Novel low-nitrogen stress-responsive long non-coding RNAs (lncRNA) in barley landrace B968 (Liuzhutouzidamai) at seedling stage

Zhiwei Chen,Panpan Jiang,Chenghong Liu,Wan Zhang,Ruiju Lu,Qi Jiang,Nigel G Halford,Jianhua Huang

doi:10.1186/s12870-020-02350-2

Abstract

BackgroundReducing the dependence of crop production on chemical fertilizer with its associated costs, carbon footprint and other environmental problems is a challenge for agriculture. New solutions are required to solve this problem, and crop breeding for high nitrogen use efficiency or tolerance of low nitrogen availability has been widely considered to be a promising approach. However, the molecular mechanisms of high nitrogen use efficiency or low-nitrogen tolerance in crop plants are still to be elucidated, including the role of long non-coding RNAs (lncRNAs).ResultsIn this study, we identified 498 lncRNAs in barley (Hordeum vulgare) landrace B968 (Liuzhutouzidamai), of which 487 were novel, and characterised 56 that were responsive to low-nitrogen stress. For functional analysis of differentially-expressed lncRNAs, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of co-expressed and co-located protein-coding genes were analyzed, and interactions with annotated co-expressed protein coding genes or micro RNAs (miRNAs) were further predicted. Target mimicry prediction between differentially-expressed lncRNAs and miRNAs identified 40 putative target mimics of lncRNAs and 58 target miRNAs. Six differentially-expressed lncRNAs were further validated by qPCR, and one in particular showed consistent differential expression using both techniques. Expression levels of most of the lncRNAs were found to be very low, and this may be the reason for the apparent inconsistency between RNA-seq and qPCR data.ConclusionsThe analysis of lncRNAs that are differentially-expressed under low-nitrogen stress, as well as their co-expressed or co-located protein coding genes and target mimics, could elucidate complex and hitherto uncharacterised mechanisms involved in the adaptation to low-nitrogen stress in barley and other crop plants.

Highlights

Reducing the dependence of crop production on chemical fertilizer with its associated costs, carbon footprint and other environmental problems is a challenge for agriculture
Identification and characterization of Long non-coding RNA (lncRNA) Shoot samples of barley landrace B968 grown under normal nitrogen (N) supply and low-nitrogen stress conditions were used for cDNA library construction and RNA-seq analysis, with two biological replicates for each sample
498 unique lncRNAs were identified in the RNA-seq data, of which 487 were novel, including 460

Summary

Introduction

Reducing the dependence of crop production on chemical fertilizer with its associated costs, carbon footprint and other environmental problems is a challenge for agriculture. New solutions are required to solve this problem, and crop breeding for high nitrogen use efficiency or tolerance of low nitrogen availability has been widely considered to be a promising approach. The concept of nitrogen use efficiency was proposed as early as the 1980s [6], the availability and low cost of chemical fertilizer, together with the focus on dwarfing/semi-dwarfing genes in crop breeding, meant that there was little progress in improving this important trait [2]. As chemical fertilizer becomes more expensive and its carbon footprint and environmental cost become increasingly unacceptable, more researchers are trying to address this and provide new solutions for improving nitrogen use efficiency of crops by conducting lownitrogen tolerance studies [8,9,10]

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