Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).

Yuanda Lv,Han Zhao,Feng Lin,Zhaohua Peng,Min Ge,Zhikai Liang,Tifu Zhang,Weicong Qi

doi:10.1186/s12864-016-2650-1

Yuanda Lv, Han Zhao + Show 6 more

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https://doi.org/10.1186/s12864-016-2650-1

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Abstract

BackgroundNitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expression.ResultsIn this study, we surveyed the intergenic/intronic lncRNAs in maize B73 leaves at the V7 stage under conditions of N-deficiency and N-sufficiency using ribosomal RNA depletion and ultra-deep total RNA sequencing approaches. By integration with mRNA expression profiles and physiological evaluations, 7245 lncRNAs and 637 nitrogen-responsive lncRNAs were identified that exhibited unique expression patterns. Co-expression network analysis showed that the nitrogen-responsive lncRNAs were enriched mainly in one of the three co-expressed modules. The genes in the enriched module are mainly involved in NADH dehydrogenase activity, oxidative phosphorylation and the nitrogen compounds metabolic process.ConclusionsWe identified a large number of lncRNAs in maize and illustrated their potential regulatory roles in response to N stress. The results lay the foundation for further in-depth understanding of the molecular mechanisms of lncRNAs’ role in response to nitrogen stresses.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2650-1) contains supplementary material, which is available to authorized users.

Highlights

Nitrogen (N) is an essential and often limiting nutrient to plant growth and development
Eighty-five differentially expressed N responsive long non-coding RNA (lncRNA) were further classified into three coexpressed modules, some of which are involved in metabolic processes associated with energy, oxidative phosphorylation, phosphorus and nitrogen compounds. These results suggest that lncRNAs might have unique roles in the response to nitrogen
The results suggested that seedlings of inbred line B73 were sensitive to the N stress and that the internal N content was altered by the N treatments (Fig. 1b)

Summary

Introduction

Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. As a major yielddetermining factor, N is a vital plant nutrient for plant growth and development. To reduce nitrogen pollution while increasing productivity, enabling crops to use nitrogen more efficiently is critical [13,14,15]. To achieve this goal, multiple quantitative trait loci (QTLs) in the related pathways have been identified [16,17,18,19] and differential gene expression studies in response to nitrogen resources and stresses have been reported [20,21,22,23,24].

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