Identification and Characterization of Verticillium nonalfalfae-Responsive MicroRNAs in the Roots of Resistant and Susceptible Hop Cultivars.

Urban Kunej,Nataša Štajner,Jernej Jakše,Sebastjan Radišek

doi:10.3390/plants10091883

Abstract

MicroRNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They can modulate various biological processes, including plant response and resistance to fungal pathogens. Hops are grown for use in the brewing industry and, recently, also for the pharmaceutical industry. Severe Verticillium wilt caused by the phytopathogenic fungus Verticillium nonalfalfae, is the main factor in yield loss in many crops, including hops (Humulus lupulus L.). In our study, we identified 56 known and 43 novel miRNAs and their expression patterns in the roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae. In response to inoculation with V. nonalfalfae, we found five known and two novel miRNAs that are differentially expressed in the susceptible cultivar and six known miRNAs in the resistant cultivar. Differentially expressed miRNAs target 49 transcripts involved in protein localization and pigment synthesis in the susceptible cultivar, whereas they are involved in transcription factor regulation and hormone signalling in the resistant cultivar. The results of our study suggest that the susceptible and resistant hop cultivars respond differently to V. nonalfalfae inoculation at the miRNA level and that miRNAs may contribute to the successful defence of the resistant cultivar.

Highlights

Accepted: 9 September 2021Hops (Humulus lupulus L.) are traditionally cultivated for use in the brewing industry as an essential ingredient that provides flavour and acts as a stabilizer or preserver of the beer [1]
To investigate the miRNA response in roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae, small RNA libraries were constructed from three control and three inoculated root samples of both hop cultivars
We identified 56 known miRNAs belonging to 30 different miRNA families and 43 novel miRNAs

Summary

Introduction

Accepted: 9 September 2021Hops (Humulus lupulus L.) are traditionally cultivated for use in the brewing industry as an essential ingredient that provides flavour and acts as a stabilizer or preserver of the beer [1]. One of the main limiting factors in hop production are fungal diseases, especially those caused by the soil-borne plant pathogenic fungus Verticillium nonalfalfae (formerly known as Verticillium albo-atrum) [4]. The symptoms of Verticillium wilt in hops caused by V. nonalfalfae vary depending on the pathogenicity of the fungal strain and the sensitivity of the cultivar. The first layer of defence is represented by pattern recognition receptors (PRRs) present at the cell membrane surface that recognize conserved pathogenassociated molecular patterns (PAMPs). This phenomenon is called PAMP-triggered immunity (PTI) or basal defence. PTI comprises both physical and chemical defence responses, e.g., the deposition of lignin-like compounds in the cell wall, the production of reactive oxygen species (ROS) and the activation of signalling cascades that modulate

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