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

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 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.

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

“…Advancements in RNA-sequencing have further expanded our understanding of N-responsive lncRNAs’ roles in N homeostasis in plants. Studies showed that changes in N supply altered the expression of lncRNAs in rice [ 38 ], Populus [ 133 ], barley [ 134 ], and maize [ 41 ]. A study on lncRNAs in the rice genome under nitrogen starvation revealed the role of two cis-NAT-lncRNAs, cis-NAT AMT1.1 and cis-NAT AMT1.2 , derived from the sense strand of AMT1 [ 38 ].…”

Novel insights into water-deficit-responsive mRNAs and lncRNAs during fiber development in Gossypium hirsutum

“…3 ), suggesting the high quality of transcriptomes. Only one lncRNA, LNC009310, showed a relatively low correlation between transcriptome and qPCR analysis ( r = 0.55), likely due to the low expression of lncRNAs [ 51 ].

Fig.

…”

Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants

“…Recently, another lncRNA, T5120 , was found to be modulated by both NLP7 and NRT1.1 to regulate N signaling and improve N use efficiency in Arabidopsis [ 126 ]. On the other hand, a genomewide survey of candidate N-responsive lncRNAs has been performed through deep sequencing in Populus [ 127 ], maize [ 128 ], and barley [ 129 ], while lncRNAs responsive to multiple nutrient stresses have also been explored by deep sequencing in Arabidopsis [ 130 ]. Such large-scale sequencing efforts not only demonstrated an interaction network among lncRNAs, miRNAs, and mRNAs, but also helped to pinpoint key lncRNAs responsible for nutrient stress response.…”