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Transcriptome profiling of GTDs symptomatic vs. asymptomatic grapevine plants

ABSTRACT: Grapevine trunk diseases (GTDs) have become a major concern to viticulture worldwide, causing a high economic impact on yield and vineyard longevity in all growing areas. The prevalence of GTDs is increasing and, together with the absence of effective treatments, is currently one of the major challenges for viticulture sustainability. Given the urgent need to identify and develop new sustainable and effective protection strategies, a better understanding of grapevine defence mechanisms is crucial to develop more tolerant plants and provide new insights for disease management. This study explored the transcriptomic profile of GTDs symptomatic and asymptomatic plants of ‘Trincadeira’, a tolerant cultivar, and ‘Alicante Bouschet’, a susceptible cultivar to GTDs, using next-generation sequencing technology. RNA-seq yielded 1 598 differentially expressed genes (DEGs) between the two cultivars, and 64 DEGs between the groups with different symptomatology, regardless of the cultivar. Transport was revealed as the main biological process involved, generally activated in the susceptible cultivar ‘Alicante Bouschet’, suggesting that the DEGs associated with these processes may play an important role in disease development. Contrarily, the relative tolerance of ‘Trincadeira’ to this disease complex might be supported by the activation of secondary and hormonal metabolism and the differential expression of a set of defence-related genes, including resistance genes, which may act as key factors to limit GTDs infection. Furthermore, this study points to an important role of PER42 gene in the inhibition of GTDs symptoms. Our results provide new insights into the resistance mechanisms of grapevine to GTDs and may help to explain the different susceptibilities of grapevine plants to GTDs. To the best of our knowledge, this is the first time that the expression of grapevine defence-related gene expression has been studied in response to different GTDs-associated fungal infections under natural field conditions. We highlight the importance of these studies for the identification of candidate genes that may allow the development of new strategies to incorporate new sources of resistance. The activation or inhibition of potential plant response regulators can be used to promote resistance, thus providing sustainable and effective alternatives to successfully manage GTDs.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE283169 | GEO | 2025/05/31

REPOSITORIES: GEO

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Project description:Background: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through three consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy. Results: Most of the berry transcriptome clustered by year of growth rather than common environmental conditions or viticulture practices, and transcripts related to secondary metabolism showed high sensitivity towards different climates, as confirmed also by metabolomic data obtained from the same samples. When analyzed in 11 vineyards during one growth year, the environmentally-sensitive berry transcriptome comprised 5% of protein-coding genes and 18% of the transcripts modulated during berry development. Plastic genes were particularly enriched in ontology categories such as transcription factors, translation, transport and secondary metabolism. Specific plastic transcripts were associated with groups of vineyards sharing common viticulture practices or environmental conditions, and plastic transcriptome reprogramming was more intense in the year characterized by extreme weather conditions. We also identified a set of genes that lacked plasticity, showing either constitutive expression or similar modulation in all berries. Conclusions: Our data reveal candidate genes potentially responsible for the phenotypic plasticity of grapevine and provide the first step towards the characterization of grapevine transcriptome plasticity under different agricultural systems. Vitis vinifera cultivar Corvina clone 48 berries were harvested from different vineyards, each located in one of the three most important wine production macro-areas of the Verona region: Bardolino, Valpolicella and Soave, on the basis of the site geographical coordinates. For each of the selected vineyards, specific environmental conditions (altitude and type of soil) and farming and agricultural practices used (training system, rows facing direction, planting layout, vineyard age and rootstock type) were recorded. Vineyards were selected in order to maximize differences in locations and in microenvironmental and farming conditions. Berries were harvested at three different developmental stages: véraison, mid-ripening and harvest; each sample was collected in three biological replicates, to cover the whole vineyard variability. The same sampling procedure had been repeated over three consecutive vintages (2006, 2007 and 2008).

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Transcriptome profiling of GTDs symptomatic vs. asymptomatic grapevine plants

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