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). 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. 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.

中文翻译：

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大麦地方品种B968（Liuzhutouzidamai）苗期的新型低氮胁迫响应性长非编码RNA（lncRNA）

减少农作物对化肥的依赖及其相关的成本，碳足迹和其他环境问题，对农业构成挑战。需要新的解决方案来解决该问题，并且对于高氮利用效率或低氮利用率的耐受性的农作物育种已被广泛认为是有前途的方法。但是，尚需阐明作物中高氮利用效率或低氮耐受性的分子机制，包括长非编码RNA（lncRNA）的作用。在这项研究中，我们在大麦（Hordeum vulgare）地方品种B968（Liuzhutouzidamai）中鉴定了498个lncRNA，其中487个是新颖的，并鉴定了56个对低氮胁迫有响应的特征。为了对差异表达的lncRNA进行功能分析，分析了共同表达和共同定位的蛋白质编码基因的基因本体论（GO）和《京都基因与基因组百科全书》（KEGG）的富集，并进一步说明了与带注释的共同表达的蛋白质编码基因或微RNA（miRNA）的相互作用。预料到的。差异表达的lncRNA和miRNA之间的靶标拟态预测确定了40个推定的lncRNA靶标拟态和58个靶标miRNA。通过qPCR进一步验证了六种差异表达的lncRNA，其中一种特别显示了使用两种技术的一致差异表达。发现大多数lncRNA的表达水平很低，这可能是RNA-seq和qPCR数据之间明显不一致的原因。分析在低氮胁迫下差异表达的lncRNA，