Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

Qi Wu,Xiaoyong Wu,Gang Zhao,Yan Wan,Dabing Xiang,Yiming Luo,Xue Bai,Liang Zou,Qiang Li,Changying Liu,Xueling Ye

doi:10.1186/s12864-021-07605-2

Qi Wu, Xiaoyong Wu + Show 9 more

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https://doi.org/10.1186/s12864-021-07605-2

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Abstract

BackgroundNight-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal.ResultsIn this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes.ConclusionsTogether, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

Highlights

Night-break (NB) has been proven to repress flowering of short-day plants (SDPs)
In long-day plants (LDPs) such as Arabidopsis (Arabidopsis thaliana) and wheat (Triticum aestivum), only when the day length exceeds a certain threshold, FLOWERING LOCUS T (FT) proteins are sufficient for flowering induction [9, 10]
In the present study, we investigated the effect of NB on quinoa flowering, and by performing strand-specific RNA sequencing (SS RNA-seq) of the plants grown under NB and SD, we identified the specific coding genes and Long-noncoding RNAs (lncRNAs) that may be involved in flowering regulation

Summary

Introduction

Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. The photoperiod pathway controls floral transition through a signal cascade involving circadian clock and florigen genes. In short-day plants (SDPs) such as rice (Oryza saltiva) and soybean (Glycine max), FT transcripts are more abundant when the night length longer than a certain threshold [7, 8]. NB responses are abolished in the phyB mutants of rice [14], phyA mutants of soybean [12] and the phyB and phyC mutants of wheat [13], indicating functional conservation and divergence of phytochromes across different plant species. The up-regulation of FT1 by NB in wheat is dependent on PHOTOPERIOD1 (PPD1), a homolog of PSEUDO RESPONSE REGULATOR 37 (PRR37) in rice, which is a core component of the circadian clock [13]. NB affects plant flowering by controlling different layers of regulators

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