Basis Of Abiotic Stress Tolerance Research Articles

Unlocking the Genetic Basis of Abiotic Stress Tolerance in Wheat: Insights from Dif- ferential Expression Analysis and Machine Learning

Abiotic stresses such as heat and cold temperatures, salinity, and drought are threatening global food security by affecting crop quality and reproductivity. Wheat is the most essential staple crop in the world, its complex genome is the main barrier to finding valuable genes responsive to different stresses. Thus, in our study we conducted differential RNA-seq analysis to identify Differentially Expressed Genes (DEGs) involved in 4 different stresses such as drought, heat, freeze resistance, and water-deficit stress, then applied two machine learning models; the "Extra-tree regressor" and LIME algorithms to accurately predict and select the highly significant genes. Our findings identified a set of 36 significant genes, many of which play important roles in various molecular functions, cellular components, and biological processes related to the response or resistance to abiotic stress in wheat. For example, Hsp101b is a member of the heat shock protein family, which protects cells against stress by stabilizing proteins. BADH, an enzyme involved in the synthesis of stress hormones, is important for the plant’s response to different stresses. AGL14 is a member of the AGL protein family, which regulates gene expression and is involved in the plant’s response to drought, cold, and salinity stresses. This study demonstrates the prospects of the integration of bioinformatics tools as well as machine learning models to assess the genes responsible for wheat stress resistance, genes’ regulatory networks, and their functions in order to save time and cost to improve wheat productivity.

The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond.

The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.

Biochemical and molecular basis of abiotic stress tolerance in barley

Environment has very critical role for the plant growth and development and it is the deciding factor for the growing time and distribution of a crop plant in a particular geographical area. The abiotic stresses are bound to increase in the time to come, because of changing climatic conditions. To sustain the agricultural system, we need to get ready with the crop plants which have durable abiotic stress tolerance. Among the cultivable cereals, barley stands out in terms of abiotic stress tolerance and has the inherent capability to grow in harsh environments with limited resources. Attempt has been made in this article to compile the available information on some of the biochemical and molecular factors contributing to drought, salinity and heat tolerance of barley species. It is expected that this compilation may be useful for the crop improvement programmes in relation to abiotic stress tolerance.

Use of hydraulic traits for modeling genotype‐specific acclimation in cotton under drought

Summary Understanding the genetic and physiological basis of abiotic stress tolerance under field conditions is key to varietal crop improvement in the face of climate variability. Here, we investigate dynamic physiological responses to water stress in silico and their relationships to genotypic variation in hydraulic traits of cotton (Gossypium hirsutum), an economically important species for renewable textile fiber production.In conjunction with an ecophysiological process‐based model, heterogeneous data (plant hydraulic traits, spatially‐distributed soil texture, soil water content and canopy temperature) were used to examine hydraulic characteristics of cotton, evaluate their consequences on whole plant performance under drought, and explore potential genotype × environment effects.Cotton was found to have R‐shaped hydraulic vulnerability curves (VCs), which were consistent under drought stress initiated at flowering. Stem VCs, expressed as percent loss of conductivity, differed across genotypes, whereas root VCs did not. Simulation results demonstrated how plant physiological stress can depend on the interaction between soil properties and irrigation management, which in turn affect genotypic rankings of transpiration in a time‐dependent manner.Our study shows how a process‐based modeling framework can be used to link genotypic variation in hydraulic traits to differential acclimating behaviors under drought.

Mechanisms and Advances in Abiotic Stress Tolerance in Crops: A Molecular and Genetic Perspective

Abiotic stresses, including drought, salinity, extreme temperatures, and heavy metals, pose significant threats to global crop production and food security. Understanding the molecular and genetic basis of abiotic stress tolerance is essential for developing resilient crop varieties. This review comprehensively examines recent advances in the molecular and genetic mechanisms underlying abiotic stress tolerance in crops. Key topics include signal perception and transduction pathways, stress-responsive gene expression, osmotic adjustment, and ion homeostasis. We explore genetic approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and functional genomics that have elucidated critical genes and regulatory networks, to discuss biotechnological interventions, including transgenic approaches, marker-assisted breeding, and synthetic biology, highlighting their applications in enhancing stress tolerance. Case studies in major crops such as rice, wheat, maize, and soybean illustrate practical advances and challenges. Finally, we address future perspectives, emphasizing the integration of multi-omics approaches, the impact of climate change, and the ethical and regulatory considerations of biotechnological advancements. This review aims to provide a comprehensive understanding of the current state of abiotic stress tolerance research and its implications for sustainable agriculture.

Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater

Microalgal Chlorella has been demonstrated to process wastewater efficiently from piggery industry, yet optimization through genetic engineering of such a bio-treatment is currently challenging, largely due to the limited data and knowledge in genomics. In this study, we first investigated the differential growth rates among three wastewater-processing Chlorella strains: Chlorella sorokiniana BD09, Chlorella sorokiniana BD08 and Chlorella sp. Dachan, and the previously published Chlorella sorokiniana UTEX 1602, showing us that BD09 maintains the best tolerance in synthetic wastewater. We then performed genome sequencing and analysis, resulting in a high-quality assembly for each genome with scaffold N50 > 2 Mb and genomic completeness ≥91%, as well as genome annotation with 9,668, 10,240, 9,821 high-confidence gene models predicted for BD09, BD08, and Dachan, respectively. Comparative genomics study unravels that metabolic pathways, which are involved in nitrogen and phosphorus assimilation, were enriched in the faster-growing strains. We found that gene structural variation and genomic rearrangement might contribute to differential capabilities in wastewater tolerance among the strains, as indicated by gene copy number variation, domain reshuffling of orthologs involved, as well as a ~1 Mb-length chromosomal inversion we observed in BD08 and Dachan. In addition, we speculated that an associated bacterium, Microbacterium chocolatum, which was identified within Dachan, play a possible role in synergizing nutrient removal. Our three newly sequenced Chlorella genomes provide a fundamental foundation to understand the molecular basis of abiotic stress tolerance in wastewater treatment, which is essential for future genetic engineering and strain improvement.

Removal of early fruit branches triggered regulations in senescence, boll attributes and yield of Bt cotton genotypes

AbstractPremature senescence, unopened and rotted bolls are the primary constrictions hampering the accomplishment of yield potential in Bt cotton. An experiment was conducted with the objectives to delay senescence, enhance boll opening and reduce the boll rotting. The experiment was conducted at two randomly selected sites of University of Agriculture Faisalabad, Pakistan, during 2015 and repeated in 2016. Each experiment was laid out in randomised complete block design with two by two factorial arrangement structure and replicated five times. Treatments were comprised of R0 = no fruit removal; R1 = removal of early fruit branches (REFB) and two genotypes, viz. V1 = FH‐142 and V2 = MNH‐886. Genotypes were selected on the basis of abiotic stress tolerance (FH‐142) and susceptibility (MNH‐886). Nodes above cracked bolls, monopodial branches, opened bolls per plant and seed cotton yield were enhanced by 23, 12, 13 and 17%, respectively, under the influence of REFB over no fruit branch removal, while the REFB‐mediated decrease in boll rotting was 27%. Moreover, the response of MNH‐886 was more remarkable than FH‐142 for all studied variables. Conclusively, REFB increased the number of nodes above a cracked boll, monopodial branches, opened bolls per plant and seed cotton yield while decreased rotted bolls per plant in both genotypes.

Molecular understandings on ‘the never thirsty’ and apomictic Cenchrus grass

The genus Cenchrus comprises around 25 species of 'bristle clade' grasses. Cenchrus ciliaris (buffel grass) is a hardy, perennial range grass that survives in poor sandy soils and limiting soil moisture conditions and, due to the very same reasons, this grass is one of the most prevalent fodder grasses of the arid and semi-arid regions. Most of the germplasms of Cenchrus produce seeds asexually through the process of apomeiosis. Therefore, the lack of sufficient sexual lines has hindered the crop improvement efforts in Cenchrus being confined to simple selection methods. Many attempts have been initiated in buffel grass to investigate the various molecular aspects such as genomic signatures of different species and genotypes, molecular basis of abiotic stress tolerance and reproductive performance. Even though it is an important fodder crop, molecular investigations in Cenchrus lack focus and the molecular information available on this grass is scanty. Cenchrus is a very good gene source for abiotic stress tolerance and apomixis studies. Biotechnological interventions in Cenchrus can help in crop improvement in Cenchrus as well as other crops through transgenic technology or marker assisted selection. To date no consolidated review on biotechnological interventions in Cenchrus grass has been published. Therefore we provide a thorough and in depth review on molecular research in Cenchrus focusing on molecular signatures of evolution, tolerance to abiotic stress and apomictic reproductive mechanism.

Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp.

BackgroundTranscription factors (TFs) and microRNAs (miRNAs) are primary gene regulators within the cell. Regulatory mechanisms of these two main regulators are of great interest to biologists and may provide insights into the abiotic and biotic stresses. However, the interaction between miRNAs and TFs in a gene regulatory network (GRN) still remains uncovered. Previous research has been mostly directed at inferring either miRNA or TF regulatory networks from data. However, networks involving a single type of regulator may not fully reveal the complex gene regulatory mechanisms, therefore study of interplay among these two regulators in gene regulation is important towards explaining the mechanism of different abiotic stresses. ResultOligonucleotide microarrays containing 51,279 transcripts were used to identify total 133 salt responsive target genes regulated by 11 TFs that are also differentially regulated by miRNA under salinity, heat and drought stresses in Oryza sativa. TF's-target interactions which are most enriched in their downstream regulation were also identified. Many genes whose encoded proteins are implicated in response to light and radiation stimulus, hormone stimuli, oxidative stress, copper ion binding and electron transport were found to be enriched. However the majority were novel for the combined abiotic stress, which indicates that there are a great number of genes induced after the exposure these abiotic stresses and regulated by miRNA. ConclusionAnalysis of the expression profile data of Oryza provides clues regarding some putative cellular and molecular processes that are undertaken in response to these stresses. The study also identified a large number of candidate functional genes that appear to be constitutively involved in salt, drought and heat stresses tolerance. Further examination of these genes may enable the molecular basis of abiotic stress tolerance in Oryza, to be elucidated.

Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement

Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed.

Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice

Drought, salt and cold are the major abiotic stresses that limit the rice production. Identification of the key functional and regulatory genes in the abiotic stress signaling pathways is important for understanding the molecular basis of abiotic stress tolerance. In this study, we investigated the transcriptomes of rice leaves and roots under cold, drought, and salt stresses using the massively parallel signature sequencing (MPSS) and sequencing by synthesis (SBS) technologies. About 1.8 to 2.6 million individual signatures were obtained from the seven abiotic-stressed and control libraries of the japonica cultivar Nipponbare. A total of 102,630 and 1,414,788 distinct signatures were obtained from the MPSS and SBS libraries, respectively. Clustering analysis identified many up- and down-regulated genes specifically and commonly expressed in the cold, drought and salt-treated plant leaves and roots. Data mining revealed the expression patterns of key functional and regulatory genes that were involved in different abiotic stress signaling pathways. Highly conserved cis-regulatory elements in the promoter of the up-regulated genes were identified. Our comprehensive and deep survey of abiotic stress transcriptome of rice has provided candidate genes for further understanding the molecular basis of abiotic stress tolerance in rice.

Positive role of a wheat HvABI5 ortholog in abiotic stress response of seedlings

ABA-responsive element binding protein (AREB) and ABA-responsive element binding factor (ABF), members of the basic region/leucine zipper (bZIP)-type protein family, act as major transcription factors in ABA-responsive gene expression under abiotic stress conditions in Arabidopsis. Barley HvABI5 and rice transcription factor responsible for ABA regulation 1 (TRAB1) are homologues of AREB/ABF and are expressed in drought- and ABA-treated seedlings. However, no direct evidence has shown an association of an AREB/ABF-type transcription factor with stress tolerance in cereals. To understand the molecular basis of abiotic stress tolerance through a cereal AREB/ABF-type transcription factor, a wheat HvABI5 ortholog, Wabi5, was isolated and characterized. Wabi5 expression was activated by low temperature, drought and exogenous ABA treatment, and its expression pattern differed between two wheat accessions with distinct levels of stress tolerance and ABA sensitivity. Wabi5-expressing transgenic tobacco plants showed a significant increase in tolerance to abiotic stresses such as freezing, osmotic and salt stresses and a hypersensitivity to exogenous ABA in the seedling stage compared with wild-type plants. Expression of a GUS reporter gene under the control of promoters of three wheat cold-responsive/late embryogenesis abundant (Cor/Lea) genes, Wdhn13, Wrab18 and Wrab19, was enhanced by ectopic Wabi5 expression in wheat callus and tobacco plants. These results clearly indicated that WABI5 functions as a transcriptional regulator of the Cor/Lea genes in multiple abiotic stress responses in common wheat.

Role of DREB transcription factors in abiotic and biotic stress tolerance in plants

Abiotic and biotic stresses negatively influence survival, biomass production and crop yield. Being multigenic as well as a quantitative trait, it is a challenge to understand the molecular basis of abiotic stress tolerance and to manipulate it as compared to biotic stresses. Lately, some transcription factor(s) that regulate the expression of several genes related to stress have been discovered. One such class of the transcription factors is DREB/CBF that binds to drought responsive cis-acting elements. DREBs belong to ERF family of transcription factors consisting of two subclasses, i.e. DREB1/CBF and DREB2 that are induced by cold and dehydration, respectively. The DREBs are apparently involved in biotic stress signaling pathway. It has been possible to engineer stress tolerance in transgenic plants by manipulating the expression of DREBs. This opens an excellent opportunity to develop stress tolerant crops in future. This review intends to focus on the structure, role of DREBs in plant stress signaling and the present status of their deployment in developing stress tolerant transgenic plants.