Identification of cold-inducible microRNAs in grapevine

Abstract

Low temperature is one of the most important environmental factors that limits the geographical distribution and productivity of grapevine. However, the molecular mechanisms on how grapevine responds to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although miRNAs and their targets have been identified in several Vitis species, their participation during cold accumulation in grapevine remains unknown. In this study, two small RNA libraries were generated from micropropagated ‘Muscat Hamburg’ (V. vinifera) plantlets under normal and low temperatures (4°C). A total of 163 known miRNAs and 67 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. The expression patterns of the 13 DEMs were verified by real-time RT-PCR analysis. The prediction of the target genes for DEMs indicated that miRNA may regulate transcription factors, including AP2, SBP, MYB, bHLH, GRAS, and bZIP under cold stress. The 5′-RLM RACE were conducted to verify the cleavage site of predicted targets. Seven predicted target genes for four known and three novel vvi-miRNAs showed specific cleavage sites corresponding to their miRNA complementary sequences. The expression pattern of these seven target genes revealed negative correlation with the expression level of the corresponding vvi-miRNAs. Our results indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response.

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

“…Recently, Sun et al (2015) described changes in grape miRNA abundance induced by cold stress and Pantaleo et al (2016) characterized novel miRNAs in virus-infected grapevine contemporaneously subjected to water stress. However, to the best of our knowledge, this is the first time that the effects of drought alone were analyzed on grape miRNA populations.…”

The ethylene response factor VaERF092 from Amur grape regulates the transcription factor VaWRKY33, improving cold tolerance

“…RNA extraction and qRT‐PCR was carried out as described by Sun et al . (). Each sample was represented by three biological replicates and three technical replicates.…”

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

“…Group IV miRNA, vvi-miR3640, exhibited suppressed expression till 8 h of cold stress. Under cold stress, these miRNAs targeted AP2, SBP, MYB, bHLH, GRAS, and bZIP TFs to regulate stress responses (Sun et al 2015a). Khraiwesh et al (2012) documented the up-regulation of miR169 and miR397 in Arabidopsis, Brachypodium, and Populus, whereas induction of miR172 was reported only for the first two species exposed to cold.…”

“…Dehydrins are the essential osmoprotectants which preserve cellular homeostasis and often act as chaperones to prevent protein misfolding and aggregation (Banerjee and Roychoudhury 2016). Sun et al (2015a) performed Solexa sequencing in salt stressed (200 mM NaCl) radish (Raphanus sativus) to identify the global expression profiles of miRNAs. They identified 22 novel miRNAs which were differentially regulated under stress.…”