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| Alternative splicing events in Bradi4g16980. (A) The IGV map of RNA-seq reads. The reads showed that the middle exon was differentially spliced. (B) Result of semi-quantitative RT-PCR. (C) Diagram of isoforms a, b, and c. Arrows in (C) indicate primers.
Source publication
Heat stress greatly affects plant growth/development and influences the output of crops. With the increased occurrence of extreme high temperature, the negative influence on cereal products from heat stress becomes severer and severer. It is urgent to reveal the molecular mechanism in response to heat stress in plants. In this research, we used RNA...
Contexts in source publication
Context 1
... verify the AS events, the two genes Bradi4g16980 and Bradi3g07286 were selected for further analysis. The AS of Bradi4g16980 can occur in a skipped exon manner, indicated by the Integrative Genomics Viewer (IGV) map of RNASeq reads ( Figure 7A). According to the predicted sites and the length of exons, primers were designed and semi-quantitative RT-PCR experiments were performed. ...
Context 2
... to the predicted sites and the length of exons, primers were designed and semi-quantitative RT-PCR experiments were performed. As shown in Figures 7B,C, in addition to bands a that included exons 10, 11, 12, and 13, and b that included exons 10, 11, and 13 that could be amplified in leaves of seedlings under normal conditions, band c, which included exons 10 and 13, was amplified in heat-treated samples. This result indicated another isoform was formed during the RNA processing by skipping the 12th exon. ...
Citations
... Plant heat tolerance is primarily mediated by a signal cascade, a transcription factor regulatory network, and the production of heat shock proteins [11]. Heat stress can be effectively decreased by these pathway responses, which include a rise in proline (Pro), soluble sugars (SS), free amino acids, malondialdehyde (MDA), and catalase (CAT), as well as an increase in the activity of enzymes that scavenge free radicals, such as catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) [12,13]. Plants activate a large number of signal transduction pathways at high temperatures. ...
Background
High temperatures significantly affect the growth, development, and yield of plants. Anoectochilus roxburghii prefers a cool and humid environment, intolerant of high temperatures. It is necessary to enhance the heat tolerance of A. roxburghii and breed heat-tolerant varieties. Therefore, we studied the physiological indexes and transcriptome of A. roxburghii under different times of high-temperature stress treatments.
Results
Under high-temperature stress, proline (Pro), H2O2 content increased, then decreased, then increased again, catalase (CAT) activity increased continuously, peroxidase (POD) activity decreased rapidly, then increased, then decreased again, superoxide dismutase (SOD) activity, malondialdehyde (MDA), and soluble sugars (SS) content all decreased, then increased, and chlorophyll and soluble proteins (SP) content increased, then decreased. Transcriptomic investigation indicated that a total of 2740 DEGs were identified and numerous DEGs were notably enriched for “Plant-pathogen interaction” and “Plant hormone signal transduction”. We identified a total of 32 genes in these two pathways that may be the key genes for resistance to high-temperature stress in A. roxburghii.
Conclusions
To sum up, the results of this study provide a reference for the molecular regulation of A. roxburghii’s tolerance to high temperatures, which is useful for further cultivation of high-temperature-tolerant A. roxburghii varieties.
... Chen and Li [127] study included Brachypodium distachyon leaf transcriptome analysis, showing DEGs participating in processes such as the spliceosome and PSI, and PSII biogenesis, or in protein folding. Notably, more than 43 upregulated genes coded machinery for alternative RNA splicing. ...
Plant transcriptomes are an extremely dynamic entities shaped spatially and temporally by many intracellular and environmental cues. In this review, we first summarize the complexity and diversity of plant genomes and transcriptomes as a start point for the multitude of transcriptomic responses. Numerous alterations within various tissue and organ‐specific transcriptomes as well as the most relevant transcriptomic responses associated with plant acclimation to selected abiotic and biotic stress conditions, from the current studies employing highthroughput
transcriptomic analysis are widely discussed. Understanding changes within plant
transcriptomes, revealed by in silico functional analysis, allows for the characterization of stress affected genes and stress acclimatory mechanisms, as well as allows to perform plant metabolic engineering. The latter allow cultivars to produce more secondary metabolites in the future, which are often desirable substances in the biomedical industry. Accordingly, in this review special attention was also paid to characterize the potential of transcriptomic analyses of medicinal species, particularly to search for new cultivars. Extensive characterization of transcriptomic responses in stress would also result in the development of new cultivars that display physiological and molecular mechanisms that allow them to cope with adverse environmental conditions more adequately.
... Environmental stresses such as heat stress can disrupt the bonds that maintain protein structure, leading to denaturation and loss of function (Freeman et al., 1999;Bischof and He, 2006;Huang and Xu, 2008). Previous studies reported the upregulation of genes related to protein folding in different plant species such as Brachypodium distachyon (Chen and Li, 2017), Orchard-grass (Luo et al., 2023) and maize (Wu et al., 2020a). During heat stress, the expression of genes that are related to protein folding and assembly, such as HSPs, can enhance heat tolerance in plants (Miernyk, 1999;Jacob et al., 2017;Ding et al., 2020). ...
Introduction
Wheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development.
Methods
This study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars.
Results and discussion
We identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain.
Conclusion
Our results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.
... Alternative splicing events have been observed in various plant species in response to heat stress. For instance, in Brachypodium distachyon, a total of 1,973 alternative splicing events were identified among 451 differentially expressed genes following exposure to a temperature of 42°C (Chen and Li, 2017). In Oryza sativa, the temperature and drought-responsive gene DREB2B undergoes alternative splicing. ...
Introduction
Increasing global warming has made heat stress a serious threat to crop productivity and global food security in recent years. One of the most promising solutions to address this issue is developing heat-stress-tolerant plants. Hence, a thorough understanding of heat stress response mechanisms, particularly molecular ones, is crucial.
Methods
Although numerous studies have used microarray expression profiling technology to explore this area, these experiments often face limitations, leading to inconsistent results. To overcome these limitations, a random effects meta-analysis was employed using advanced statistical methods. A meta-analysis of 16 microarray datasets related to heat stress response in Arabidopsis thaliana was conducted.
Results
The analysis revealed 1,972 significant differentially expressed genes between control and heat-stressed plants (826 over-expressed and 1,146 down-expressed), including 128 differentially expressed transcription factors from different families. The most significantly enriched biological processes, molecular functions, and KEGG pathways for over-expressed genes included heat response, mRNA splicing via spliceosome pathways, unfolded protein binding, and heat shock protein binding. Conversely, for down-expressed genes, the most significantly enriched categories included cell wall organization or biogenesis, protein phosphorylation, transmembrane transporter activity, ion transmembrane transporter, biosynthesis of secondary metabolites, and metabolic pathways.
Discussion
Through our comprehensive meta-analysis of heat stress transcriptomics, we have identified pivotal genes integral to the heat stress response, offering profound insights into the molecular mechanisms by which plants counteract such stressors. Our findings elucidate that heat stress influences gene expression both at the transcriptional phase and post-transcriptionally, thereby substantially augmenting our comprehension of plant adaptive strategies to heat stress.
... We found that the number of downregulated genes was greater than the number of upregulated genes after heat stress at both the seedling and adult plant stages. Previous research has shown that the number of downregulated genes was greater than the number of upregulated genes after heat stress in wheat seeds, and the number of downregulated genes was also greater than the number of upregulated genes after heat stress in Brachypodium distachyon [31,32]. This is consistent with our findings. ...
Heat stress is a major abiotic stress that can cause serious losses of a crop. Our previous work identified a gene involved in heat stress tolerance in wheat, TaPLC1-2B. To further investigate its mechanisms, in the present study, TaPLC1-2B RNAi-silenced transgenic wheat and the wild type were comparatively analyzed at both the seedling and adult stages, with or without heat stress, using transcriptome sequencing. A total of 15,549 differentially expressed genes (DEGs) were identified at the adult stage and 20,535 DEGs were detected at the seedling stage. After heat stress, an enrichment of pathways such as phytohormones and mitogen-activated protein kinase signaling was mainly found in the seedling stage, and pathways related to metabolism, glycerophospholipid metabolism, circadian rhythms, and ABC transporter were enriched in the adult stage. Auxin and abscisic acid were downregulated in the seedling stage and vice versa in the adult stage; and the MYB, WRKY, and no apical meristem gene families were downregulated in the seedling stage in response to heat stress and upregulated in the adult stage in response to heat stress. This study deepens our understanding of the mechanisms of TaPLC1-2B in regard to heat stress in wheat at the seedling and adult stages.
... Plants initiate multiple physiological and molecular responses to enhance heat tolerance [3,4]. On the one hand, plants recruit antioxidant enzymes to eliminate reactive oxygen species; increase the transpiration rate to cool down; and increase soluble sugars, proteins, and proline to maintain cell membrane homeostasis [5,6]. On the other hand, plants sense via sensors and transduce heat stress signals to transcriptional regulators. ...
Affected by global warming; heat stress is the main limiting factor for crop growth and development. Brassica rapa prefers cool weather, and heat stress has a significant negative impact on its growth, development, and metabolism. Understanding the regulatory patterns of heat–resistant and heat–sensitive varieties under heat stress can help deepen understanding of plant heat tolerance mechanisms. In this study, an integrative analysis of transcriptome and metabolome was performed on the heat–tolerant (‘WYM’) and heat–sensitive (‘AJH’) lines of Brassica rapa to reveal the regulatory networks correlated to heat tolerance and to identify key regulatory genes. Heat stress was applied to two Brassica rapa cultivars, and the leaves were analyzed at the transcriptional and metabolic levels. The results suggest that the heat shock protein (HSP) family, plant hormone transduction, chlorophyll degradation, photosynthetic pathway, and reactive oxygen species (ROS) metabolism play an outstanding role in the adaptation mechanism of plant heat tolerance. Our discovery lays the foundation for future breeding of horticultural crops for heat resistance.
... C306 shown 14.2 and 19.5-fold change under heat stress at anthesis stage (Vishwakarma and Sharma 2018). Another study, also proved higher expression of MBF1c gene in Brachypodium distachyon (2751.3 and 358.9-folds at seedling and anthesis stage) (Chen and Li 2017). This confirmed the role of MBF1c gene in combating heat stress tolerance plants especially at anthesis stage. ...
Enhancement of crop productivity under various abiotic stresses is a major objective for researchers in the current scenario. Heat stress adversely affects yield of wheat (Triticum aestivum L.) plants. To cope up with stress conditions, plants respond by overexpressing their heat stress-related genes and transcription factors. Wheat is one of the world’s most staple food crops which is highly sensitive to heat stress especially during anthesis stage, thereby affecting both yield and quality. During abiotic stress, plant heat shock factors (Hsfs) play a crucial role and confers stress tolerance. In this study, we have isolated highly heat stress-responsive transcription factor from wheat cultivar HD3086, after checking the gene expression using real-time PCR in contrasting wheat genotypes (HD2894 and HD3086). The candidate gene (TaMBF1c) was cloned in pJET1.2/blunt vector and then further into binary vector followed by transformation in tobacco (Nicotiana tabacum) via Agrobacterium mediated genetic transformation. The transgenic tobacco plants raised were validated for heat stress tolerance using different physiological and biochemical assays (RWC, MDA, proline content and chlorophyll content). The gene expression was checked in transgenic plants using qRT-PCR. At T1 generation, seeds of transgenic plants were germinated on MS selection media and a segregation inheritance of 3:1 (resistance: susceptible) ratio was obtained which, followed the Mendelian inheritance pattern. For future research work, TaMBF1c would be taken in different crop plants to develop heat stress tolerant crops for sustainable development under globally changing climate conditions.
... The development of next-generation sequencing technology [9] has made it possible to identify heat stress-responsive genes and transcripts more accurately and rapidly at the transcriptome level. This technology facilitates in-depth analysis of the molecular mechanism of heat stress [10,11]. ...
Heat stress has been a big challenge for animal survival and health due to global warming. However, the molecular processes driving heat stress response were unclear. In this study, we exposed the control group rats (n = 5) at 22 °C and the other three heat stress groups (five rats in each group) at 42 °C lasting 30, 60, and 120 min, separately. We performed RNA sequencing in the adrenal glands and liver and detected the levels of hormones related to heat stress in the adrenal gland, liver, and blood tissues. Weighted gene co-expression network analysis (WGCNA) was also performed. Results showed that rectal temperature and adrenal corticosterone levels were significantly negatively related to genes in the black module, which was significantly enriched in thermogenesis and RNA metabolism. The genes in the green-yellow module were strongly positively associated with rectal temperature and dopamine, norepinephrine, epinephrine, and corticosterone levels in the adrenal glands and were enriched in transcriptional regulatory activities under stress. Finally, 17 and 13 key genes in the black and green-yellow modules were identified, respectively, and shared common patterns of changes. Methyltransferase 3 (Mettl3), poly(ADP-ribose) polymerase 2 (Parp2), and zinc finger protein 36-like 1 (Zfp36l1) occupied pivotal positions in the protein–protein interaction network and were involved in a number of heat stress-related processes. Therefore, Parp2, Mettl3, and Zfp36l1 could be considered candidate genes for heat stress regulation. Our findings shed new light on the molecular processes underpinning heat stress.
... They also affect cell division and differentiation, reducing plant growth and development (Qi and Zhang, 2020;Liu et al., 2022). It should be noted that the majority of studies carried out to understand shoot and/or root responses to heat or warming have grown whole plants (shoots and roots) at homogeneous high temperatures and, in some cases, have heated detached shoots and roots (Heckathorn et al., 2013;Valdé s-Ló pez et al., 2016;Chen and Li, 2017;Estravis-Barcala et al., 2021). However, waves of high atmospheric temperature have different effects on shoots than on roots. ...
... In this work, we used a novel approach that reflects natural soil properties in many aspects to demonstrate that a temperature gradient in the root ecosystem is essential for studying and understanding the whole-plant response to heat stress. In general, in vitro and greenhouse studies have not considered the temperature in the root zone when analyzing the effect of heat stress (Heckathorn et al., 2013;Valdé s-Ló pez et al., 2016;Chen and Li, 2017;Estravis-Barcala et al., 2021;Pei et al., 2021). In response to warming temperatures, which are normally optimal and nondetrimental for plant growth, one of the thermomorphogenetic responses is the elongation of roots. ...
Climate change is increasing the frequency of extreme heat events that aggravate its negative impact on plant development and agricultural yield. Most of the experiments designed to study plant adaption to heat stress apply homogeneous high temperatures to both shoot and root. However, this treatment does not mimic the conditions in natural fields where roots grow in a dark and in a temperature descendent-gradient environment. Excessively high temperatures severely reduce cell division in the root meristem, compromising root growth, while increase cell division of quiescent center cells, likely in an attempt to maintain the stem cell niche in such harsh conditions. Here, we engineered the TGRooZ, a device that generates a temperature gradient for in vitro or greenhouse growth assays. The root system of plants exposed to high temperatures in the shoot, but cultivated in the TGRooZ, grows efficiently and maintains its functionality to sustain a proper shoot growth and development. Furthermore, gene expression and rhizosphere or root microbiomes composition of TGRooZ-grown roots is significantly less affected than high temperature-grown roots, correlating with a higher root functionality. Our data indicate that by using TGRooZ in heat stress studies, we can improve our knowledge on the plant response to high temperatures and the applicability from laboratory studies to the field.
... Highest number of identified genes was belonged to biological processes and lowest was in molecular function in two contrasting genotypes [9]. According to Chen and Li [27], in Brachypodium distachyon, highest genes were annotated to biological processes while lowest were in cellular components. Li et al. [28] also used GO analysis in switch grass. ...
Hexaploid wheat is the main cereal food crop for most people but it is highly influenced by climatic variations. The influence of these climatic variations was studies in wheat genotype WH -1184 in field conditions under two different environments (normal and late sown) and it was found that the genotype is less yielding under late sown conditions. To study the effects of heat stress at transcript level, it was grown under two different conditions (WH-1184 control and heat treated) in pots and transcriptome analysis based on Illumina Novoseq 6000 was carried out for the identification of the differentially expressed genes (DEGs) and metabolic processes or gene regulations influenced by heat stress which lead to a reduction in both quality and quantity of wheat production. These DEGs were utilized to set up a subsequent unigene assembly and GO analysis was performed using unigenes to analyze functions of DEGs which were classified into three main domains, i.e., biological process, cellular component, and molecular function. KEGG (Kyoto Encyclopedia of Genes and Genomes) ontology was used to visualize the physiological processes or to identify KEGG pathways that provide plants their ability to shield in adverse conditions of heat stress. From KEGG ontology, it was reported that genes which encoded protein detoxification and ABC1 domain-containing protein were upregulated while genes thatencoded glutathione transferase (GST), peroxidase, and chitinase enzymes were downregulated. Downregulation of these enzymes during heat stress causes oxidative damages in plants while upregulated proteins play a main role in detoxification to protect plants from heat stress. It was hypothesized that the yield of WH-1184 decreased 44% under heat stress due to the downregulation of genes that encoded GST, peroxidase, and chitinase enzymes which can protect plants from oxidative damage. Hence, upregulation of these genes might be helpful for the adaptation of this genotype under heat stress condition.
