Role of phytohormones in regulating cold stress tolerance: Physiological and molecular approaches for developing cold-smart crop plants

Plant Stress, Journal Year: 2023, Volume and Issue: 8, P. 100152 - 100152

Published: March 23, 2023

Global climate variations induce extreme temperatures and significantly decrease crop production, leading to food insecurity worldwide. Temperature extremes (mainly cold stress (CS): chilling 0–15 °C freezing <0 temperatures) limit plant growth development severely affect physiology biochemical molecular processes. Subsequently, plants execute numerous endogenous mechanisms, including phytohormone biosynthesis (i.e., abscisic acid, cytokinins, jasmonic salicylic gibberellic brassinosteroids, indole-3-acetic ethylene, strigolactones) tolerate stressful environments. Phytohormones are vital for managing diverse events associated with under CS as important signaling substances that dynamically arbitrate many physiological, biochemical, responses through a stress-responsive regulatory cascade. This review briefly appraises adaptation mechanisms then comprehensively reports on the crucial role of several phytohormones in adjusting response acclimation. We also discuss phytohormone-regulated genes controlling tolerance their genetic engineering combat species develop future CS-smart plants. The potential state-of-the-art omics approaches help identify phytohormone-induced novel genes, metabolites, metabolic pathways is discussed. In short, we conclude exogenous application phytohormones-regulated promising techniques developing cold-smart

Language: Английский

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Fillable and unfillable gaps in plant transcriptome under field and controlled environments

Plant Cell & Environment, Journal Year: 2022, Volume and Issue: 45(8), P. 2410 - 2427

Published: May 25, 2022

The differences between plants grown in field and controlled environments have long been recognized. However, few studies addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces irradiance, temperature humidity of environments. We analysed massive transcriptome data rice under SmartGC conditions clarify Rice dynamics mimicked those field, particularly during morning evening but conventional did not. Further analysis revealed fluctuation irradiance affects evening, while only morning. found upregulation genes related biotic abiotic stress, their expression was affected by environmental factors cannot be SmartGC. Our results reveal fillable unfillable gaps transcriptomes can accelerate understanding for both basic biology agricultural applications.

Language: Английский

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Beyond heat waves: Unlocking epigenetic heat stress memory in Arabidopsis

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 194(4), P. 1934 - 1951

Published: Oct. 25, 2023

Abstract Plants remember their exposure to environmental changes and respond more effectively the next time they encounter a similar change by flexibly altering gene expression. Epigenetic mechanisms play crucial role in establishing such memory of fine-tuning With recent advancements biochemistry sequencing technologies, it has become possible characterize dynamics epigenetic on scales ranging from short term (minutes) long (generations). Here, our main focus is describing current understanding temporal regulation histone modifications chromatin during short-term recurring high temperatures reevaluating them context natural environments. Investigations structural Arabidopsis after repeated heat at intervals have revealed detailed molecular stress memory, which include modification enzymes, remodelers, key transcription factors. In addition, we summarize spatial responses. Based temperature patterns summer, discuss how plants cope with occurring various utilizing 2 distinct types mechanisms. We also explore future research directions provide precise memory.

Language: Английский

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Simulation study of factors affecting the accuracy of transcriptome models under complex environments

Plant Molecular Biology, Journal Year: 2025, Volume and Issue: 115(2)

Published: March 28, 2025

Language: Английский

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Field plus lab experiments help identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees: A case study of Camellia oleifera

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 22, 2023

The molecular mechanisms of freezing tolerance are unresolved in the perennial trees that can survive under much lower temperatures than annual herbs. Since natural conditions involve many factors and temperature usually cannot be controlled, field experiments alone directly identify effects stress. Lab insufficient for to complete cold acclimation reflect freezing-stress responses. In this study, a new method was proposed using plus lab associated genes subtropical evergreen broadleaf Camellia oleifera as case. Cultivated C. is dominant woody oil crop China. Wild at high-elevation site Lu Mountain could below -30°C, providing valuable genetic resource breeding tolerance. experiment, air monitored from autumn winter on wild Mountain. Leave samples were taken before acclimation, during temperature. Leaf transcriptome analyses indicated gene functions expression patterns very different experiments, leaves after placed -10°C climate chambers. A cultivated variety "Ganwu 1" used control. According relative conductivity changes leaves, showed more freezing-tolerant oleifera. between experiment. Combing results both common with responses identified. Key flg22, Ca2+ gibberellin signal transduction pathways lignin biosynthesis pathway may involved Most had highest levels experiment higher stronger Our study help underlying trees.

Language: Английский

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Circadian and environmental signal integration in a natural population of Arabidopsis

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(35)

Published: Aug. 22, 2024

Plants sense and respond to environmental cues during 24 h fluctuations in their environment. This requires the integration of internal such as circadian timing with light temperature elicit cellular responses through signal transduction. However, transduction signals by plants growing natural environments remains poorly understood. To gain insights into dynamics signaling nature, we performed a field study from nucleus chloroplasts population Arabidopsis halleri. Using several modeling approaches interpret data, identified that clock are key regulators this pathway under conditions. We potential time-delay steps between components, diel response reminiscent process gating. found our framework can be extended other pathways undergo oscillations cues. approach combining studies gene expression allowed us identify dynamic cues, plant cells, naturally fluctuating cycles.

Language: Английский

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A low-coverage 3′ RNA-seq to detect homeolog expression in polyploid wheat

NAR Genomics and Bioinformatics, Journal Year: 2023, Volume and Issue: 5(3)

Published: July 5, 2023

Abstract Although allopolyploid species are common among natural and crop species, it is not easy to distinguish duplicated genes, known as homeologs, during their genomic analysis. Yet, cost-efficient RNA sequencing (RNA-seq) be developed for large-scale transcriptomic studies such time-series analysis genome-wide association in allopolyploids. In this study, we employed a 3′ RNA-seq utilizing untranslated regions (UTRs) containing frequent mutations homeologous compared coding sequence. Among the protocols, examined low-cost method Lasy-Seq using an allohexaploid bread wheat, Triticum aestivum. HISAT2 showed best performance with least mapping errors quick computational time. The number of detected homeologs was further improved by extending 1 kb UTR annotation. Differentially expressed genes response mild cold treatment were verified high-coverage conventional RNA-seq, although latter more differentially genes. Finally, downsampling that even 2 million depth can still detect than half identifiable 32 reads. These data demonstrate facilitates wheat indicate potential application other species.

Language: Английский

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Cross-species transcriptomics reveals differential regulation of essential photosynthesis genes in Hirschfeldia incana

G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: 14(10)

Published: Aug. 8, 2024

Abstract Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established H. incana as model for high photosynthetic light-use efficiency (LUE). Now aim to unravel genetic basis of this in incana, potentially contributing improvement LUE other species. Here, compare its transcriptomic response light with that Arabidopsis thaliana, Brassica rapa, and nigra, 3 fellow Brassicaceae members lower LUE. We built a high-light, high-uniformity growing environment, which plants developed normally without signs stress. compared gene expression contrasting conditions across species, utilizing panproteome identify orthologous proteins. In-depth analysis key pathways showed general trend under high-light all 4 However, several photosynthesis-related genes break trend. observed cases constitutive higher (like antenna protein LHCB8), treatment-dependent differential (as PSBE), cumulative through simultaneous multiple copies LHCA6). Thus, shows regulation essential photosynthesis genes, light-harvesting complex first point deviation. The effect these differences on abundance turnover, ultimately phenotype relevant further investigation. Furthermore, resource fully grown under, rather than briefly exposed to, very irradiance, will support development highly efficient crops.

Language: Английский

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Comparative transcriptomics of Hirschfeldia incana and relatives highlights differences in photosynthetic pathways

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 20, 2023

Abstract Photosynthesis is the only yield-related trait that has not yet been substantially improved by plant breeding. The limited results of previous attempts to increase yield via improvement photosynthetic pathways suggest more knowledge still needed achieve this goal. To learn about genetic and physiological basis high light-use efficiency (LUE) at irradiance, we study Hirschfeldia incana . Here, compare transcriptomic response light H. with three other members Brassicaceae, Arabidopsis thaliana, Brassica rapa , nigra which have a lower LUE. First, built high-light, high-uniformity growing environment in climate-controlled room. Plants grown system developed normally showed no signs stress during whole growth period. Then compared gene expression low high-light conditions across four species, utilizing panproteome group homologous proteins efficiently. As expected, all species actively regulate genes related process. An in-depth analysis on involved key revealed general trend conditions. However, distinguishes itself from through higher certain these pathways, either constitutive expression, as for LHCB8 ordinary differential PSBE or cumulative obtained simultaneous multiple copies, seen LHCA6 These differentially expressed path-ways are interesting leads further investigate exact relationship between protein abundance turnover, ultimately LUE phenotype. In addition, can also exclude thousands “explaining” phenotype, because they do show both Finally, deliver resource fully under, rather than briefly exposed to, very supporting efforts develop highly efficient photosynthesis crop plants.

Language: Английский

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Time of Day Analysis over a Field Grown Developmental Time Course in Rice

Plants, Journal Year: 2022, Volume and Issue: 12(1), P. 166 - 166

Published: Dec. 30, 2022

Plants integrate time of day (TOD) information over an entire season to ensure optimal growth, flowering time, and grain fill. However, most TOD expression studies have focused on a limited number combinations daylength temperature under laboratory conditions. Here, Oryza sativa (rice) study that followed in the field growing was re-analyzed. Similar Arabidopsis thaliana, almost all rice genes TOD-specific developmental course. As has been suggested other grasses, thermocycles were stronger cue for than photocycles season. All core circadian clock display consistent with interesting exception two grass paralogs EARLY FLOWERING 3 (ELF3) distinct phasing based interaction between thermo- photo-cycles. The dataset also revealed how specific pathways are modulated changing biology. data presented here provide resource researchers changes natural conditions course, which will guide approaches engineer more resilient prolific crops.

Language: Английский

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