Long non-coding RNAs (lncRNAs) play important roles in response to various biotic and abiotic stresses. So far, systematic identification and characterization of lncRNAs have been reported in a few model plant species and major crops, but their roles in abiotic stress response have not yet been reported in common wild rice (Oryza rufipogon). Dongxiang wild rice (DXWR) possesses a high degree of drought resistance and has been well recognized as a precious genetic resource for drought resistant rice breeding. We presented the reference catalog of 1 655 novel lncRNA transcripts in DXWR using strand-specific RNA sequencing and bioinformatics approaches. Meanwhile, a total of 1 092 lncRNAs were determined as differentially expressed lncRNAs under drought stress. Quantitative real-time PCR results exhibited a high concordance with RNA sequencing data, which confirmed that the expression patterns of lncRNAs based on RNA sequencing were highly reliable. Furthermore, 8 711 transcripts were predicted as target genes of the differentially expressed lncRNAs. Functional annotation analysis based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases showed that the target genes were significantly enriched in cellular and metabolic processes, cell part, binding and plant hormone signal transduction, as well as many other terms related to abiotic stress resistance. These results expanded our understanding of lncRNA biology and provided candidate regulators for genetic improvement of drought resistance in rice cultivars.

长的非编码RNA（lncRNA）在应对各种生物和非生物胁迫时发挥着重要作用。到目前为止，已经在一些典型的植物物种和主要农作物中报告了lncRNA的系统鉴定和表征，但尚未在普通野生稻中报道它们在非生物胁迫响应中的作用（Oryza rufipogon）。东乡野生稻（DXWR）具有高度的抗旱性，已被公认为是抗旱水稻育种的宝贵遗传资源。我们使用链特异性RNA测序和生物信息学方法介绍了DXWR中1 655种新lncRNA转录本的参考目录。同时，在干旱胁迫下，总共确定了1092个lncRNAs为差异表达的lncRNAs。实时定量PCR结果显示与RNA测序数据高度一致，这证明基于RNA测序的lncRNA的表达模式是高度可靠的。此外，预测了8711个转录物作为差异表达的lncRNA的靶基因。基于基因本体论和《京都议定书》的基因和基因组百科全书的功能注释分析表明，目标基因在细胞和代谢过程，细胞部分，结合和植物激素信号转导以及许多其他与非生物胁迫抗性有关的术语上显着丰富。这些结果扩大了我们对lncRNA生物学的理解，并为水稻品种的抗旱性遗传改良提供了候选调控因子。