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"Many research works have unveiled how grapevine cultivars respond to environmental conditions; however, the molecular mechanisms underlying the interplay between clones (vegetatively propagated lines of selected mother plants) and environment need to be elucidated. This study was aimed to explore the complexity of the clone x environment interaction by investigating changes controlled by clone, vineyard or developmental stage. The transcriptome of berries collected over ripening in different vineyards from three 'Nebbiolo' clones was analyzed by integrating RNA-seq data with analysis of candidate genes, quantification of secondary metabolites and agronomical parameters. Transcripts associated to sugar transport and anthocyanin biosynthesis were differently modulated among clones, while genes involved in secondary metabolism and defence, such as stilbene synthase genes, were affected by vineyard, consistently with stilbenoid accumulation. This attests that clone-specific responses exert a role in shaping agronomic performances of a grape variety in different environments, thus providing indications for orienting viticultural practices in light of both cultivation area and clone choice."

"During the last years, several research works were addressed to uncover how different grapevine cultivars respond to environmental conditions, nevertheless the molecular mechanisms tuning this phenomenon needs to be further deepened. In particular, little is known on the molecular processes underlying the interplay between clones of the same cultivar and vineyard. In order to investigate this point, we analyzed the transcriptome of berries collected over the ripening period from three 'Nebbiolo' clones (CVT 71, CVT 423, CVT 185, whose respective genome sequences have recently been released) grown in three different vineyards of the Langhe area (Piedmont, North-West Italy), in two years. Transcriptomic data obtained through RNA-sequencing analysis were integrated by: i) real-time RT-qPCR of candidate genes; ii) HPLC quantification of abscisic acid, flavonoid and stilbenoid contents; iii) agronomical parameters; and iv) climate conditions. This multidisciplinary approach was instrumental for exploring the whole complexity of the genotype-environment interaction and identifying the molecular changes controlled by clone, vineyard, phenological phase or a combination of them. The results showed that transcript categories associated to sugar mediated-signalling, anthocyanin biosynthesis and transport can be differently modulated among diverse clones of the same cultivar, thus influencing related yields in terms of berry quality and agronomical features. Conversely, genes involved in the production of secondary metabolites, typically playing a role in stress response such as stilbenoids, were significantly affected by the vineyard location, consistently with the accumulation patterns of different stilbenoids.We thus demonstrated that clone-specific molecular responses exert a key role in determining the agronomic performances of a grapevine variety in different environments. These results provide valuable indications also for directing viticulture practices aimed at enhancing the typicality of grapevine productions in light of both the cultivation area and clone choice."

The role of plant tyrosyl-DNA phosphodiesterase 1? in genome stability is studied using a Medicago truncatula MtTdp1?-depleted line. Lack of MtTdp1? results in a 39% reduction of methylated cytosines as compared to control. RNA-Seq analyses revealed that 11 DNA transposons and 22 retrotransposons were differentially expressed in the Tdp1?-2a line. And among them all DNA transposons (MuDR, hAT, DNA3-11_Mad) and seven retrotransposons (LTR/Gipsy, LTR/Copia, LTR and NonLTR/L1) were down-regulated, while remaining 15 retrotransposons were up-regulated. Results suggest that the occurrence of stress-responsive cis-elements as well as changes in the methylation pattern at the LTR promoters might be responsible for the enhanced retrotransposon transcription.

Grapevine (Vitis vinifera L.) is one of the major fruit crop worldwide with thousands of cultivated varieties. Among the important Italian cultivars, 'Nebbiolo' is characterized by a wide genetic variability expressed by a high number of clones (i.e. vegetatively propagated lines of selected mother plants) registered in the National Catalogue. However, little morphological differences exist between clones and often it is very difficult to visually distinguish the different clones, and the Simple Sequence Repeats (SSRs) extensively used as markers, showed low or no success in discriminating clones. The aim of this on-going study is to identify a set of single nucleotide polymorphisms (SNPs) able to discriminate the registered 'Nebbiolo' clones, setting up an effective and rapid SNP genotyping protocol based on the TaqMan® probes technology. Three 'Nebbiolo' clones were sequenced by Illumina technology (CVT 71, CVT 185 and CVT 423) and processed reads were mapped against the PN40024 reference genome. SNPs were first detected using the GATK-UnifiedGenotyper tool with default parameters followed by filtering and by a calibration step. SNPs were validated as true positive by Sanger sequencing, and nine of the 11 SNPs confirmed to date were successfully used to perform TaqMan® genotyping assays in genomic DNA from 37 'Nebbiolo' clones. Combining results obtained from each single SNP assay, we classified the 'Nebbiolo' clones in six main groups linked to the geographical origin of accessions. Furthermore, these SNPs were tested in other grapevine cultivars, and interestingly in some case, these markers are polymorphic also in clones of 'Brachetto' and 'Nebbiolo rosè'. This work is in progress and the methodology will be applied in the vine supply chain to ensure a traceability from grape nurseries up to wine industry, providing a product of sure origin to the consumers. This research was funded by Fondazione Cassa di Risparmio di Cuneo: "Nebbiolo Genomics"; Fondazione Cassa di Risparmio di Torino: "Track W/Vine"; and Regione Piemonte: "MicroGenVine".

The success of the grape and wine-related agribusiness depends on yield and quality of the grapes produced, which is heavily influenced by genetic diversity (cultivars and clones) and environment (terroir). Among the important Italian varieties, 'Nebbiolo' is one of the best examples of this connection. The behavior of three 'Nebbiolo' clones (CVT71, CVT185, CVT423) grafted on the same rootstock (Kober 5BB) and grown in three different experimental vineyards in the typical growing areas of Piedmont (Italy), was analyzed in relation to the different soil and environmental conditions. In two years (2013 and 2014) the agronomical and biochemical performances of those vines were monitored from winter pruning to harvest, recording vigor, yield, juice composition and anthocyanin profile. RNA-Seq analyses were performed on berries collected in three different developmental stages during the vegetative season: berry pea size stage, veraison and at harvest (24 °Brix). RNA-seq data were analyzed through a data mining process with the aim of investigating the relationships between time course of gene expression profiles and environmental variables, and of quantifying how much these variables affect the gene expression. The most important changes in the berry transcriptome are related to the different developmental stages. However, also vineyard and genotype induce significant modulation of several genes. For example, in a vineyard with a less favorable exposure we observed the activation of many genes related to stress responses. Another example is given by the clone CVT423, which showed different agronomic and metabolic performances with respect to the other two clones as well as different modulation of several genes. This research was funded by Fondazione Cassa di Risparmio di Cuneo, Project "Nebbiolo Genomics".

Climate change phenomenon, soil qualities and rootstocks are among the main factors that influence grape development as well as fruit and wine composition. The relationships between scion and biotic/abiotic factors are rootstock-mediated. Studies investigating the molecular network of rootstock and scion interactions are still scarce and the selection of the appropriate rootstock is and will be one of the key factor for the development of a more sustainable viticulture. In this work, the rootstock/scion interactions were studied using a whole-transcriptome approach on leaves of wine red variety 'Gaglioppo', grafted onto thirteen different rootstocks growing in the same vineyard in adjacent rows. The experiments were performed during the summer season 2014 in a vineyard located in Calabria Region (South-east Italy) that falls to Mediterranean climate characterized by warm and dry summers. Leaf transcriptome of 'Gaglioppo' grafted on five selected rootstocks showed high variability in gene expression. In particular, significant modulation of transcripts linked to primary (e.g. carbohydrate and transport) and secondary metabolism (e.g. phenylpropanoids pathways and response to stress) was observed. Interestingly, genes involved in the priming defense responses (e.g stilbenes and defense genes) were strongly activated only in some graft combinations. These results were further confirmed by the quantification of stilbene contents by HPLC-MS/MS. The adopted approach allowed to point out an interesting result among the others: the leaves of 'Gaglioppo' grafted on 1103 Paulsen showed the lowest levels of stilbene synthase transcripts and stilbene compound and revealed interestingly the greater sensitivity to downy mildew in in vitro assay. This study carrying out an extensive analysis of the rootstock effects on scion leaves open the possibility to unravel this complex interaction in a useful way considering the ongoing climate changes.

Nell'ampia gamma delle cultivar di vite il Nebbiolo riveste un ruolo di particolare rilevanza. Le eccellenti caratteristiche qualitative di questo vitigno derivano dall'interazione tra la sua nota variabilità intravarietale (cloni) e le differenti caratteristiche pedoclimatiche degli ambienti in cui esso è coltivato (terroir). A fronte dell'interesse anche economico, erano disponibili poche informazioni a livello genomico per il Nebbiolo e mancavano dati fondamentali per comprendere in modo organico vari aspetti patologici e qualitativi della cultivar. Per colmare questa lacuna, nel 2012 è stato avviato il progetto triennale "Nebbiolo Genomics: genomica strutturale e funzionale su aspetti patologici e qualitativi", finanziato dalla Fondazione Cassa di Risparmio di Cuneo e finalizzato alla caratterizzazione genetica approfondita del Nebbiolo. Il progetto prevedeva in primo luogo il sequenziamento del genoma di 3 cloni di Nebbiolo; tale sequenziamento ha rappresentato la base di partenza per l'approfondimento di alcune importanti tematiche: 1) lo studio delle interazioni tra la biodiversità genetica esistente e l'ambiente di coltivazione (clima, microclima e terreno); 2) lo studio dei meccanismi di interazione vite/fitoplasma attraverso la caratterizzazione del trascrittoma; 3) l'individuazione di marcatori genetici clone-specifici. In questa sede vengono riportati i risultati ottenuti in particolare per quanto riguarda quest'ultima tematica.