Genome Wide Transcriptome Investigation of Fruit Development and Ripening in Apple

Ripening represents the final stage of fruit development, during which the important structural, biochemical and physiological modifications occurs. In order to unravel the physiological machinery deputed in this process, two genomic tools were employed in order to characterize the overall transcriptomic variation. The functional regulation was initially investigated by the use of a candidate based gene Combimatrix array, composed by a subset of selected genes mostly involved in fruit ripening processes. The gene activity showed a specific regulation over the time course, in particular during the postharvest ripening phase. To better characterize the late ripening, a second tool was employed in the study, represented by a genome wide Nimblegen array. This platform was, moreover, enriched of genes specifically involved in the final phase of the fruit ripening, by sequencing RNA-seq analysis. During the investigation a particular attention was given to the effect played by the hormone ethylene, comparing the control postharvest samples with those treated with 1-MCP, an ethylene competitor largely used to extend the fruit shelf-life.

The genome wide approaches used in this work have shown a global and complete aspect of the regulatory networks operating during fruit development, ripening and post harvest stages of apple fruit. From this gene wide expression, a subset of genes have been selected and currently used as functional biomarkers for the physiological characterization of the climacteric ripening of apple fruits.