W_ i Heterologous Comparative Genomics to Identify Candidate Genes Impacting Fruit Quality in Apple (Malus x domestica Borkh.) F. Costa', G. Costa', S. Sansavini', V. Soglio 2 , L. Gianfranceschi 2 . N.J. Schouten', R. Alha 4 and J. Giovannoni 'Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fan in 46. 40127 Bologna, Italy 2 Dept. of Biornolecular Sciences and Biotechnologies, Università degli Studi di Milano, via Celoria 26, 20133 Milano. Italy 'Plant Research International, Droevendaalscsteeg I. 6700 AA Wageningen, The Netherlands 4 Boyce Thompson Institute for Plant Research, Cornell campus, 14850 Ithaca, New York, USA 5U S. Department of Agriculture, Agricultural Research Service, Plant, Soil and Nutrition Laboratory, Ithaca, New York, 14853, USA Keywords: comparative and translational genomic, microarray, fruit ripening, I -MCP (I - rnethyleyclopropane), gene mapping Abstract Fruits are an important source of healthy compounds in the human diet, such as fibers, organic acids, vitamins, and antioxidants. All these metabolites are developed during fruit ripening, a complex process characterized by dramatic physiological changes. Fruit ripening is normally distinguished as climacteric or non-climacteric, depending on the direct effect of the hormone ethylene in the control of these processes, especially on fruit softening. Variation in fruit firmness, one of the most evident phenomena, strongly influences the general fruit quality, limiting the shelf life due to a minor resistance to post-harvest diseases. To investigate the transcription dynamics over the apple ripening, two wide genomic eDNA microarrays were used: an apple specific homologous system, and a tomato heterologous platform. In this study, we assessed the potential of the heterologous array to analyze the apple ripening physiology. The normal ripening transcriptome was compared with the distorted one obtained with I-MCP treatment (an ethylene competitor), allowing for the identification of a comprehensive gene set, developmental and ethylene dependent. INTRODUCTION Fruits, in general, are an essential component of the human diet providing healthy nutraceutical compounds (Giovannoni, 2004). All the features defining high quality fruits are determined and developed during the ripening process (Lelièvre et al., 1997), a physiological syndrome distinguished in two general behaviors: climacteric or non- climacteric (Alexander and Grierson, 2002). The first category, to which apple and tomato belong, differs from the second for the starch accumulation occurring during the maturation phase, and the characteristic ethylene burst at the climacteric stage. Ethylene is a gaseous hormone able to trigger and coordinate all the physiological changes of fruit ripening (Alexander and Greirson, 2002). controlling in particular the action of several cell wall enzymes, responsible for the loss of firmness. This aspect highly impacts the fruit economic value, limiting fruit shipping and storability, because a fruit with a reduced shelf life becomes more prone to post-harvest diseases and mechanical damage. To unravel the genetic bases responsible for all these ripening changes. the identification of the gene set putatively involved in these pathways is challenging. To date, microarray technique is one of the most promising available technologies for candidate gene discovery at a wide genomie scale. This strategy has already been used for studying gene expression related to fruit ripening in strawberry (Aharoni et al.. 2002) and peach (Trainotti et al., 2006). Proc. XIlh Eucarpia Symp. on Fniit Breeding and Genetics 517 Eds.: R. Socias i Compan y ci al. Acta 1-Ion. 814, ISIIS 2009