RNA-Seq Time Series of<i>Vitis vinifera</i>Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile

Pucker, Boas; Schwandner, Anna; Becker, Sarah; Hausmann, Ludger; Viehöver, Prisca; Töpfer, Reinhard; Weißhaar, Bernd; Holtgräwe, Daniela

doi:10.1101/2020.10.18.344176

Cited by 5 publications

(1 citation statement)

References 54 publications

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“…Pearson correlation was moderate, but this is expected considering the conditions of the free field environment. Exposure of the vines to external factors like biotic or abiotic stressors, including weather conditions that differ significantly between the years, also affect the transcriptome which reduces the level of correlation [38]. In a PCA, almost all data points lie on the same intended track, and biological replicates (subsamples) from both years are located close to each other.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time

Theine

Holtgräwe

Herzog

et al. 2021

Preprint

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BackgroundGrapevine cultivars of the Pinot family represent in the broader sense clonally propagated mutants with clear-cut phenotypes, such as different color or shifted ripening time, that result in major phenotypic and physiological differences as well as changes in important viticultural traits. Specifically, the cultivars ‘Pinot Noir’ (PN) and ‘Pinot Noir Precoce’ (PNP, early ripening) flower at the same time, but vary for the beginning of berry ripening (véraison) and consequently for the harvest time. Apart from the genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible ripening-regulatory genes affecting the timing of the start of ripening, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and in two years.ResultsThe difference in the duration of berry formation between PN and PNP was quantified to be about two weeks under the growth conditions applied, using plant material with a proven clonal relationship of PN and PNP. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the beginning of ripening at the level of gene expression profiles. Functional annotation of these DEGs fits to phenotypic and physiological changes during berry development. In total, we observed between PN and PNP 3,342 DEGs in 2014 and 2,745 DEGs in 2017. The intersection of both years comprises 1,923 DEGs. Among these, 388 DEGs were identified as véraison-specific and 12 were considered as candidates for a regulatory effect on berry ripening time. The expression profiles revealed two candidate genes for Ripening Time Control, designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively) that may contribute to controlling the phenotypic difference between PN and PNP.ConclusionsMany of the 1,923 DEGs identified show highly similar expression profiles in both cultivars as far as accelerated berry formation of PNP is concerned. Putative ripening-regulatory genes differentially expressed between PNP and PN as well as véraison-specific genes were identified. We point out potential connections of these genes to molecular events during berry development and discuss potential ripening time controlling candidate genes, two of which are already differentially expressed in the early berry development phase. Several down-regulated genes are annotated to encode auxin response factors / ARFs. Conceivably, changes in auxin signaling may realize the earlier ripening phenotype of PNP.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time

Theine

Holtgräwe

Herzog

et al. 2021

Preprint

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DNA-Based Technologies for Grapevine Biodiversity Exploitation: State of the Art and Future Perspectives

et al. 2022

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The cultivated grapevine, Vitis vinifera subsp. vinifera L., is represented by an enormous population of varieties and clones. They arise from the accumulation of gametic and somatic mutations during centuries of sexual and asexual propagation. These varieties represent a vast reservoir of traits/alleles that could be useful in improving the berry quality as well as against environmental stresses. However, most of them are still unexploited. For this reason, an efficient characterization system is essential to define the varietal identity, avoid cases of synonymy (identical genotypes but different names) and homonymy (same names but different genotypes) and deepen our understanding of the existing diversity within the grape germplasm. The plethora of DNA-based high-throughput technologies currently available provides promising tools for the analysis of diversity, overcoming many of the limitations of phenotypic-based diversity analyses. However, the analysis of intra-varietal diversity remains challenging. In this scenario, after summarizing the causes and consequences of grapevine genetic inter- and intra-varietal diversity, we review the DNA-based technologies used for varietal genotyping, emphasizing those able to distinguish clones within a variety. This review provides an update on the technologies used to explore grapevine diversity, the knowledge of which is necessary for an efficient exploitation and conservation of the grapevine germplasm.

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Transcriptome Analysis of ‘Kyoho’ Grapevine Leaves Identifies Heat Response Genes Involved in the Transcriptional Regulation of Photosynthesis and Abscisic Acid

Guo

Huang

et al. 2022

Agronomy

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Grapevine is a popular cultivated fruit throughout the world and heat stress is one of the most serious threats to viticulture. However, transcriptional responses, such as molecular properties of photosynthesis and abscisic acid biosynthesis, metabolism and signal transduction pathway of grapevine to heat stress, are still poorly understood. In this study, RNA-seq was carried out for thermostabilized grapevine ‘Kyoho’ leaves. Results showed that 685 and 469 genes were commonly down-regulated and up-regulated at three sampling time-points. The light-dependent reactions of photosynthesis was significantly enriched in up-regulated DEGs at 1 hpt and down-regulated DEGs at R24 hpt. Heat stress impaired the photosynthetic capacity of grapevine leaves, and there was a significant positive relationship between photosynthesis and stomatal conductance at short-term post-heat stress treatment, but the inhibition of HS on Pn was non-stomata limitation for a longer period. Photosystem (PS)Ⅱ was more sensitive to heat stress than PSⅠ, and PsbP, as well as Psb28, played important roles in response to heat stress. The abscisic acid (ABA) content in heat-stress-treated Kyoho plants was higher than that in the control at 1 hpt, but less in heat-stress-treated plants at 4 and R24 hpt, which was regulated by numerous genes involved in the ABA biosynthesis and catabolism pathways. These results help to understand the influence of heat stress on photosynthesis and ABA biosynthesis, metabolism and signal transduction pathway.

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RNA-Seq Time Series ofVitis viniferaBud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile

Cited by 5 publications

References 54 publications

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time

Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time

DNA-Based Technologies for Grapevine Biodiversity Exploitation: State of the Art and Future Perspectives

Transcriptome Analysis of ‘Kyoho’ Grapevine Leaves Identifies Heat Response Genes Involved in the Transcriptional Regulation of Photosynthesis and Abscisic Acid

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