Gene and Metabolite Integration Analysis through Transcriptome and Metabolome Brings New Insight into Heat Stress Tolerance in Potato (Solanum tuberosum L.)

Cotton under heat stress: a comprehensive review of molecular breeding, genomics, and multi-omics strategies

Cotton is a vital fiber crop for the global textile industry, but rising temperatures due to climate change threaten its growth, fiber quality and yields. Heat stress disrupts key physiological and biochemical processes, affecting carbohydrate metabolism, hormone signaling, calcium and gene regulation and expression. This review article explores cotton's defense mechanism against heat stress, including epigenetic regulations and transgenic approaches, with a focus on genome editing tools. Given the limitations of traditional breeding, advanced omics technologies such as GWAS, transcriptomics, proteomics, ionomics, metabolomics, phenomics and CRISPR-Cas9 offer promising solutions for developing heat-resistant cotton varieties. This review highlights the need for innovative strategies to ensure sustainable cotton production under climate change.

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat. In this study, the global transcriptomic and metabolomics profiles were employed to investigate the mechanisms of roots responding to water stresses using the drought-tolerant (DT) and drought-susceptible (DS) wheat genotypes. The results showed that compared with the control group, wheat roots exposed to polyethylene glycol (PEG) had 25941 differentially expressed genes (DEGs) and more upregulated genes were found in DT (8610) than DS (7141). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the drought-tolerant genotype were preferably enriched in the flavonoid biosynthetic process, anthocyanin biosynthesis and suberin biosynthesis. The integrated analysis of the transcriptome and metabolome showed that in DT, the KEGG pathways, including flavonoid biosynthesis and arginine and proline metabolism, were shared by differentially accumulated metabolites (DAMs) and DEGs at 6 h after treatment (HAT) and pathways including alanine, aspartate, glutamate metabolism and carbon metabolism were shared at 48 HAT, while in DS, the KEGG pathways shared by DAMs and DEGs only included arginine and proline metabolism at 6 HAT and the biosynthesis of amino acids at 48 HAT. Our results suggest that the drought-tolerant genotype may relieve the drought stress by producing more ROS scavengers, osmoprotectants, energy and larger roots. Interestingly, hormone signaling plays an important role in promoting the development of larger roots and a higher capability to absorb and transport water in drought-tolerant genotypes.

Transcriptomic and physiological analyses reveal different grape varieties response to high temperature stress

High temperatures affect grape yield and quality. Grapes can develop thermotolerance under extreme temperature stress. However, little is known about the changes in transcription that occur because of high-temperature stress. The heat resistance indices and transcriptome data of five grape cultivars, 'Xinyu' (XY), 'Miguang' (MG), 'Summer Black' (XH), 'Beihong' (BH), and 'Flame seedless' (FL), were compared in this study to evaluate the similarities and differences between the regulatory genes and to understand the mechanisms of heat stress resistance differences. High temperatures caused varying degrees of damage in five grape cultivars, with substantial changes observed in gene expression patterns and enriched pathway responses between natural environmental conditions (35 °C ± 2 °C) and extreme high temperature stress (40 °C ± 2 °C). Genes belonging to the HSPs, HSFs, WRKYs, MYBs, and NACs transcription factor families, and those involved in auxin (IAA) signaling, abscisic acid (ABA) signaling, starch and sucrose pathways, and protein processing in the endoplasmic reticulum pathway, were found to be differentially regulated and may play important roles in the response of grape plants to high-temperature stress. In conclusion, the comparison of transcriptional changes among the five grape cultivars revealed a significant variability in the activation of key pathways that influence grape response to high temperatures. This enhances our understanding of the molecular mechanisms underlying grape response to high-temperature stress.

Yield reduction caused by elevated temperatures and high nitrogen fertilization is mitigated by SP6A overexpression in potato (Solanum tuberosum L.)

Potatoes (Solanum tuberosum L.) are a fundamental staple for millions of people worldwide. They provide essential amino acids, vitamins, and starch - a vital component of the human diet, providing energy and serving as a source of fiber. Unfortunately, global warming is posing a severe threat to this crop, leading to significant yield losses, and thereby endangering global food security. Industrial agriculture traditionally relies on excessive nitrogen (N) fertilization to boost yields. However, it remains uncertain whether this is effective in combating heat-related yield losses of potato. Therefore, our study aimed to investigate the combinatory effects of heat stress and N fertilization on potato tuber formation. We demonstrate that N levels and heat significantly impact tuber development. The combination of high N and heat delays tuberization, while N deficiency initiates early tuberization, likely through starvation-induced signals, independent of SELF-PRUNING 6A (SP6A), a critical regulator of tuberization. We also found that high N levels in combination with heat reduce tuber yield rather than improve it. However, our study revealed that SP6A overexpression can promote tuberization under these inhibiting conditions. By utilizing the excess of N for accumulating tuber biomass, SP6A overexpressing plants exhibit a shift in biomass distribution towards the tubers. This results in an increased yield compared to wild-type plants. Our results highlight the role of SP6A overexpression as a viable strategy for ensuring stable potato yields in the face of global warming. As such, our findings provide insights into the complex factors impacting potato crop productivity.

Multivariate Analysis Compares and Evaluates Heat Tolerance of Potato Germplasm

High temperature is the most important environmental factor limiting potato (Solanum tuberosum L.) yield. The tuber yield has been used to evaluate the heat tolerance of some potato cultivars, but potato yield was closely correlated with the maturation period. Therefore, it is necessary to employ different parameters to comprehensively analyze and evaluate potato tolerance to heat stress. This study aimed to investigate physiologic changes during growth and development, and develop accurate heat tolerance evaluation methods of potato cultivars under heat stress. About 93 cultivars (including foreign elite lines, local landraces and cultivars) were screened using an in vitro tuber-inducing system (continuous darkness and 8% sucrose in the culture medium) under heat stress (30 °C) and normal (22 °C) conditions for 30 days. The tuber yield and number decreased significantly under heat stress compared to the control. A total of 42 cultivars were initially selected depending on tuber formation, after in vitro screening, further testing of selected cultivars was conducted in ex vitro conditions. The screened cultivars were further exposed to heat stress (35 °C/28 °C, day/night) for 60 days. Heat stress led to an increase in the plant height growth rate, fourth internode growth rate, and membrane damage, and due to heat-induced damage to chloroplasts, decrease in chlorophyll biosynthesis and photosynthetic efficiency. Three principal components were extracted by principal component analysis. Correlation and regression analysis showed that heat tolerance is positively correlated with the plant height growth rate, fourth internode growth rate, the content of chlorophyll b, photosynthetic rate, stomatal conductance, transpiration rate, tuber number, and tuber yield, and negatively correlated with the cell membrane injury level. The nine traits are accurate and representative indicators for evaluating potato tolerance to heat stress and could determine a relatively high mean forecast accuracy of 100.0% for the comprehensive evaluation value. Through cluster analysis and screening, cultivar FA, D73, and C132 had the highest heat comprehensive evaluation value, which could be further selected as heat-resistant varieties. This study provides insights into the different physiological mechanisms and accurate evaluation methods of potato cultivars under heat stress, which could be valuable for further research and breeding.

Plant hormones and secondary metabolites under environmental stresses: Enlightening defense molecules

The climatic changes have great threats to sustainable agriculture and require efforts to ensure global food and nutritional security. In this regard, the plant strategic responses, including the induction of plant hormones/plant growth regulators (PGRs), play a substantial role in boosting plant immunity against environmental stress-induced adversities. In addition, secondary metabolites (SMs) have emerged as potential 'stress alleviators' that help plants to adapt against environmental stressors imposing detrimental impacts on plant health and survival. The introduction of SMs in plant biology has shed light on their beneficial effects in mitigating environmental crises. This review explores SMs-mediated plant defense responses and highlights the crosstalk between PGRs and SMs under diverse environmental stressors. In addition, genetic engineering approaches are discussed as a potential revenue to enhance plant hormone-mediated SM production in response to environmental cues. Thus, the present review aims to emphasize the significance of SMs implications with PGRs association and genetic approachability, which could aid in shaping the future strategies that favor agro-ecosystem compatibility under unpredictable environmental conditions.

Rapid Identification of High-Temperature Responsive Genes Using Large-Scale Yeast Functional Screening System in Potato

As the third largest global food crop, potato plays an important role in ensuring food security. However, it is particularly sensitive to high temperatures, which seriously inhibits its growth and development, thereby reducing yield and quality and severely limiting its planting area. Therefore, rapid, and high-throughput screening for high-temperature response genes is highly significant for analyzing potato high-temperature tolerance molecular mechanisms and cultivating new high-temperature-tolerant potato varieties. We screened genes that respond to high temperature by constructing a potato cDNA yeast library. After high-temperature treatment at 39 °C, the yeast library was subjected to high-throughput sequencing, and a total of 1931 heat resistance candidate genes were screened. Through GO and KEGG analysis, we found they were mainly enriched in "photosynthesis" and "response to stimuli" pathways. Subsequently, 12 randomly selected genes were validated under high temperature, drought, and salt stress using qRT-PCR. All genes were responsive to high temperature, and most were also induced by drought and salt stress. Among them, five genes ectopically expressed in yeast enhance yeast's tolerance to high temperatures. We provide numerous candidate genes for potato response to high temperature stress, laying the foundation for subsequent analysis of the molecular mechanism of potato response to high temperature.

Abiotic Stress in Crop Production

The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.

Biochemical, transcriptomic and metabolomic responses to total dissolved gas supersaturation and their underlying molecular mechanisms in Yangtze sturgeon (Acipenser dabryanus)

With the rapid development of hydropower facility construction, the total dissolved gas (TDG) generated by dam discharge is seriously threatening the survival of fish and has become an ecological environmental issue of global concern. However, how TDG affects fish physiology and the underlying molecular mechanism remain poorly known. In this study, Acipenser dabryanus, an ancient living fossil that is a flagship species of the Yangtze River, was exposed to water supersaturated with TDG at a level of 116% for 48 h. A comprehensive analysis was performed to study the effect of TDG supersaturation stress on A. dabryanus, including histopathological, biochemical, transcriptomic and metabolomic analyses. The histopathological results showed that mucosal-associated lymphoid tissues were seriously damaged after TDG supersaturation stress. Plasma catalase levels increased significantly under TDG supersaturation stress, while superoxide dismutase levels decreased significantly. Transcriptomic analysis revealed 289 upregulated genes and 162 downregulated genes in gill tissue and 535 upregulated and 104 downregulated genes in liver tissue. Metabolomic analysis revealed 63 and 164 differentially abundant metabolites between the control group and TDG group in gill and liver, respectively. The majority of heat shock proteins and genes related to ubiquitin and various immune-related pathways were significantly upregulated by TDG supersaturation stress. Integrated transcriptomic and metabolomic analyses revealed the upregulation of amino acid metabolism and glycometabolism pathways under TDG supersaturation stress. Glycerophospholipid metabolism was increased which might be associated with maintaining cell membrane integrity. This is the first study revealing the underlying molecular mechanisms of effects of TDG supersaturation on fish. Our results suggested that acute TDG supersaturation stress could enhance immune and antioxidative functions and activate energy metabolic pathways as an adaptive mechanism in A. dabryanus.

Mechanistic Concept of Physiological, Biochemical, and Molecular Responses of the Potato Crop to Heat and Drought Stress

Most cultivated potatoes are tetraploid, and the tuber is the main economic part that is consumed due to its calorific and nutritional values. Recent trends in climate change led to the frequent occurrence of heat and drought stress in major potato-growing regions worldwide. The optimum temperature for tuber production is 15-20 °C. High-temperature and water-deficient conditions during the growing season result in several morphological, physiological, biochemical, and molecular alterations. The morphological changes under stress conditions may affect the process of stolon formation, tuberization, and bulking, ultimately affecting the tuber yield. This condition also affects the physiological responses, including an imbalance in the allocation of photoassimilates, respiration, water use efficiency, transpiration, carbon partitioning, and the source-sink relationship. The biochemical responses under stress conditions involve maintaining ionic homeostasis, synthesizing heat shock proteins, achieving osmolyte balance, and generating reactive oxygen species, ultimately affecting various biochemical pathways. Different networks that include both gene regulation and transcription factors are involved at the molecular level due to the combination of hot and water-deficient conditions. This article attempts to present an integrative content of physio-biochemical and molecular responses under the combined effects of heat and drought, prominent factors in climate change. Taking into account all of these aspects and responses, there is an immediate need for comprehensive screening of germplasm and the application of appropriate approaches and tactics to produce potato cultivars that perform well under drought and in heat-affected areas.

Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement

Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.

Design and Analysis of Native Photorespiration Gene Motifs of Promoter Untranslated Region Combinations Under Short Term Abiotic Stress Conditions

Quantitative traits are rarely controlled by a single gene, thereby making multi-gene transformation an indispensable component of modern synthetic biology approaches. However, the shortage of unique gene regulatory elements (GREs) for the robust simultaneous expression of multiple nuclear transgenes is a major bottleneck that impedes the engineering of complex pathways in plants. In this study, we compared the transcriptional efficacies of a comprehensive list of well-documented promoter and untranslated region (UTR) sequences side by side. The strength of GREs was examined by a dual-luciferase assay in conjunction with transient expression in tobacco. In addition, we created suites of new GREs with higher transcriptional efficacies by combining the best performing promoter-UTR sequences. We also tested the impact of elevated temperature and high irradiance on the effectiveness of these GREs. While constitutive promoters ensure robust expression of transgenes, they lack spatiotemporal regulations exhibited by native promoters. Here, we present a proof-of-principle study on the characterization of synthetic promoters based on cis-regulatory elements of three key photorespiratory genes. This conserved biochemical process normally increases under elevated temperature, low CO2, and high irradiance stress conditions and results in ∼25% loss in fixed CO2. To select stress-responsive cis-regulatory elements involved in photorespiration, we analyzed promoters of two chloroplast transporters (AtPLGG1 and AtBASS6) and a key plastidial enzyme, AtPGLP using PlantPAN3.0 and AthaMap. Our results suggest that these motifs play a critical role for PLGG1, BASS6, and PGLP in mediating response to elevated temperature and high-intensity light stress. These findings will not only enable the advancement of metabolic and genetic engineering of photorespiration but will also be instrumental in related synthetic biology approaches.

Germplasm, Breeding, and Genomics in Potato Improvement of Biotic and Abiotic Stresses Tolerance

Potato is one of the most important food crops in the world. Late blight, viruses, soil and tuber-borne diseases, insect-pests mainly aphids, whiteflies, and potato tuber moths are the major biotic stresses affecting potato production. Potato is an irrigated and highly fertilizer-responsive crop, and therefore, heat, drought, and nutrient stresses are the key abiotic stresses. The genus Solanum is a reservoir of genetic diversity, however, a little fraction of total diversity has been utilized in potato breeding. The conventional breeding has contributed significantly to the development of potato varieties. In recent years, a tremendous progress has been achieved in the sequencing technologies from short-reads to long-reads sequence data, genomes of Solanum species (i.e., pan-genomics), bioinformatics and multi-omics platforms such as genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics. As such, genome editing has been extensively explored as a next-generation breeding tool. With the available high-throughput genotyping facilities and tetraploid allele calling softwares, genomic selection would be a reality in potato in the near future. This mini-review covers an update on germplasm, breeding, and genomics in potato improvement for biotic and abiotic stress tolerance.

High Temperature Alters Secondary Metabolites and Photosynthetic Efficiency in Heracleum sosnowskyi

Due to global warming, invasive species have spread across the world. We therefore studied the impact of short-term (1 day or 2 days) and longer (7 days) heat stress on photosynthesis and secondary metabolites in Heracleum sosnowskyi, one of the important invasive species in the European Union. H. sosnowskyi leaves exposed to short-term heat stress (35 °C/1 d) showed a decrease in chlorophyll and maximum potential quantum efficiency of photosystem II (Fv/Fm) compared to control, 35 °C/2 d, or 30 °C/7 d treatments. In turn, the high level of lipid peroxidation and increased H₂O₂ accumulation indicated that the 30 °C/7 d stress induced oxidative damage. The contents of xanthotoxin and bergapten were elevated in the 2 d and 7 d treatments, while isopimpinellin was detected only in the heat-stressed plants. Additionally, the levels of free proline and anthocyanins significantly increased in response to high temperature, with a substantially higher increase in the 7 d (30 °C) treatment. The results indicate that the accumulation of proline, anthocyanins, and furanocoumarins, but not of phenolic acids or flavonols, contributes to protection of H. sosnowskyi plants against heat stress. Further studies could focus on the suppression of these metabolites to suppress the spread of this invasive species.