Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.).

Shengchun Xu,Guofu Wang,Qizan Hu,Yaming Gong,Weihua Mao,Na Liu

doi:10.1038/srep26619

Shengchun Xu, Guofu Wang + Show 4 more

Open Access

https://doi.org/10.1038/srep26619

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Abstract

Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. In the present study, systematic identification and functional analysis of miRNAs under chilling stress were carried out to clarify the molecular mechanism of chilling resistance. Two independent small RNA libraries from leaves of soybean were constructed and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and 3 novel miRNAs were identified. Thirty-five miRNAs were verified by qRT-PCR analysis. Furthermore, their gene targets were identified via high-throughput degradome sequencing. A total of 898 transcripts were targeted by 54 miRNA families attributed to five categories. More importantly, we identified 51 miRNAs differentially expressed between chilling stress and control conditions. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. Our qRT-PCR analysis confirmed a negative relationship among the miRNAs and their targets under chilling stress. Our work thus provides comprehensive molecular evidence supporting the involvement of miRNAs in chilling-stress responses in vegetable soybean.

Highlights

Vegetable soybean (Glycine max L.) is a food-type soybean[1]
Most known miRNAs are involved in regulating developmental processes[13,14,15], a group of miRNAs have been identified to function under chilling stress in Arabidopsis thaliana[16], Populus[17], and Prunus persica[18]
The results showed that the exact fold changes varied between quantitative reverse transcription PCR (qRT-PCR) and miRNA-sequencing data, possibly due to differences in the sensitivity and specificity between the two approaches, the miRNA expression trends are similar

Summary

Introduction

Vegetable soybean (Glycine max L.) is a food-type soybean[1]. Largely due to its higher nutritional content and better flavor compared to grain soybean, vegetable soybean has become very popular in China (300,000 ha planted each year), Southeast Asia, and some Western countries[2,3,4]. Chilling stress affects vegetable soybean plant growth and results in severe yield reduction[5]. MicroRNAs (miRNAs), a group of small endogenous noncoding RNAs, play significant roles in post-transcriptional processes by degrading mRNA or inhibiting its translation in plants[11,12]. A systematic study on chilling-responsive miRNAs is an important step to understanding small RNA-mediated gene regulation in vegetable soybean. Degradome sequencing, which has been successfully confirmed to validate large-scale discovery of miRNA targets[27,28], was used to validate the targets of these detected miRNAs. The aims of this study were 1) to identify conserved and novel miRNAs and their targets in vegetable soybean; 2) to reveal the relationships between miRNAs and their targets under chilling stress. The results provide insights into the regulatory roles of miRNAs under chilling stress in vegetable soybean

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