Combining QTL mapping and gene expression analysis to elucidate the genetic control of ‘crumbly’ fruit in red raspberry
Ontology highlight
ABSTRACT:
INSTRUMENT(S): G2505B scanner (Agilent)
ORGANISM(S): Rubus idaeus
SUBMITTER: Pete Hedley
PROVIDER: E-MTAB-10049 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2012-07-02 | E-GEOD-38535 | biostudies-arrayexpress
Project description:In order to circumvent environmental changes throughout fruit development, young and ripening berries were sampled simultaneously on continuously flowering microvines acclimated to controlled circadian light and temperature changes. Gene expression profiles along fruit development were monitored during both day and night with whole genome microarray Nimbelgen® vitis 12x, yielding a total number of 9273 developmentally modulated probesets. All day-detected transcripts were modulated at night, whereas 1755 genes were night-specific. Very similar developmental patterns of gene expression were observed upon independent hierarchical clustering of day and night data, whereas functional categories of allocated transcripts varied according to time of the day. Many transcripts within pathways, known to be upregulated during ripening, in particular those linked to secondary metabolism exhibited a clearer developmental regulation at night than during the day. Functional enrichment analysis also indicated that diurnally modulated genes considerably varied during fruit development, with a shift from cellular organization and photosynthesis in green berries to secondary metabolism and stress-related genes in ripening ones. These results reveal critical changes in gene expression during night development that differ from day development which have not been observed in other transcriptomic studies on fruit development so far. A total of 24 samples were analyzed representing four berry developmental stages (two during green development, two during ripening). Sample were drawn simultaneously in triplicates at day and night on the microvine dwarf (DRCF) GAI mutant.
2013-12-20 | E-GEOD-52829 | biostudies-arrayexpress
Project description:Tomato pollen production and viability is highly vulnerable to higher temperature. Hot summers with temperature reaching above 32°C can disrupt production of viable pollens and fruit set, resulting in yield loss. In recent years, temperature above 35-38oC has become a norm during mid-summer with potential adverse impacts on the production of tomatoes and many other crop species. Pollens are developed through the microsporogenesis and micro-gametogenesis stages. The most heat sensitive period is from the meiotic process of the microsporocytes, at the young microspore stage (uninucleate stage of microspore) to during late pollen development (pollen mitosis). This project studied the heat-induced proteomes in microsporocyte, also called pollen mother cells (PMC). Homogenous PMC samples were collected from cross-sectioned frozen fresh anther tissues of tomato ‘Maxifort’ using laser capture microdissection (LCM). Tandem mass tag (TMT) proteomics analysis was conducted to identify proteomics changes related to heat tolerance during pollen development.
2022-04-07 | PXD018915 | Pride
Project description:Comparison of endogenous small RNA profiles from different developmental stages of tomato fruits Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
2011-06-02 | E-GEOD-18110 | biostudies-arrayexpress
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2011-07-26 | E-GEOD-29037 | biostudies-arrayexpress
Project description:The vacuole occupies a large portion of plant cell volume, it is especially true to fruit tissues. Berry flesh cell vacuole serves as storage organelle for water, sugars, acids, secondary metabolites and others, which largely determining berry quality (Fontes et al., 2011a, b; Shiratake and Martinoia, 2007, Conde et al., 2006). However, the molecular basis of these compartmentation processes is still poorly understood. As in many species, the major bottle neck to study these aspects in grapevine is to obtain highly purified vacuoles with a good yield (Fontes et al., 2010). Up to date, several vacuole or tonoplast proteome researches were applied on a few plants mainly on Arabidopsis thaliana, vacuoles or tonoplast were derived from mesophyll cells (Carter et al., 2004, Endler et al., 2006, Schulze, et al., 2012) or cell culture (Jaquinod et al 2006, Shimaoka et al 2004), cauliflower buds (Schmidt et al., 2007) and sugar beet taproots (Jung et al., 2015). Though the grape berry protoplasts and intact vacuoles were successfully isolated from Cabernet Sauvignon berry suspension-cultured cells (Fontes et al., 2010), the vacuoles isolated from grape berry or different development and ripening stages of grape berry mesocarp tissues were not achieved.
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Project description:Background: Global climate change, in particular the entailed predicted temperature increase, will noticeably affect plants vegetative and reproductive development. High temperatures alter the composition of the grapevine fruit, one of the most important fruits produced worldwide. This is leading to variable yield and quality, already observed in many growing regions in recent years. However, physiological processes underlying temperature response and tolerance of the grapevine fruit have hardly been investigated. Currently, all studies on fleshy fruits investigating their abiotic stress response on a molecular level were conducted during the day but possible night-specific variations were overlooked. The present study explores the grapevine fruit transcriptomic response at different developmental stages upon heat stress at day and night. Methodology/Principal Results: Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axis. The recently proposed microvine model was grown in climatic chambers in order to circumvent common constraints and biases introduced in field experiments with perennial vines. Post-véraison berry heterogeneity inside clusters was evaded upon constituting homogenous batches following organic acid and sugar measurements on individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbelGen® 090918 12X microarrays (30K). Results revealed important differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes within phenylpropanoid metabolism. Precise distinction of post-véraison stages led to a stage-specific detection of anthocyanin-related transcripts repressed by heat. Important modifications in cell wall-related processes as well as indications for a heat-induced delay of ripening and sugar accumulation were observed at véraison and reversed in later stages. Conclusion: This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity to include different developmental stages and especially different time points in transcriptomic studies. A total of 12 samples were analyzed representing three berry developmental stages (two after the onset of ripening, one during green growth). At each stage, heat stress was applied at day and night. Controls and treated berry samples were drawn in triplicates (two in duplicates) at day and at night on the microvine dwarf (Dwarf Rapid Cycling and Continous Flowering; DRCF) gibberellin-insensitive (GAI) mutant.
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