SRA

To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process. Overall design: As a first step to screen for genes involved in oil palm ripe fruit abscission, we examined the short-term gene expression response in the fruit abscission zone (AZ) at 150 Days after pollination (DAP) to an exogenous ethylene treatment. Transcriptome analysis was assessed every 3h over a period of 12h, while cell separation was already observed after 9h of treatment. We identified 1957 differentially expressed genes (DEGs) during at least one time point of the ethylene treatment in the 150 DAP sample (AZ150) compared to the control (time 0h AZ150). As a second step to screen the 1957 DEGs for AZ specific expression, we compared the short-term response of AZ150 to exogenous ethylene with those from the AZ from immature fruit at 30 DAP (AZ30) and the pedicel from ripe fruit (P150) samples (also treated with ethylene at same time intervals) at each ethylene treatment time point. From this analysis, a total of 502 DEG candidates were retained based on their higher or lower expression level in AZ150 compared to that observed in both AZ30 and P150. As a third step to screen for AZ genes involved in abscission, we analysed gene expression in the AZ of ripe fruit undergoing natural abscission in the field and aimed at finding genes with similar expression profiles between ethylene induced and natural abscission in the field. The natural abscission study (RNA-Seq) was conducted with AZ samples collected in the field at 30 DAP, 120 DAP, during which time no abscission was observed, and 160 DAP collected from a fruit bunch where abscission was observed.