Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb)

Tao Hu,Tao Wang,Liang Chen,Misganaw Wassie,Huawei Xu,Huiying Li

doi:10.1186/s12864-020-07103-x

Abstract

BackgroundTall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) and two types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing.ResultsA total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out of the three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound and associated with tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 28,927 potential target genes were discovered for all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways. In addition, bdi-miR167e-3p targets two kinase proteins EIF2AK4 and IRAK4, and osa-miR397a targets auxin response factor 5, which may be the significant miRNA-genes controllers in tillering development.ConclusionsThis is the first genome-wide miRNA profiles analysis to identify regulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.

Highlights

Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species
The difference in tiller number between the two tall fescue genotypes reached its maximum during this growth stage, which was the most appropriate period to collect for small RNAs (sRNAs) sequencing
The current study presented the genome-wide sRNA profiles of two tall fescue genotypes contrasting for tillering production rate and the tissue at both vegetative and tillering stages based on full-length transcriptome data

Summary

Introduction

Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. Tall fescue (Festuca arundinacea Schreb.) is a main cool-season grass species, widely applied as forage and turf for gardens, parks, residential and sports grounds [1, 2]. The low tiller density and size are the major factor limiting its turf performance and dry matter yield of forage. Tiller number is the most important agronomic trait for cool-season grass and is responsible for high shoot density and biomass production [3, 4]. The morphological observation of tillering development in monocot grass showed that tiller production is normally formed in two distinct developmental stages including axillary bud formation and its subsequent outgrowth or extension [4, 5]. It is well reported that tillering is a complex trait that can be regulated by multiple factors such as endogenous hormones level, water, fertilizer, light, temperature, genes, and miRNA [6, 7]

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