Novel low-nitrogen stress-responsive long non-coding RNAs (lncRNA) in barley landrace B968 (Liuzhutouzidamai) at seedling stage
Novel low-nitrogen stress-responsive long non-coding RNAs (lncRNA) in barley landrace B968 (Liuzhutouzidamai) at seedling stage
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DOI：
10.1186/s12870-020-02350-2
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发表时间：
2020-04-06
影响因子：
5.3
通讯作者：
Lu, Ruiju
中科院分区：
文献类型：
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作者：
Chen, Zhiwei;Jiang, Qi;Lu, Ruiju
减少作物生产对化肥的依赖及其相关成本、碳足迹和其他环境问题是农业面临的一项挑战。需要新的解决方案来解决这一问题，并且作物育种以获得高氮利用效率或耐受低氮可用性已被广泛认为是一种有前途的方法。然而，作物高氮利用效率或耐低氮的分子机制仍有待阐明，包括长链非编码RNA（lncRNA）的作用。结果在大麦地方品种B 968中共鉴定出498个lncRNA，其中487个为新发现，56个为低氮胁迫响应的lncRNA。对于差异表达的lncRNA的功能分析，分析了共表达和共定位的蛋白质编码基因的基因本体论（GO）和京都基因和基因组百科全书（KEGG）富集，并进一步预测与注释的共表达蛋白质编码基因或微小RNA（miRNA）的相互作用。差异表达的lncRNA和miRNA之间的靶模拟预测鉴定了40种lncRNA和58种靶miRNA的推定靶模拟物。通过qPCR进一步验证了六种差异表达的lncRNA，特别是一种使用两种技术显示出一致的差异表达。发现大多数lncRNA的表达水平非常低，这可能是RNA-seq和qPCR数据之间明显不一致的原因。结论对低氮胁迫下差异表达的lncRNA及其共表达或共定位的蛋白质编码基因和靶标模拟物的分析，可以阐明大麦等作物适应低氮胁迫的复杂机制。
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.