Development of an oligo-based microarray (µPEACH 1.0) for genomics studies in peach fruit

The first peach oligo-based microarray has been constructed by the Italian Consortium for Genomics in Prunus (ESTree, www.itb.cnr.it/ESTree) starting from Expressed Sequence Tags (ESTs) isolated in peach fruit. Four cDNA libraries have been synthesized from mesocarp of cv. ‘Fantasia’, ‘Redhaven’, ‘OroB’ and ‘Bolero’ and 1261 and 1133 ESTs were generated from S3 (second exponential growth) and S4 (maturation and ripening) stages, respectively. These 2394 sequences have been processed and combined with other 8807 ESTs retrived from NCBI GenBank and GDR (Genome Database for Rosaceae) at Clemson University Genomics Institute (CUGI) to create a gene dataset of 11201 entries. After sequence assembling, an unigene set composed of 4818 independent sequences has been obtained. Of these, 1442 contigs contain 2 or more ESTs, while the others 3376 represent single sequences (singletons). About 40% of the 4818 unigenes showed homology higher than 1.0e-10 with Arabidopsis proteome and have been grouped according to MIPS functional categorization. 70-mer oligo-probes corresponding to 4806 unigenes expressed in peach fruit have been designed, synthesised, and deposited onto glass slides to create a microarray (µPEACH 1.0). The first trials performed with µPEACH 1.0 revealed that more than 70% of the probes give a positive signal when hybridized with RNA extracted from peach ripe fruits.