Submitted to: Genome Biology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/15/2012
Publication Date: 6/15/2012
Publication URL: http://genomebioloby.com/2012/13/6/R47
Citation: Xia, R., Zhu, H., An, Y., Beers, E., Liu, Z. 2012. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology. 13(6):R47. Interpretive Summary: Gene regulation and gene function control fruit quality, productivity, and their resistance to biotic and abiotic stresses. Small RNAs have been found to play a critical role in gene regulation in model and crop species. To understand whether small RNAs are involved in the regulation of genes controlling many agronomical traits in apple, we took genomic and genetic tools to identify novel small RNA regulators - microRNAs (miRNAs) in apple plants. We found that these miRNAs display distinct gene expression patterns which could regulate biological processes such as fruit development and tree growth. Further elucidation of the miRNAs function would provide insight into understanding mechanisms underlying fruit development and their responses to biotic and abiotic stresses in the field.
Technical Abstract: MiRNAs, negatively affecting gene expression at the post-transcriptional levels, have been shown to control numerous genes involved in various biological and metabolic processes. To date, the identification of miRNAs in plants focused on certain model plants, such as Arabidopsis and rice. Investigation on important agricultural crops is limited. In this study, we identify both conserved and species-specific miRNAs in apple by employing the next generation sequencing (NGS) technology. The sequencing results showed that apples have a complex small RNA population in which the 24-nt long small RNAs are predominant. A total of 22 conserved miRNA families were identified and 24 known but non-conserved miRNAs were also found. In addition to known miRNAs, 21 novel apple-specific non-conserved miRNAs were found together with their corresponding star stands, and 21 other putative miRNA candidates without star stands found were also reported. A novel miRNA is found to be located in a single stem-loop structure with the conserved mdo-miR319b. A total of 121 targets have been identified for many apple miRNAs by degradome sequencing. Most of the targets are transcription factors associated with diverse metabolic processes and signaling pathways in plants. Two TAS orthologs are also found to be conserved in apple.