Long non-coding RNAs (lncRNAs) play an important function in plant growth and development as well as response to stresses. However, little information was known in foxtail millet; no study was reported on lncRNAs in plant response to herbicide treatment. In this study, by using deep sequencing and advanced bioinformatic analysis, a total of 2547 lncRNAs were identified, including 787 known and 1760 novel lncRNAs. These lncRNAs are distributed across all 9 chromosomes, and the majority were located in the intergenic region with 1–2 exons. These lncRNAs were differentially expressed between different genotypes under different herbicide treatments. lncRNAs regulate plant growth and development as well as response to herbicide treatments through targeting protein-coding genes that directly relate to chemical metabolism and defense system. Multiple potential target genes and lncRNA-mRNA-miRNA gene networks were discovered. These results elucidate the potential roles of lncRNAs in plant response to herbicides.

长链非编码 RNA (lncRNAs) 在植物生长发育以及胁迫响应中发挥重要作用。然而，关于谷子的信息知之甚少。没有关于 lncRNA 在植物对除草剂处理的反应中的研究报告。本研究通过深度测序和先进的生物信息学分析，共鉴定出 2547 条 lncRNA，其中已知 787 条 lncRNA 和 1760 条新型 lncRNA。这些 lncRNA 分布在所有 9 条染色体上，大多数位于具有 1-2 个外显子的基因间区域。这些 lncRNA 在不同除草剂处理下的不同基因型之间差异表达。lncRNAs通过靶向与化学代谢和防御系统直接相关的蛋白质编码基因来调节植物生长和发育以及对除草剂处理的反应。发现了多个潜在的靶基因和lncRNA-mRNA-miRNA基因网络。这些结果阐明了 lncRNA 在植物对除草剂反应中的潜在作用。