alias: E-MTAB-8756:F_2_B_s
title: Illumina Genome Analyzer IIx sequencing; miRNome investigations supports the role of rootstock-scion interaction in grapevine berry quality
design: miRNome investigations supports the role of rootstock-scion interaction in grapevine berry quality
library_construction_protocol: 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  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 are 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).  Small RNA libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina®), following all manufacturers' instructions. Thirty-six Eighteen bar-coded small RNA libraries were constructed starting from 1 µg  of total RNAs. The quality of each library was assessed using an Agilent DNA 1000 kit.
identifiers.namespace: Council for Agricultural Research and Economics (CREA) Research Centre for Genomics and Bioinformatics
identifiers.id: E-MTAB-8756:F_2_B_s
attributes.tag: Experimental Factor: developmental stage
attributes.value: Maturity
attributes.tag: Experimental Factor: genotype
attributes.value: Not grafted Pinot Noir