Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing

Waqas Ahmed,Hua Zhang,Yanshi Xia,Peiguo Guo,Kadambot H M Siddique,Guihua Bai,Ronghua Li

doi:10.1038/s41598-019-51443-y

Abstract

Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.

Highlights

Plant microRNAs are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development
Superoxide dismutase (SOD) and peroxidase (POD) activities in heat treated plants increased at 1 h, 6 h and 12 h compared to 0 h control plants (Fig. 1C,D)
The findings showed that heat stress significantly increased CAT, superoxide dismutase (SOD) and POD activities in flowering Chinese cabbage

Summary

Introduction

Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Flowering Chinese cabbage is a cryophilic vegetable crop that has been planted year-round in southern China since its domestication several hundred years ago It often suffers from high-temperature stress in summer[6], which influences www.nature.com/scientificreports plant growth and performance but results in yield reductions and even death[7]. Plant noncoding RNAs play a significant role in the response to various abiotic and biotic stresses and are categorized into classes including microRNAs (miRNAs ~21–24 nucleotides in length), circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and small interfering RNAs (siRNAs)[11], which use various molecular mechanisms to perform their important functions, ranging from modulation of RNA stability, translation, post-transcriptional and transcriptional regulation of gene expression[12,13]. Using genomic and sequencing technologies, several miRNAs and their potential targets that play key roles in heat stress have been extensively studied in model plant species of various agricultural and vegetable crops[21]. This study aimed to identify novel miRNAs involved in heat stress, their differential expression, putative targets, and miRNA-related regulatory pathways linked to heat stress in flowering Chinese cabbage

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