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

A - Papers appearing in refereed journals

Chen, Z., Jiang, Q., Jiang, P., Zhang, W, Huang, J., Liu, C, Halford, N. G. and Lu, R. 2020. Novel low-nitrogen stress-responsive long non-coding RNAs (lncRNA) in barley landrace B968 (Liuzhutouzidamai) at seedling stage. BMC Plant Biology. 20, p. 142. https://doi.org/10.1186/s12870-020-02350-2

AuthorsChen, Z., Jiang, Q., Jiang, P., Zhang, W, Huang, J., Liu, C, Halford, N. G. and Lu, R.
Abstract

Background: 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. 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.

Results: In 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.

Conclusions: The analysis of lncRNAs that are differentially-expressed under low-nitrogen stress, as well as their coexpressed 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.

KeywordsLong non-coding RNAs; Barley; Hordeum vulgare; Low-nitrogen stress; Nitrogen use efficiency; RNA-seq
Year of Publication2020
JournalBMC Plant Biology
Journal citation20, p. 142
Digital Object Identifier (DOI)https://doi.org/10.1186/s12870-020-02350-2
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeDesigning Future Wheat (DFW) [ISPG]
Publisher's version
Output statusPublished
Publication dates
Online08 Apr 2020
PublisherBiomed Central Ltd
ISSN1471-2229

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