MicroRNAs (miRNAs), interfering RNAs (siRNA, phase-based siRNAs (phasiRNA) and trans-acting siRNAs (tasiRNAs) are recently emerged as powerful regulators in plants. However, how they operate and function, in context of fruit productivity, in fruit crops remain largely unknown. Recently, we took advantage of a deep sequencing approach, in combination with computation and molecular analyses, to thoroughly characterize the profile of miRNASs, tasiRNAs, phasiRNAs and other types of siRNAs as well as their interaction in apple and peach, respectively. Our work showed that both apple and peach shared the conserved miRNAs with model species as well as evolved a large number of unique ones. We also demonstrated that a multitude of apple and peach miRNAs were capable of triggering phasiRNA production in a few gene families, and many of the produced phasiRNAs were able to target genes inside and outside the families. These miRNA-triggered, phasiRNA-cascaded robust networks represent novel regulatory mechanisms that have not been elucidated in other species. The potential function of the sRNA-based regulatory networks in regulation of plant growth, development, productivity and defense will be discussed.
