Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality

Although DNA methylation has largely been shown to be stable in plants, mounting evidence indicates methylation patterns may reflect environmental sensitivity. Perennial plants experience seasonal and inter-annual environmental variation, and clonal replicates of some long-lived plants, including many perennial crops, survive in a broad range of environments. This makes perennial crops a compelling study system to investigate links between the plant epigenome and environmental variation. In this study, we used whole genome bisulfite sequencing and small RNA sequencing to characterize the epigenome in 12 clonal replicates of the winegrape cultivar ‘Chambourcin.’ We asked whether DNA methylation varied in response to a full factorial combination of irrigation and grafting treatments. We found signatures of both irrigation and grafting in the ‘Chambourcin’ epigenome, as well as compelling evidence for a unique interaction effect whereby grafting appeared to override or mitigate epigenomic changes associated with irrigation in ungrafted vines. These findings indicate that the epigenome responds to environmental and agronomic manipulations, suggesting the epigenome might be a mechanism underlying how long-lived, clonal plants respond at the molecular level to their environment. Further research is needed to assess the potential relevance of variation in DNA methylation to plant form and function, and to address the implications of environmentally-inducible patterns of DNA methylation on the adaptive capacity of long-lived woody perennials in nature and under cultivation.

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“…1H). The few DE sRNA detected in this study are consistent with published results from other work in grapevine (Zombardo et al, 2020).…”

Section: Characterization Of Small Rnas (Srna)supporting

confidence: 93%

Epigenomic patterns reflect irrigation and grafting in the grapevine clone ‘Chambourcin’

Williams

Edwards

Kwasniewski

et al. 2020

Preprint

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“…In contrast, other studies have found signatures of rootstock genotype in the transcriptome in early berry development, although this distinction was lost in later development (Berdeja et al, 2015;Corso et al, 2016), but see (Zombardo et al, 2020). Collectively, these studies suggest the effects of grafting are diverse and may vary over the course of vine development.…”

Section: Introductionmentioning

confidence: 66%

“…For example, a study of ‘Cabernet Sauvignon’ grafted to different rootstocks identified transcriptome reprogramming in the scion of grafted plants; this appeared to be a general effect of grafting to a rootstock and was not rootstock-specific (Cookson & Ollat, 2013). In contrast, other studies have found signatures of rootstock genotype in the transcriptome in early berry development, although this distinction was lost in later development (Berdeja et al ., 2015; Corso et al ., 2016), but see (Zombardo et al ., 2020). Collectively, these studies suggest the effects of grafting are diverse and may vary over the course of vine development.…”

Section: Introductionmentioning

confidence: 99%

Root system influence on high dimensional leaf phenotypes over the grapevine growing season

Harris

Klein

Awale

et al. 2020

Preprint

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SummaryIn many perennial crops, grafting the root system of one individual to the shoot system of another individual has become an integral part of propagation performed at industrial scales to enhance pest, disease, and stress tolerance and to regulate yield and vigor. Grafted plants offer important experimental systems for understanding the extent and seasonality of root system effects on shoot system biology.Using an experimental vineyard where a common scion ‘Chambourcin’ is growing ungrafted and grafted to three different rootstocks, we explore associations between root system genotype and leaf phenotypes in grafted grapevines across a growing season. We quantified five high-dimensional leaf phenotyping modalities: ionomics, metabolomics, transcriptomics, morphometrics, and physiology and show that rootstock influence is subtle but ubiquitous across modalities.We find strong signatures of rootstock influence on the leaf ionome, with unique signatures detected at each phenological stage. Moreover, all phenotypes and patterns of phenotypic covariation were highly dynamic across the season.These findings expand upon previously identified patterns to suggest that the influence of root system on shoot system phenotypes is complex and broad understanding necessitates volumes of high-dimensional, multi-scale data previously unmet.

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“…While 80% of the same miRNAs were similarly differentially expressed either early or late in the growing season, 20% of all miRNAs changed their mode of up-regulation or down-regulation through the year (Figure 2). Among these, there are the most prominent isomiRs with sequences that varied with respect to the reference sequences of vvi-miR166 and vvi-miR3623 that regulate genes that encode proteins involved in disease resistance [45]. All of the differentially expressed miRNAs in grapevines infected with 'Ca.…”

Section: Resultsmentioning

confidence: 99%

Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes

Dermastia

Škrlj

Strah

et al. 2021

IJMS

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Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.

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Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality

Cited by 32 publications

References 96 publications

Epigenomic patterns reflect irrigation and grafting in the grapevine clone ‘Chambourcin’

Epigenomic patterns reflect irrigation and grafting in the grapevine clone ‘Chambourcin’

Root system influence on high dimensional leaf phenotypes over the grapevine growing season

Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes

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