Unique miRNAs and their targets in tomato leaf responding to combined drought and heat stress

Abstract

Background: Both drought and heat stress are serious global problems, leading to agricultural production loss. MicroRNAs (miRNAs) play important roles in plant species responding to individual drought and heat stress. However, the miRNAs and mRNAs in association with combined drought and heat in crops like tomato remains unclear.

Results: We studied the crosstalk of miRNAs and their target genes in tomato plants grown under simultaneous drought and heat stress that frequently happen in field conditions. In total, 335 known miRNAs representing 55 miRNA families and 430 potential novel miRNAs were identified in Solanum lycopersicum L. using small RNA deep sequencing. Through expression analysis, miRNAs in association with drought, heat and the combination of these were investigated. In total, 61, 74 and 37 miRNAs were differentially regulated for combination (of both stresses) vs control, combination vs drought and combination vs heat, respectively. Target genes with different expression levels were found using degradome sequencing, which were mainly involved in transcription factor activity, sequence-specific DNA binding, transcription, regulation of transcription, nucleus, DNA binding etc. The quantitative real-time polymerase chain reaction (qRT-PCR) results confirmed the accuracy of sequencing.

Conclusions: Our study serves as valuable knowledge on how crop adapted to combined drought and heat stress by regulating miRNAs and mRNAs, which provide information for crop improvement to deal with future climate changes.

Keywords: Combined abiotic stress; Degradome; Functional analysis; Solanum lycopersicum L.; miRNAs.

Fig. 1

Melatonin content in tomatoes treated after control, drought, heat and combined stress for 24 h, 36 h and 48 h

Fig. 2

a Length distribution of the unique miRNAs; b percentage of first nucleotide bias in the unique miRNAs; c venn diagrams of conserved miRNAs; d venn diagrams of novel miRNAs and e significantly up−/down regulated miRNAs identified in tomatoes at control, drought, heat and their combination

Fig. 3

GO enrichment of target genes with significantly different expression level for combined stress vs drought and combined stress vs heat

Fig. 4

qRT-PCR validation of four miRNAs and four target genes

Fig. 5

Network of miRNAs-mRNAs in tomato leaf at combined drought and heat stress as compared with control and individual stress. The miRNAs were shown in square box, while the target genes were shown in circle. The yellow color indicated that the miRNAs from the family /target genes were up-regulated; the blue color indicated that the miRNAs from the family /target genes were down-regulated; the green color indicated that the miRNAs from the family showed both up−/down- regulation. The shared response of the same genes was marked in the grey background