Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination

Shabari Sarkar Das,Ananda K Sarkar,Archita Singh,Vibhav Gautam,Prakash Karmakar,Neeti Sanan-Mishra,Asis K Nandi,Manoj Majee,Sandeep Yadav

doi:10.1038/s41598-017-18823-8

Abstract

Seed germination paves the way for the dormant embryo to establish itself as a new plant marking the first critical step in postembryonic plant growth and development. Germination starts with the uptake of water (imbibition), followed by induction of transcription, translation, energy metabolism, and cell division processes. Although small RNAs have been implicated in many developmental processes, their role during seed germination stages and conditions remained elusive. Here we show that seed germination conditions, like imbibition and temperature, dynamically regulate the expression of many developmentally important miRNAs and their targets. We have identified 58 miRNAs belonging to 30 different families at different seed germination conditions. Amongst these, 15 miRNAs and their targets were significantly differentially expressed in Arabidopsis seeds in dry and 12 h, 24 h and 48 h of imbibition. Interestingly, differential expression of miR390, which targets trans-acting siRNA locus (TAS3) derived transcripts, resulted in alteration of tasiR-ARF mediated regulation of expression of target AUXIN RESPONSE FACTORs (ARF2/3/4). Our results suggest that the dynamic expression of several miRNAs, their targets, and a crosstalk between miRNA and ta-siRNA pathways contribute to the regulation of seed germination in Arabidopsis thaliana.

Highlights

Seed germination process, which marks the transition from seed to seedling stage, plays a crucial role in the complete life cycle of higher plants
In order to identify miRNAs that are involved in seed germination process in Arabidopsis, we used miRNA microarray approach
We identified a total of 58 miRNAs differently expressed in (i) imbibed seeds (IS)-4 °C vs. dry seeds (DS) (Fig. 1a), (ii) IS-room temperature (RT) vs. DS (Fig. 1b) and lastly, (iii) IS-4 °C vs. IS-RT (Fig. 1c)

Summary

Introduction

Seed germination process, which marks the transition from seed to seedling stage, plays a crucial role in the complete life cycle of higher plants. Deep sequencing of small RNAs from rice seed embryos identified 59 known and 230 novel miRNAs differentially regulated in the early stages of seed germination[21]. In eudicot (Nelumbo nucifera) seed germination, 145 known and 78 novel miRNAs were identified[22] These reports indicate the association of more number of small RNAs in the dynamic seed germination procedure. Little is known about the condition specific regulation of small RNAs and their targets, which are potentially important contributors to the early stages of Arabidopsis seed germination. The correlation of altered expression of miR390 and ARF2/3/4 indicate that a crosstalk of both miRNAs, ta-siRNAs, and their targets contributes to the dynamic seed germination process

Methods

Results

Conclusion