Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum

Xu Yang,Lu Wang,Yu Zhang,Fei Liu,Yu-Fu Cheng

doi:10.1186/s12864-017-4341-y

Abstract

BackgroundLow temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response 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 the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance.ResultsHere, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association.ConclusionsIn summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level.

Highlights

Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants
The small RNA library was established, and the expression of miRNAs and target genes was calculated by RPKM and Expdiff, that searched the differential expression of miRNAs and its target genes
Plant miRNAs are involved in a range of activities, including adverse environmental responses to temperature, drought, salt, nutrient starvation, heavy metal stress [2,3,4,5], and defensive responses to pathogenic infection [6]. miRNAs that respond to low temperature stress are divided into three categories according to their target gene types

Summary

Introduction

Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Plants have modified their own cold tolerance by evolving various adaptive mechanisms, which lead to changes in gene expression and subsequent physiological enhancement These physiological responses include induction of transient increases in Ca2+ and ABA levels, Yang et al BMC Genomics (2017) 18:1000 alterations in lipid composition, increases in antioxidant levels, and the accumulation of osmoprotectants [1]. The C-repeat binding factor (CBF)/dehydration responsive element provides one of the most important pathways for cold response for a large number of cold regulatory genes that encode transcription factors or proteins involved in transcription It has been shown in transgenic eggplants that heterologous expression of Arabidopsis C-repeat binding factor 3(AtCBF3) and cold-regulated 15A (AtCOR15A) enhanced chilling tolerance [1, 8]

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