Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits

In addition to 7 novel miRNA families, 103 conserved miRNAs belonging to 24 families and 10 non-conserved miRNAs matching 9 families were identified in our libraries. The targets of many these miRNAs were predicted to be transcriptional factors. Other targets are known to play roles in the regulation of metabolic processes. Interestingly, some targets were predicted to be involved in fruit ripening and softening, such as Pectate Lyase, beta-galactosidase, while a few others were predicted to be involved in ethylene biosynthesis and signaling pathway, such as ACS, EIN2 and CTR1. The expression patterns of a number of such miRNAs at three ripening stages were confirmed by stem-loop RT-PCR, which showed a strong negative correlation with that of their targets. The regulation of exogenous ethylene on miRNAs expression profiles were analyzed simultaneously, and 3 down-regulated, 5 up-regulated miRNAs were found in this study.A combination of high throughput sequencing and molecular biology approaches was used to explore the involvement of miRNAs during fruit ripening. Several miRNAs showed differential expression profiles during fruit ripening, and a number of miRNAs were influenced by ethylene treatment. The results suggest the importance of miRNAs in fruit ripening and ethylene response.Gene expression is regulated by transcriptional and post-transcriptional pathways, which are crucial for optimizing gene output and for coordinating cellular programs [1]. One of the recently discovered mechanisms in plants was short non-coding RNAs mediated gene silencing at post-transcriptional (PTGS) level [2]. Short RNAs (sRNAs) are diverse and can be categorized into two major classes: short interfering RNAs (siRNAs) and microRNAs (miRNAs) [3,4]. SiRNAs, processed from perfectly double-stranded RNA (dsRNA), posttranscriptionally silence transposons, viruses, and transgenes are important for DNA methylation [5-7]. MicroRNAs (miRNAs), a near ubiquitous class of short RNAs in plants,