Illumina Genome Analyzer IIx sequencing; Transcriptome investigations supports the role of rootstock-scion interaction in grapevine berry quality
Transcriptome investigations supports the role of rootstock-scion interaction in grapevine berry quality
grape samples for molecular analyses were collected at two ripening times: veraison (75% of colored berries, T1) and at maturity (maturity, T2). Berries (15 per plant, 3 plants per replicate) were randomly hand-picked at different positions of the clusters, dissected to separate skin tissues, stored in Falcon tubes and immediately frozen at -80°C for further processing.  At harvest, technological maturity was evaluated on musts according to O.I.V. official methods (O.I.V., 2009), confirming commercial ripeness. A pot system for grapevines monitoring was set up in Arezzo (43°28'36'' N, 11°49'27'' E, Italy). It consists of plastic pots of 70 liters, filled by a silty-clay texture soil (40% clay, 41% silt, 19% sand), with a volumetric soil water content of 34% at field capacity, collected from a real vineyard of the Chianti Classico D.O.C.G. district (Tuscany - Italy). The grapevines in the pots  were 7-year-old Pinot noir plants, clone ENTAV 115 with two different rootstock combinations: 1103 Paulsen (P) V. berlandieri x V. rupestris,  and Mgt 101-14 (M) V. riparia x V. rupestris,  not grafted plants were used as control (F). The vines were trained on vertical shoot positioned trellis, with spur cordon pruning and an average of 10 buds per vine. The pots were positioned in an open field, spaced at the distance of 1 m within the row and 2,5 m between the rows, with orientation north to south, and were arranged in a randomized block design with 9 replicates for each root system. The plants were maintained in the same agronomic conditions: all the pots were fertilized before the beginning of the vegetative season with 40g of Nitrophoska (12N-12P-17K, EurochemAgro) and were abundantly irrigated by drip emitters during the summer period, with the same water regime.  Total RNA extraction from the berry skins  was performed using Plant RNA Isolation Reagent (PRIR – Life TechnologiesTM) starting from 200 mg of ground berries skin tissue in 1 ml of reagent, followed by RNA Clean up and Concentration kit (NorgenBiotek Corp) according to manufacturers' protocols. Total RNA was then subjected to Dnase I treatment (DNA-freeTM Kit, Applied Biosystems).      mRNA seq libraries were prepared from  total RNA (1 µg) , using TruSeq RNA sample preparation kit (Illumina), according to manufacturers' instructions. Libraries were quantified through qRT-PCR, as recommended by the protocol
Experimental Factor: developmental stage
veraison
Experimental Factor: genotype
Pinot Noir / 1103 Paulsen