he standard deviation of their PCR efficiencies among the accessions under study was less than 10%. PCR pri mers that distinguished individual paleologous copies, as well as highly similar paralogues, and passed the thresh olds set for the qPCR experiment, could be developed for nine out of the sixteen F35H copies. The remaining copies were either highly identical in sequence or con tained only a few polymorphic sites within DNA seg ments unsuitable for primer design. The range of variation in average PCR efficiency of primer pairs among the accessions tested was within the bounds of 87% in Marzemino and 102% in Nebbiolo, with a similar average efficiency of 93% in Aglianico and Grignolino.

This excluded a substantial cultivar effect of the efficiency of primer annealing during qPCR on the estimation of transcript levels of the whole gene family among cultivars, caused by possible SNPs in the annealing sites across haplotypes. Experimental design and statistics in expression and metabolite analyses Variation in anthocyanin profile and in transcriptional level of duplicate genes among developmental stages and cultivars was studied using a complete randomized design, and Cilengitide tested for significance using ANOVA run by COSTAT statistical package. Each plot consisted of 10 in a row clonally replicated plants in north south oriented rows. Vines were grown at the germplasm repository of Vivai Cooperativi Rauscedo, northeastern Italy. Vines were trained using the Syl voz system. Three biological replicates of 20 berries per cultivar were collected at each developmental stage.

Berries of each replicate were col lected in the vineyard on both sides of canopy by ran dom sampling on every plant within each plot. Samples were frozen immediately in liquid nitrogen and stored at 80 C until processed. Skin of each biological replicate was peeled from frozen berries, powdered in liquid nitrogen, and split to obtain a 100 mg aliquot for RNA extraction and a 200 mg aliquot for anthocyanin extrac tion. A three way ANOVA was used to partition the factors that contributed to expression divergence in ripening fruit, gene copy, cultivar and developmental stage, and their interactions. A two way ANOVA was used to assess the effect of gene copy and developmen tal stage on expression level, regardless of the cultivar.

A one way ANOVA was used to assess the same effect in each cultivar, as well as the differences in metabolite content and composition among cultivars. Statistically significant differences were determined using the Stu dent Newman Keuls test. Anthocyanin profiling Anthocyanins were extracted by sonication of 200 mg berry skin in 1. 8 mL of 1,1 methanol H2O for 30 minutes. After centrifugation at 13,000 �� g for 15 min, samples were filtered with a 0. 2 um cellulose membrane. Anthocyanins were separated by an Agilent 1200 Series HPLC system equipped with a C18 Purospher RP 18 column, according to the procedure reported by, and detected at 520 nm by a UV detector. C