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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
Grant R. Cramer
University of Nevada, Reno
Corresponding Author
ORCiD: https://orcid.org/0000-0002-2374-4091
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Plant Biology.
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition.
Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis.
Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.
Keywords
abiotic stress, biotic stress, grape berry development, RNA-Seq, transcriptomics, Vitis vinifera L.
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CURRENT STATUS: Published
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Editorial decision: Major revision
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Reviewer #1 agreed
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Editorial decision: Major revision
On 08 Jul, 2019
Review #2 received
Received 06 Jul, 2019
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Received 05 Jul, 2019
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Reviewer #8 agreed
On 27 Jun, 2019
Reviewer #9 agreed
On 27 Jun, 2019
Reviewer #7 agreed
On 24 Jun, 2019
Reviewer #5 agreed
On 24 Jun, 2019
Reviewer #6 agreed
On 24 Jun, 2019
Editor assigned
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Reviewers invited
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Reviewer #1 agreed
On 23 Jun, 2019
Reviewer #2 agreed
On 23 Jun, 2019
Reviewer #3 agreed
On 23 Jun, 2019
Reviewer #4 agreed
On 23 Jun, 2019
Submission checks complete
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This preprint is under consideration at BMC Plant Biology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
Grant R. Cramer
University of Nevada, Reno
Corresponding Author
ORCiD: https://orcid.org/0000-0002-2374-4091
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 5
Posted 15 Jan, 2020
Published
On 28 Jan, 2020
No community comments so far
Submission checks complete
On 14 Jan, 2020
Editorial decision: Accept
On 14 Jan, 2020
No comments provided
Submission checks complete
On 08 Jan, 2020
Editorial decision: Minor revision
On 08 Jan, 2020
No comments provided
Editorial decision: Minor revision
On 03 Jan, 2020
Editor assigned
On 25 Dec, 2019
Submission checks complete
On 24 Dec, 2019
Editor invited
On 24 Dec, 2019
No comments provided
Editorial decision: Major revision
On 21 Nov, 2019
Review #2 received
Received 15 Nov, 2019
Review #1 received
Received 10 Nov, 2019
Reviewer #2 agreed
On 01 Nov, 2019
Reviewer #1 agreed
On 25 Oct, 2019
Reviewers invited
Invitations sent on 21 Oct, 2019
Editor assigned
On 07 Oct, 2019
Submission checks complete
On 06 Oct, 2019
Editor invited
On 06 Oct, 2019
No comments provided
Editorial decision: Major revision
On 08 Jul, 2019
Review #2 received
Received 06 Jul, 2019
Review #3 received
Received 05 Jul, 2019
Review #5 received
Received 05 Jul, 2019
Review #1 received
Received 02 Jul, 2019
Reviewer #8 agreed
On 27 Jun, 2019
Reviewer #9 agreed
On 27 Jun, 2019
Reviewer #7 agreed
On 24 Jun, 2019
Reviewer #5 agreed
On 24 Jun, 2019
Reviewer #6 agreed
On 24 Jun, 2019
Editor assigned
On 23 Jun, 2019
Reviewers invited
Invitations sent on 23 Jun, 2019
Reviewer #1 agreed
On 23 Jun, 2019
Reviewer #2 agreed
On 23 Jun, 2019
Reviewer #3 agreed
On 23 Jun, 2019
Reviewer #4 agreed
On 23 Jun, 2019
Submission checks complete
On 11 Jun, 2019
Editor invited
On 11 Jun, 2019
First submitted
On 20 May, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Plant Biology.
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition.
Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis.
Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.
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