Fig. 2

A multi-scale comparative transcriptome analysis approach was used to screen for genes activated or repressed in the ripe fruit AZ during abscission. a We first used ethylene to induce abscission in ripe fruit, and compared the expression profiles of the ripe fruit AZ (AZ150) with that of adjacent pedicel tissue (P150) and immature fruit AZ (AZ30), in which no cell separation occurs under ethylene treatments. To screen for preferential ripe fruit AZ expression, differential expression in the AZ150 was first identified (blue arrows, screen step 1), then DEGs with similar profiles in the AZ30 and P150 were eliminated (red arrows, screen step 2). Candidate DEGs were retained when there was a statistical difference between their expression in the AZ150 DAP samples compared with the P150 DAP and AZ30 DAP for at least one time point (0 h, 3 h, 6 h or 9 h). b A transcriptome developmental time course (30, 120 and 160 DAP) of the AZ from fruit during natural abscission was then obtained (step 3) to provide a comparison with the DEGs found in the AZ during ethylene induced abscission (screen step 4) that resulted in the identification of 168 DEGs common to both ethylene induced and natural abscission (black arrow). c From these DEGs, 126 were up regulated and (d) 42 were down regulated in the AZ during abscission in both contexts