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Investigating the phenotypic plasticity of two red grapevine varieties: an integrated study of transcriptome and environmentome by WGCNA

ABSTRACT: Grapevine (Vitis spp., family Vitaceae) is characterized by a marked phenotypic plasticity and its ability to withstand various environmental conditions depends on the activation of highly coordinated responses, resulting from the interaction among genotypes (G) and environmental factors (E). Understanding genotype by environment (GxE) interplays is highly complex and challenging, and often the outcome of the genetic responses to field performance is not straightforward also due to the difficulties to reach a precise definition of the E component in field studies. In this work, the transcriptome of commercially ripe berries of Cabernet sauvignon and Aglianico genotypes grown in open-field at three different sites of central-southern Italy (Campania, Molise and Sicily) was analyzed by RNAseq. These transcriptomic data were integrated with a comprehensive set of climatic indices, forming an “environmentome”, through Weighted Gene Co-expression Network Analysis (WGCNA). A total of 11,887 differentially expressed genes (DEGs) have been retrieved, most of them found in the Aglianico genotype, suggesting that Aglianico transcriptome is largely influenced by the environment. Furthermore, the comparisons involving the Sicilian site exhibited the highest number of DEGs for both genotypes. WGCNA suggested that most of the climatic data (such as daily maximum air temperature, relative humidity, air pressure, dew point, hours of sun radiation) significantly correlated with “lightcyan1” module. Among these eingengenes, the low expression of ACA10 cation transporter is suggested to be indirectly related to the low anthocyanin content in Cabernet sauvignon in Campania, thus confirming WGCNA as powerful approach to identify gene of high biological interest. Similarly, transcriptome was also correlated with quality trait, such as total soluble solids and polyphenol content, leading to the discovery of hub genes that might function as markers of wine quality.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE261685 | GEO | 2024/04/14

REPOSITORIES: GEO

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Project description:Background: Grapevine is a major food crop that is affected by global climate change. Consistent with field studies, dehydration assays of grapevine leaves can reveal valuable information of the plant’s response at physiological, transcript, and protein levels. There are well-known differences in grapevine rootstocks responses to dehydration. We used time-series transcriptomic approaches combined with network analyses to elucidate and identify important physiological processes and network hubs that respond to dehydration in three different grapevine species differing in their drought tolerance. Results: Transcriptomic analyses of the leaves of Cabernet Sauvignon, Riparia Gloire, and Ramsey were evaluated at different times during a 24-h controlled dehydration. ANOVA revealed that 11,000 transcripts changed significantly with respect to the genotype x treatment interaction term and 6,000 transcripts changed significantly according to the genotype x treatment x time interaction term indicating massive differential changes in gene expression over time. Standard analyses determined substantial effects on the transcript abundance of genes involved in the metabolism and signaling of two known plant stress hormones, ABA and ethylene. ABA and ethylene signaling maps were constructed and revealed specific changes in transcript abundance that were associated with the known drought tolerance of the genotypes including genes such as VviABI5, VviABF2, VviACS2, and VviWRKY22. Weighted-gene coexpression network analysis (WGCNA) confirmed these results. In particular, WGCNA identified 30 different modules, some of which had highly enriched gene ontology categories for photosynthesis, phenylpropanoid metabolism, ABA and ethylene signaling. The ABA signaling transcription factors, VviABI5 and VviABF2, were highly connected hubs in two modules, one having overrepresentation in gaseous transport and the other in ethylene signaling. VviABI5 was distinctly correlated with an early response and high expression for the drought tolerant Ramsey and with little response from the drought sensitive Riparia Gloire. These ABA signaling transcription factors were highly connected to VviSNRK1 and other gene hubs associated with sugar, ethylene and ABA signaling. The ABA and ethylene signaling hubs were highly connected, supporting the hypothesis that there is substantial cross-talk between the two hormone pathways. This study identifies solid gene candidates for future investigations of drought tolerance in grapevine.

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Investigating the phenotypic plasticity of two red grapevine varieties: an integrated study of transcriptome and environmentome by WGCNA

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