Quantitative and qualitative post-harvest losses occur worldwide up to 50%. It would be of great benefit to control fruit senescence thereby improving fruit quality and storability. Tomato (Solanum lycopersicum L.) is probably the best model for understanding the fleshy climacteric fruit ripening process. However, it is still unclear whether fruit ripening is a process of organ senescence or fruit senescence is a distinct process downstream the ripening. To accomplish a comprehensive investigation on the senescence-related processes, a multi-omics approach including RNA-seq for coding and non-coding RNAs, BS-seq for DNA methylation, and ChIP-seq for histone post-translational modifications (H3K4me3, H3K27me3, H3K9K14ac) was planned in tomato by using the landrace Lucariello (LUC), recognized as 'Pomodorino del Piennolo del Vesuvio', that has a shelf-life higher than 150 days. Fruit pericarps were sampled at the red ripe stage, 60 and 150 days in post-harvest (dph). Dry weight, soluble solids content and firmness decreased in LUC fruits at 150 dph by 13%, 10% and 67%, respectively, in comparison with the earliest time point. Differentially expressed genes (DEGs, n=10285) from RNA-seq included many transcription factor genes involved in fruit ripening-related processes. The occurrence of a genome-wide hypermethylation at CG and CHG sites in 150 dph fruits was concomitant with a progressive silencing of the fruit-specific DNA demethylase, SlDML2, thereby suggesting a role for the epigenome in fruit senescence. We focused on DEGs that were likely regulated by DNA methylation as well as by the abovementioned histone marks or miRNAs. In particular, more than 2000 putative miRNAs were associated with anti-correlated DEG targets in a predictive manner. Among the regions of significant H3K4me3, H3K27me3, H3K9K14ac ChIP enrichment, the peaks of read counts that were different between time points and located around the transcription start site were correlated with DEGs. Similarly, the regions that significantly gained/lost DNA methylation across time points (Differentially Methylated Regions) were analysed for the association with DEGs. Based on the identified DEGs, co-expression analysis is currently underway to find activator and/or repressor candidates in the regulatory pathways underlying tomato fruit senescence. Furthermore, all the data are being reconciled in a web-based platform.
Multi-Omics analysis of tomato fruit senescence
Termolino P;Cammareri M;Consiglio MF;Della Ragione F;D'Esposito M;Grandillo S;Matarazzo MR;Conicella C
2018
Abstract
Quantitative and qualitative post-harvest losses occur worldwide up to 50%. It would be of great benefit to control fruit senescence thereby improving fruit quality and storability. Tomato (Solanum lycopersicum L.) is probably the best model for understanding the fleshy climacteric fruit ripening process. However, it is still unclear whether fruit ripening is a process of organ senescence or fruit senescence is a distinct process downstream the ripening. To accomplish a comprehensive investigation on the senescence-related processes, a multi-omics approach including RNA-seq for coding and non-coding RNAs, BS-seq for DNA methylation, and ChIP-seq for histone post-translational modifications (H3K4me3, H3K27me3, H3K9K14ac) was planned in tomato by using the landrace Lucariello (LUC), recognized as 'Pomodorino del Piennolo del Vesuvio', that has a shelf-life higher than 150 days. Fruit pericarps were sampled at the red ripe stage, 60 and 150 days in post-harvest (dph). Dry weight, soluble solids content and firmness decreased in LUC fruits at 150 dph by 13%, 10% and 67%, respectively, in comparison with the earliest time point. Differentially expressed genes (DEGs, n=10285) from RNA-seq included many transcription factor genes involved in fruit ripening-related processes. The occurrence of a genome-wide hypermethylation at CG and CHG sites in 150 dph fruits was concomitant with a progressive silencing of the fruit-specific DNA demethylase, SlDML2, thereby suggesting a role for the epigenome in fruit senescence. We focused on DEGs that were likely regulated by DNA methylation as well as by the abovementioned histone marks or miRNAs. In particular, more than 2000 putative miRNAs were associated with anti-correlated DEG targets in a predictive manner. Among the regions of significant H3K4me3, H3K27me3, H3K9K14ac ChIP enrichment, the peaks of read counts that were different between time points and located around the transcription start site were correlated with DEGs. Similarly, the regions that significantly gained/lost DNA methylation across time points (Differentially Methylated Regions) were analysed for the association with DEGs. Based on the identified DEGs, co-expression analysis is currently underway to find activator and/or repressor candidates in the regulatory pathways underlying tomato fruit senescence. Furthermore, all the data are being reconciled in a web-based platform.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
