Molecular characterization of flower bud dormancy under constrained temperatures
Ontology highlight
ABSTRACT:
ORGANISM(S): Prunus avium
PROVIDER: GSE301282 | GEO | 2026/07/01
REPOSITORIES: GEO
Similar Datasets
Project description:Temperate perennial plants have to adapt their growth in order to survive over winter conditions and protect their tissues by entering into dormancy. The dormancy phenomenon is a complex process regulated by many factors, externals (photoperiod and temperature) or internals through the transport towards the buds. In order to better understand the molecular mechanisms involved in the regulation of dormancy, we conducted a transcriptomic analysis of flower buds from the late flowering sweet cherry cultivar 'Fertard' during dormancy, from October 2017 to March 2018.
2023-04-15 | GSE229429 | GEO
Project description:Bud dormancy is a crucial stage in perennial trees and allows survival over winter and optimal subsequent flowering and fruit production. Environmental conditions, and in particular temperature, have been shown to influence bud dormancy. Recent work highlighted some physiological and molecular events happening during bud dormancy in trees. However, we still lack a global understanding of transcriptional changes happening during bud dormancy. We conducted a fine tune temporal transcriptomic analysis of sweet cherry (Prunus avium L.) flower buds from bud organogenesis until the end of bud dormancy using next-generation sequencing. We observe that buds in organogenesis, paradormancy, endodormancy and ecodormancy are characterised by distinct transcriptional states, and associated with different pathways. We further identified that endodormancy can be separated in two phases based on its transcriptomic state: early and late endodormancy. We also found that transcriptional profiles of just 7 genes are enough to predict the main cherry tree flower buds dormancy stages. Our results indicate that transcriptional changes happening during dormancy are robust and conserved between different sweet cherry cultivars. Our work also sets the stage for the development of a fast and cost effective diagnostic tool to molecularly define the flower bud stage in cherry trees.
2019-12-16 | GSE130426 | GEO
Project description:Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.
2021-11-30 | GSE189658 | GEO
Project description:Buds were collected at equivalent branch positions and always at the same time of the day. Samples corresponding to May (MAY), June (JUN), July (JUL), September (SEP), November (NOV), January (JAN), March (MAR) and April (APR) buds were analyzed. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jose Diaz-Riquelme. The equivalent experiment is VV36 at PLEXdb.]
2012-11-17 | GSE42345 | GEO
Project description:Leafy spurge (Euphorbia esula) is an herbaceous perennial weed that produces vegetatively from an abundance of underground adventitious buds. The objectives of this study were to determine how mimicking natural seasonal conditions (photoperiod and temperature) under controlled environmental conditions affect dormancy and flowering competence; to determine molecular mechanisms associated with well-defined phases of seasonal dormancy transitions based on transcript profiles obtained by microarray analysis; and to link mechanisms regulating induction and release of endodormancy and flowering competence. Reduction in temperature (27 to 10°C) and photoperiod (16 to 8 h) over a three-month period induced a para- to endo-dormant transition in crown buds. An additional eleven weeks of prolonged cold (5-7°C) and short-photoperiod treatment resulted in accelerated shoot growth from crown buds, and 99% floral competence when plants were returned to growth promoting conditions. Exposure of paradormant plants to short-photoperiod and prolonged cold treatment alone had minimal affect growth potential or on flowering (~1%); whereas endodormant crown buds without prolonged cold treatment, had delayed shoot growth and approximately 2% flowering when returned to growth promoting conditions. Transcriptome analyses revealed that 373 and 260 genes were differentially expressed (p<0.005) during para- to endo-dormant and endo- to eco-dormant transitions, respectively. Transcripts from flower competent vs. non-flower competent crown buds identified 607 differentially expressed genes, and genes involved in cell cycle and DNA processing, oxidative stress, flower regulation, and proteolysis were over-represented. Further, sub-network analysis identified expression targets and binding partners associated with circadian clock, dehydration/cold signaling, phosphorylation cascades, and response to abscisic acid, ethylene, gibberellic acid, and jasmonic acid, suggesting these central regulators affect well-defined phases of dormancy. Potential genetic pathways associated with these dormancy transitions and flowering were used to develop a proposed conceptual model.
2009-12-01 | GSE19217 | GEO
Project description:Leafy spurge (Euphorbia esula) is an herbaceous perennial weed that produces vegetatively from an abundance of underground adventitious buds. The objectives of this study were to determine how mimicking natural seasonal conditions (photoperiod and temperature) under controlled environmental conditions affect dormancy and flowering competence; to determine molecular mechanisms associated with well-defined phases of seasonal dormancy transitions based on transcript profiles obtained by microarray analysis; and to link mechanisms regulating induction and release of endodormancy and flowering competence. Reduction in temperature (27 to 10°C) and photoperiod (16 to 8 h) over a three-month period induced a para- to endo-dormant transition in crown buds. An additional eleven weeks of prolonged cold (5-7°C) and short-photoperiod treatment resulted in accelerated shoot growth from crown buds, and 99% floral competence when plants were returned to growth promoting conditions. Exposure of paradormant plants to short-photoperiod and prolonged cold treatment alone had minimal affect growth potential or on flowering (~1%); whereas endodormant crown buds without prolonged cold treatment, had delayed shoot growth and approximately 2% flowering when returned to growth promoting conditions. Transcriptome analyses revealed that 373 and 260 genes were differentially expressed (p<0.005) during para- to endo-dormant and endo- to eco-dormant transitions, respectively. Transcripts from flower competent vs. non-flower competent crown buds identified 607 differentially expressed genes, and genes involved in cell cycle and DNA processing, oxidative stress, flower regulation, and proteolysis were over-represented. Further, sub-network analysis identified expression targets and binding partners associated with circadian clock, dehydration/cold signaling, phosphorylation cascades, and response to abscisic acid, ethylene, gibberellic acid, and jasmonic acid, suggesting these central regulators affect well-defined phases of dormancy. Potential genetic pathways associated with these dormancy transitions and flowering were used to develop a proposed conceptual model. Leafy spurge is an herbaceous perennial weed that undergoes vegetative reproduction from an abundance of underground adventitious buds which exhibit phases of para-, endo-, and eco-dormancy (defined by Lang et al. 1987) during summer, fall, and winter, respectively (Anderson et al. 2005). In this study a population of leafy spurge plants were propagated through random cuttings from the genetically uniform biotype 1984-ND001. Paradormant crown buds from three-month old greenhouse plants were collected after one week of acclimation under growth chamber conditions. Induction of endodormancy in crown buds was accomplished by subjecting greenhouse grown and growth chamber acclimated plants to a ramp down (RD) treatment consisting of a reduction in temperature of 1.42°C week-1 (27°C â 10°C) and a decreasing photoperiod of 40 min week-1 (16h â 8h light) for 12 weeks as previously established by Foley et al. (2009). These conditions mimic the average seasonal environmental conditions experienced in Fargo, ND (46°54â² N, 96°48â² W) during the transition from para- to endo-dormancy (Anderson et al. 2005). To induce a transition of crown buds from endo- to eco-dormancy, plants subjected to the RD treatment were given prolonged cold treatment for 11 weeks at 5-7°C, under constant 8 h:16 h day:night cycle; light fluencies were approximately 250 μmol m-2 s-1. To compare the effects of the prolonged cold with or without RD treatment on dormancy status and flowering competence in crown buds, greenhouse-grown and growth chamber acclimated plants were subjected directly to an extended cold treatment for 11 weeks at 5-7°C, as previously described, without a RD treatment. For microarray hybridizations, labeled cDNAs were prepared from 30 µg of total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA, USA) according to manufacturer's protocols. Labeled cDNAs were hybridized to a custom made 23K element microarray that contained 19,808 unigenes from a leafy spurge EST database (Anderson et al. 2007) and an additional 4,129 unigenes from a cassava EST database (Lokko et al. 2007). Comparison of gene expression between samples was accomplished using a rolling circle dye swap hybridization scheme (Churchill 2002) to provide every biological replicate with technical replicates. In our microarray analyses experiment, each of the four biological replicates included four technical replicates using two different dyes, resulting in a total of 16 technical replicates for each treatment. Microarray hybridization was visualized using a GenePix 4000B scanner and probe intensities and background were quantified using GenePix 6.0 software (Molecular Devices, Sunnyvale, California, USA). A quality control value of â1â was assigned to all probes that had intensity values greater than 2 times the standard deviation over average of the negative control and empty probe intensities (after deletion of 1% of the most intense negative/empty probe values). Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other.
2010-05-19 | E-GEOD-19217 | biostudies-arrayexpress
Project description:We explored seasonal gene expression profiles in the Yoshino cherry trees (Cerasus × yedoensis ‘Somei-yoshino’) at three distinct sites, each situated at varying latitudes in Japan. Our goal was to gather molecular phenology data that could provide insights into mechanism of bud dormancy. The molecular phenology approach, which monitors the seasonal dynamics of global gene expression profiles in leaves and buds under natural conditions, enables the study of physiological responses to seasonal environmental changes at the molecular level.
2024-09-19 | GSE246255 | GEO
Project description:In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Generally speaking, dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. In this work we focused our attention on flower bud development during winter in peach. In order to understand how bud development progress is regulated during winter we integrated cytological epigenetic and chromatin genome wide data with transcriptional outputs to obtained a complete picture of the main regulatory pathways involved in endodormancy.
2022-04-06 | GSE190586 | GEO