Genome-wide small RNA profiling reveals tiller development in tall fescue ( Festuca arundinacea Schreb)
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RESEARCH ARTICLE
Open Access
Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb) Tao Hu1,2* , Tao Wang3, Huiying Li1,2, Misganaw Wassie1,2,4, Huawei Xu3 and Liang Chen1,2*
Abstract Background: 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. 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 highthroughput RNA sequencing. Results: A 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 “ubiquitinmediated 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. Conclusions: This 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. Keywords: MicroRNAs, Tiller development, Small RNA deep sequencing, Stem-loop qRT-PCR, Tall fescue
* Correspondence: [email protected]; [email protected] 1 CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430074, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Att
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