Transcriptome-wide analysis of dynamic variations in regulation modes of grapevine microRNAs on their target genes during grapevine development

Abstract

MicroRNAs (miRNAs) play critical regulatory roles mainly through cleaving their target mRNAs or repressing gene translation during plant development. Grapevines are among the most economically important fruit crops with available whole genome sequences. Studies on grapevine miRNAs (Vv-miRNAs) are also widely available. However, studies on the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development have not been studied well, especially at the transcriptome-wide level. Here, six small RNA and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, we systematically analyzed the spatiotemporal variations in the regulation of the target genes of regulation of Vv-miRNAs. In total, 242 known and 132 novel Vv-miRNAs and 193 target mRNAs were identified, including 103 target mRNAs for known and 90 target mRNAs for novel miRNAs, were validated in one or more of the tissues examined. More than 50 % of novel miRNAs were expressed exclusively in the flowers and berries, where they cleaved their target genes in a tissue-specific manner, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries responded to exogenous gibberellin and/or ethylene under a quantitative real time RT-PCR analysis, which confirmed their regulatory functions during berry development. Up to 93.6 % of the known miRNAs were highly conserved in various tissues, where their expression levels exhibited dynamic variations during grapevine development. Significantly, some Vv-miRNA families had one key member that acted as the main regulator of their target genes during grapevine development.

Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

“…Since the key role of miRNAs in regulating fruit and seed development is of great applied interest for crop development (Han et al, 2014), identified a number of conserved and non-conserved grapevine miRNAs responsive to exogenous gibberellin and showed that they play a potential role in mediating gibberellin-induced regulation of berry growth, development and response to various environments. Another study identified six novel miRNAs expressed in berries during exogenous gibberellin application and/or ethylene treatment, supporting a role for miRNAs in grapevine fruit development and ripening (Wang et al, 2014). In line with the growing evidence that miRNAs play critical roles in both biotic and abiotic stress responses, a recent study reported that a diverse set of grapevine miRNAs are cold-inducible and may play an important role in cold stress response (Sun X. et al, 2015).…”

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

“…The NAC33 expression profile is generally inversely correlated with that of Vv-miR164, which would be expected for a miRNA target (Sun et al, 2012). The recent transcriptome-wide analysis of grapevine miRNAs in six different organs during development revealed the spatiotemporal expression profile of the miRNAs involved in the predicted miRNA/switch gene pairs (Wang et al, 2014). We were therefore able to confirm that 26 switch genes showed the opposite expression profiles to those of their putative miRNA regulators, e.g., Vv-miR166 and ZFWD2 (VIT_13s0047g01130), Vv-miR172d and caffeic acid 3-O-methyltransferase (VIT_02s0025g02920), and Vv-miR482 and dehydration-responsive protein (VIT_16s0100g00570).…”

Grapevine microRNAs responsive to exogenous gibberellin

“…All sRNAs sequences from 18nt to 30nt obtained were removed from the vector sequences, then the modified sequences were further subjected to removal of rRNA, tRNA, snRNA, snoRNA and those containing the polyA tails, and finally the remaining sequences were compared against known plant Vvi-miRNAs in the miRBase [33]. Only the high matching (0-3mismatches) sequences were considered as conserved Vvi-miRNAs.…”