Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing

Abstract

Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress.

Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

“…For instance, in sorghum, 526 novel miRNAs were identified, and 96 were found to be drought-responsive miRNAs [143]. In tomato, stress-responsive miRNAs were recently identified, and 10 miRNAs were found to have stress-specific expression responses [144]. miRNAs are ideal candidates to investigate the crosstalk between gene expression networks and signaling pathways, because many miRNAs target TFs that are master regulators of gene expression [145].…”

Chilling stress tolerance of two soya bean cultivars: Phenotypic and molecular responses

“…It is therefore of paramount significance to describe the functions of miRNAs in plant adaptation to environmental stresses. This endeavour can be initiated by the identification of miRNAs that are differentially expressed in response to such stresses (López-Galiano et al, 2019). In this study, an attempt was undertaken to characterize the expression patterns of 5 miRNAs and their target genes in 2 chilling-tolerant soya bean cultivars.…”

Role of ATP‐binding cassette transporters in maintaining plant homeostasis under abiotic and biotic stresses

“…It also manipulates the membrane lipid composition based on external thermal temperature. Similarly, López‐Galiano et al (2019) identified stress‐associated miRNAs and characterized their role in regulating the expression of ABC transporter under heat stress. The expression of ABC transporters has been established as one of the coping mechanisms against heat stress.…”