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Comparative transcriptomic analyses of Spring OilSeed Rape (SOSR)accessions in response to warm temperature.

ABSTRACT: Elevated growth temperatures are negatively affecting crop productivity and increasing yield losses. Root traits associated with improved adaptation to rising temperatures are a promising approach to generate new varieties better suited to face the environmental constrains caused by climate change. In this study, we identified various Brassica napus roots traits altered in response to warm temperature. Thus, different combination of changes in specific root traits results in an extended and deeper root system. This overall root growth expansion facilitates root adaptation by maximizing root-soil surface interaction and increasing its ability to explore extended soil areas. We associated these traits to coordinated cellular events, including changes in cell division and elongation rates, that drive the increase in root growth triggered by warm temperature. Comparative genome wide transcriptomic analysis revealed the main genetic determinants of these RSA changes and uncovered the necessity of a tight regulation of the heat shock stress response to adjust root growth to warm temperature. Our work provides a phenotypic, cellular and genetic framework of root response to warming temperatures that will help to harness root adaptation mechanisms for crop yield improvement under the future climatic scenario.

ORGANISM(S): Brassica napus

PROVIDER: GSE173272 | GEO | 2023/01/25

REPOSITORIES: GEO

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Increased protein solubility contributes to heat priming of the plant pathogenic fungus Botrytis cinerea

Project description:Botrytis cinerea causes grey mold disease in leading crop plants. The disease develops only at cool temperatures, but the fungus remains viable in warm climates and can survive periods of extreme heat. We discovered a strong heat priming effect in which the exposure of B. cinerea to moderately high temperatures greatly improves its ability to cope with subsequent, potentially lethal temperature conditions. We showed that priming promotes protein solubility during heat stress and discovered a group of priming-induced serine-type peptidases. Several lines of evidence, including transcriptomics, proteomics, pharmacology and mutagenesis data, link these peptidases to the B. cinerea priming response, highlighting their important roles in regulating priming-mediated heat adaptation. By imposing a series of sub-lethal temperature pulses that subverted the priming effect, we managed to eliminate the fungus and prevent disease development, demonstrating the potential for developing temperature-based plant protection methods by targeting the fungal heat priming response.

2023-06-18 | GSE216541 | GEO

Increased protein solubility contributes to heat priming of the plant pathogenic fungus Botrytis cinerea

2023-06-18 | PXD037173 | Pride

Effect of high temperature on Arabidopsis thaliana root tips

Project description:Plant roots located in the upper soil layers are prone to experience high temperatures. To gain insight into the effect of high temperature on root development and functioning, we exposed five-day-old Arabidopsis thaliana seedlings grown on agar plates to 30 °C for 48 hours, and compared the gene expression profile in the root tip with that from seedlings that remained at 22 °C.

2024-02-07 | GSE254973 | GEO

Transcriptome analysis of N2 and flp-6 Caenorhabditis elegans at 25 °C

Project description:Temperature is a prominent environmental stimulus that influences life span. Previous studies indicate that in Caenorhabditis elegans, thermosensory perception in the AFD neuron maintains life span at warm temperatures. How thermosensation is translated into neuronal signals that shape aging remains elusive. We found that the Caenorhabditis elegans CREB crh-1, as well as several key genes in AFD thermosensory transduction, were specifically required for normal life span at warm temperatures. crh-1 acted in the AFD to increase transcription of the CRE-containing neuropeptide gene flp-6 in a temperature-dependent manner. Both crh-1 and flp-6 were necessary and sufficient for longevity at warm temperatures, and their effects depended on the AIY interneuron. Moreover, flp-6 signaling downregulated ins-7/insulin and several insulin pathway genes, whose activity compromised life span. We postulate that temperature experience is integrated in the thermosensory neurons to generate CREB-dependent neuropeptide signals that antagonize insulin signaling and promote temperature-specific longevity.

2018-05-01 | GSE68464 | GEO

MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis (miRNA-Seq)

Project description:MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remains ambiguous. Here we show that HYPONASTIC LEAVES1 (HYL1) – a key component of microRNA biogenesis – acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 (dcl1) allele, dcl1-24, which rescues hyl1-2’s defects in miRNA biosynthesis and warm temperature-induced hypocotyl elongation. Genome-wide miRNA and transcriptome analysis reveal microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-LIKE 9 (SPL9) as critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, the miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miRNA156/SPL9 module as a previously-uncharacterized genetic circuitry that enables plant growth plasticity in response to environmental temperature and light changes.

2023-02-11 | GSE216361 | GEO

MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis (RNA-Seq)

Project description:MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remains ambiguous. Here we show that HYPONASTIC LEAVES1 (HYL1) – a key component of microRNA biogenesis – acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 (dcl1) allele, dcl1-24, that rescues hyl1-2’s defects in miRNA biosynthesis and warm temperature-induced hypocotyl elongation. Genome-wide miRNA and transcriptome analysis reveal microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-LIKE 9 (SPL9) as critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, the miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miRNA156/SPL9 module as a previously-uncharacterized genetic circuitry that enables plant growth plasticity in response to environmental temperature and light changes.

2023-02-11 | GSE216360 | GEO

PIF7 is the master regulator of thermomorphogenesis in shade [RNA-seq]

Project description:The size and shape of plant organs are highly responsive to the local environmental conditions. The embryonic stem, or hypocotyl, of the plant is one such organ that displays impressive phenotypic plasticity, and its length is affected by both light and temperature. After sensing surrounding vegetation, hypocotyls of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. A similar elongation response occurs when the plants are grown in high ambient temperatures. Previous studies have shown that this response is mediated by a family of transcription factors called PHYTOCHROME-INTERACTING FACTORS (PIFs). However, it is poorly understood how environmental light and temperature interact to affect plants at the morphological and molecular levels. Here, we examine the genetic and molecular basis of the response to low R/FR under warm ambient temperatures. We found that low R/FR combined with warm temperature dominantly regulate by PIF7 and exhibit a synergistic effect on hypocotyl growth, greater than either stimulus alone. While the synergistic response was dependent on PIF7 and the plant hormone auxin, we demonstrate that additional, yet unknown key factor/s must be involved, likely working downstream of the phyB-PIF-auxin module. As shade responses are known to affect crop yield and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs. In addition, we point out key factors in this response that can potentially be modulated to minimize the negative effect on yield.

2022-07-26 | GSE196725 | GEO

The preceding root system drives the rhizosphere microbiome

Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.

2020-03-06 | GSE146427 | GEO

Chloroplast signalling gates thermotolerance in Arabidopsis

Project description:Temperature has a major role in plant growth and survival, for example wheat yields decrease by about 6% for every 1°C rise in global temperature [1]. High temperatures induce the expression of protective chaperones and modulate growth responses. Key players in the heat protection response are transcription factors of the HEAT SHOCK FACTOR A1 (HSFA1) family [2]. However the pathways that activate the HSFA1 class TFs, and how these perceive temperature and integrate it with other environmental signals are not clear. Plants are exposed to considerable diurnal temperature variation, and have evolved pathways to anticipate likely future conditions. For example, the cold response pathway is gated by the circadian clock, enabling the degree of responsiveness to cold to be controlled in the context of the environment [3, 4] and genes promoting elongation growth and flowering in response to warm temperature are induced during the night via thermosensory phytochromes [5 ,6]. It is not known in Arabidopsis if the warm temperature protective pathways are gated. In this study we find that there is strong diurnal variation in the heat stress response of Arabidopsis, and we show that this correlates with the expression of HSP70 in the day night cycle. The dark to light transition is in fact sufficient to robustly induce expression of warm temperature protective genes such as HSP70. A forward genetic screen with a HSP70-Luciferase reporter line revealed genes necessary for controlling this process and identified a central role for chloroplast signalling in the warm temperature response that accounts for diurnal variation in thermotolerance.

2018-02-13 | GSE96041 | GEO

Transcriptomic response of 6 Propionibacterium freudenreichii strains during cold storage

Project description:Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It produces flavor compounds over the whole ripening period. During cheese ripening, P. freudenreichii is exposed to a temperature downshift, especially when cheeses are transferred from warm temperature (about 24°C) to cold temperature (about 4°C). The cold adaptation of the type strain was studied previously. The aim of this study was to investigate the adaptation of 6 other P. freudenreichii strains at cold temperature by means of a global gene expression profile. The temporal transcriptomic response of 6 P. freudenreichii strains was analyzed at 2 times of growth, during growth at 30°C then after 3 days 4°C, in the constant presence of lactate as the main carbon source.

2012-07-06 | GSE34227 | GEO

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