Drought is one of the common environmental stresses limiting plant growth and development. Stress-specific miRNAs and their GRAS gene targets were validated to understand the role of miRNAs in response to osmotic stress.

RESULTS

In this study, expression patterns of the ten stress-responsive miRNAs involved in osmotic stress adaptation were examined in order to undertand the regulation behavior of abiotic stress and miRNAs in two contrasting wheat genotype C-306 (drought tolerant) and WL-711 (drought sensitive). Three miRNAs were discovered to be upregulated under stress, whereas seven miRNAs were showed to be down-regulated as a consequence of the study. In contrast to miRNA, it was also discovered that GRAS genes as their targets were up-regulated during osmotic stress. In addition, the expression level of miR159, miR408 along with their targets, TaGRAS178 and TaGRAS84 increased in response to osmotic stress. Nevertheless, miR408 is highly conserved miRNA that regulates plant growth, development and stress response. As a result, variation in the expression levels of studied miRNAs in the presence of target genes provides a plausible explanation for miRNA-based abiotic stress regulation. A regulatory network of miRNA and their targets revealed that fourteen miRNA interact with 55 GRAS targets from various subfamilies that contribute in the plant growth and development.

CONCLUSIONS

These findings provide evidence for temporal and variety-specific differential regulation of miRNAs and their targets in wheat in response to osmotic shock, and they may aid in determining the potential.

Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum

Leaf scald caused by Xanthomonas albilineans (Xa) is a major bacterial disease in sugarcane that represents a threat to the global sugar industry. Little is known about the population structure and genetic evolution of this pathogen. In this study, 39 Xa strains were collected from 6 provinces in China. Of these strains, 15 and 24 were isolated from Saccharum spp. hybrid and S. officinarum plants, respectively. Based on multilocus sequence analysis (MLSA), with five housekeeping genes, these strains were clustered into two distinct phylogenetic groups (I and II). Group I included 26 strains from 2 host plants, Saccharum spp. hybrid and S. officinarum collected from 6 provinces, while Group II consisted of 13 strains from S. officinarum plants in the Zhejiang province. Among the 39 Xa strains, nucleotide sequence identities from 5 housekeeping genes were: ABC (99.6-100%), gyrB (99.3-100%), rpoD (98.4-100%), atpD (97.0-100%), and glnA (97.6-100%). These strains were clustered into six groups (A-F), based on the rep-PCR fingerprinting, using primers for ERIC2, BOX A1R, and (GTG)5. UPGMA and PCoA analyses revealed that group A had the most strains (24), followed by group C with 11 strains, while there was 1 strain each in groups B and D-F. Neutral tests showed that the Xa population in S. officinarum had a trend toward population expansion. Selection pressure analysis showed purification selection on five concatenated housekeeping genes from all tested strains. Significant genetic differentiation and infrequent gene flow were found between two Xa populations hosted in Saccharum spp. hybrids and S. officinarum. Altogether, these results provide evidence of obvious genetic divergence and population structures among Xa strains from China.

The role of melatonin in plant growth and metabolism, and its interplay with nitric oxide and auxin in plants under different types of abiotic stress

Melatonin is a pleiotropic signaling molecule that reduces the adverse effects of abiotic stresses, and enhances the growth and physiological function of many plant species. Several recent studies have demonstrated the pivotal role of melatonin in plant functions, specifically its regulation of crop growth and yield. However, a comprehensive understanding of melatonin, which regulates crop growth and yield under abiotic stress conditions, is not yet available. This review focuses on the progress of research on the biosynthesis, distribution, and metabolism of melatonin, and its multiple complex functions in plants and its role in the mechanisms of metabolism regulation in plants grown under abiotic stresses. In this review, we focused on the pivotal role of melatonin in the enhancement of plant growth and regulation of crop yield, and elucidated its interactions with nitric oxide (NO) and auxin (IAA, indole-3-acetic acid) when plants are grown under various abiotic stresses. The present review revealed that the endogenousapplication of melatonin to plants, and its interactions with NO and IAA, enhanced plant growth and yield under various abiotic stresses. The interaction of melatonin with NO regulated plant morphophysiological and biochemical activities, mediated by the G protein-coupled receptor and synthesis genes. The interaction of melatonin with IAA enhanced plant growth and physiological function by increasing the levels of IAA, synthesis, and polar transport. Our aim was to provide a comprehensive review of the performance of melatonin under various abiotic stresses, and, therefore, further explicate the mechanisms that plant hormones use to regulate plant growth and yield under abiotic stresses.

Crop germplasm: Current challenges, physiological-molecular perspective, and advance strategies towards development of climate-resilient crops

Germplasm is a long-term resource management mission and investment for civilization. An estimated ∼7.4 million accessions are held in 1750 plant germplasm centres around the world; yet, only 2% of these assets have been utilized as plant genetic resources (PGRs). According to recent studies, the current food yield trajectory will be insufficient to feed the world's population in 2050. Additionally, possible negative effects in terms of crop failure because of climate change are already being experienced across the world. Therefore, it is necessary to reconciliation of research advancement and innovation of practices for further exploration of the potential of crop germplasm especially for the complex traits associated with yield such as water- and nitrogen use efficiency. In this review, we tried to address current challenges, research gaps, physiological and molecular aspects of two broad spectrum complex traits such as water- and nitrogen-use efficiency, and advanced integrated strategies that could provide a platform for combined stress management for climate-smart crop development. Additionally, recent development in technologies that are directly related to germplasm characterization was highlighted for further molecular utilization towards the development of elite varieties.

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Challenging the water stress index concept: Thermographic assessment of Arabidopsis transpiration

Water stress may greatly limit plant functionality and growth. Stomatal closure and consequently reduced transpiration are considered as early and sensitive plant responses to drought and salinity stress. An important consequence of stomatal closure under water stress is the rise of leaf temperature (Tleaf ), yet Tleaf is not only fluctuating with stomatal closure. It is regulated by several plant parameters and environmental factors. Thermal imaging and different stress indices, incorporating actual leaf/crop temperature and reference temperatures, were developed in previous studies toward normalizing for effects unassociated to water stress on Tleaf , aiming at a more efficient water stress assessment. The concept of stress indices has not been extensively studied on the model plant Arabidopsis thaliana. Therefore, the aim of this study was to examine the different indices employed in previous studies in assessing rosette transpiration rate (E) in Arabidopsis plants grown under two different light environments and subjected to salinity. After salinity imposition, E was gravimetrically quantified, and thermal imaging was employed to quantify rosette (Trosette ) and artificial reference temperature (Twet, Tdry ). Trosette and several water stress indices were tested for their relation to E. Among the microclimatic growth conditions tested, RWSI1 ([Trosette  - Twet ]/[Tdry  - Twet ]) and RWSI2 ([Tdry  - Trosette ]/[Tdry  - Twet ]) were well linearly-related to E, irrespective of the light environment, while the sole use of either Twet or Tdry in different combinations with Trosette returned less accurate results. This study provides evidence that selected combinations of Trosette , Tdry , and Twet can be utilized to assess E under water stress irrespective of the light environment.

Genome-wide characterization of cys-tathionine-β-synthase domain-containing proteins in sugarcane reveals their role in defense responses under multiple stressors

Cys-tathionine-β-synthase (CBS) domain-containing proteins (CDCPs) are essential for regulating plant responses to various biotic and abiotic stressors. This study describes the systematic identification and characterization of CDCP family genes in Saccharum spontaneum. A total of 95 SsCDCP genes and eight phylogenetic groups were identified that were distributed over 29 chromosomes of the AP85-441 genome. Most (78/95) SsCDCPs underwent fragment duplication events, and 64 gene pairs were located in synteny blocks. Expression profiling of nine ShCDCPs was also carried out in the Saccharum spp. cultivars ROC22 and MT11-611 that are resistant and susceptible to red stripe, respectively, in response to: (i) Infection by the bacterial pathogen Acidovorax avenue subsp. avenae (Aaa); (ii) abiotic stressors (drought and salinity); and (iii) exogenous salicylic acid (SA) treatment. Members of one gene pair (ShCBSD-PB1-5A and ShCBSD-PB1-7A-1) with a fragment duplication event acted as negative regulators in sugarcane under four stresses, as supported by the significantly decreased expression levels of ShCBSD-PB1-5A (23-83%) and ShCBSD-PB1-7A-1 (15-75%) at all-time points, suggesting that they have functional redundancy. Genes in another pair, ShCBS-4C and ShCBS-4D-1, which have a fragment duplication event, play opposing regulatory roles in sugarcane exposed to multiple stresses, particularly Aaa and NaCl treatments. ShCBS-4C expression was significantly decreased by 32-77%, but ShCBS-4D-1 expression was dramatically upregulated by 1.2-6.2-fold in response to Aaa treatment of both cultivars across all-time points. This result suggested that both genes exhibited functional divergence. Meanwhile, the expression of SsCBSDCBS-5A was significantly upregulated in ROC22 by 1.4-4.6-fold in response to the four stressors. These findings provide important clues for further elucidating the function of ShCDCP genes in sugarcane responding to a diverse range of stresses.

Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience

In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.