Comparative translational genomics to target candidate genes impacting fruit quality in apple (Malus x domestica Borkh.)

The important features defining high quality fruits are determined during maturation and ripening; two physiological events in which fruits undergo several biochemical and structural modification. During those stages, one of the most important changes concerns fruit softening, controlled by the action of several enzymes that modify cell wall polysaccharides complex. Loss of firmness has a relevant economic impact, affecting shipping and fruit storage, reducing shelf-life and fruit healthy aspects. In climacteric fruit (such as apple and tomato) most of these physiological modifications (firmness in particular) are under the control of ethylene, a gaseous hormone known to trigger and coordinate the climacteric ripening evolution. To target the genes impacting apple fruit ripening and quality, and to assess their transcription dynamics, we have performed a translational comparative genomics with tomato. Tomato is considered as the model species for fruit ripening investigation thanks to the availability of highly informative genomic tools, as microarray platforms and other public resources. To study gene expression profiles during fruit maturation and ripening we have characterized ethylene and firmness physiological evolution of the apple cultivar Mondial Gala. Furthermore, to create a more controlled type of experiment, 1-MCP (an ethylene competitor) was applied, after harvest, to specifically analyze the gene transcription ethylene related. Each cDNA sample was hybridized on two different arrays: one heterologous (TOM1 – tomato) and one homologous (HiDRAS apple specific array). cDNA microarray have been used thus to characterized the global gene expression pattern, in a high throughput fashion. Functional comparison between control and 1-MCP-treated samples allowed the identification of ethylene responsive genes. The comparison of heterologous and homologous expression patterns allowed to define orthologous genes involved in the ripening of climacteric fruits. Moreover, the homologous array was investigated to create functional markers based on candidate genes for breeding purposes. We show the identification and the genomic mapping of four genes, two involved in the cell wall disassembling (Md-PG1 and Md-Exp7) and two involved in ethylene biosynthesis and perception (Md-ACO1 and Md-ERS1), in relation to fruit quality QTLs discovered in a Fuji x Mondial Gala segregating population.