Transcriptome analysis of miRNAs expression reveals novel insights into root formation under Root restriction cultivation in grapevine (Vitis vinifera L.)

Background: Root restriction cultivation not only promotes maturation and quality of fruit, but optimizes the architecture of root, especially in enhancing the occurrence of adventitious and lateral roots. While the molecular mechanism of this phenotype is still unknown. Results: In this study, the development of roots was observed at 12 different time points under Root restriction and normal cultivations (control). Root phenotype showed a significantly different feature start from the seventh sampling, mainly in the increasing of adventitious roots numbers, degeneration of root tip and subsequent mass of lateral roots development. The 7th and 12th sampling of two different cultivations, named nR7, nR12, RR7, and RR12, were selected for small RNA sequencing. 214,439,588 raw reads were obtained and 168,741,687 clean reads were remained after the quality control steps, and finally got a total of 153 known miRNAs, and 119 predicted novel miRNAs. The predicted novel miRNAs blasted with the miRVIT and miRBase databases simultaneously. 96 new family members of grapevine miRNA and 23 grapevine-specific novel miRNAs were obtained. Differentially expressed miRNAs (DEMs) analysis showed that 26 and 33 miRNAs were differentially expressed in two different cultivation models (RR7 vs nR7; RR12 vs nR12), while 26 and 32 DEMs were obtained in different root development stages (nR12 vs nR7; RR12 vs RR7). MiRNA expression levels analysis found that conserved miRNA s were in higher expression level than novel miRNAs. The predicted target genes of DEMs were annotated on a variety of biological processes, and 24 participated in root development. An analysis of vvi-miR160 family members revealed that vvi-miR160c was highly expressed in grapevine root, indicating the potential role of miR160c in root development, which in accordance with the previous report in Arabidopsis . Conclusions: Multiple miRNAs were jointly to regulate root development on Root restriction condition, mainly in lateral root development. And the specific expression of vvi-miR160c in the apex may be the main cause of apical degradation. Moreover, there were multiple miRNAs related to biotic or abiotic stresses, which indicated that multiple minor stresses exist in root development after Root restriction cultivation.