Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues in rice. However, studies on the critical regulatory factor lncRNA in cultivated rice, wild rice and their BIL progenies were poorly reported. Here, high-throughput RNA sequencing technology was used to explore the functional characteristics and differences of lncRNAs in O. sativa, O. longistaminata and their three BC2F12 progenies. A total of 1254 lncRNAs were screened out, and the number of differentially expressed lncRNAs between progenies and O. sativa were significantly less than that between progenies and O. longistaminata. Some lncRNAs regulated more than one mRNA, and 89.5% of lncRNAs regulated the expression of target genes through cis-acting. A total of 78 lncRNAs and 271 mRNAs were targeted by 280 miRNAs, and 22 lncRNAs were predicted to be the precursor of 20 microRNAs. Some miRNAs were found to target their own potential precursor lncRNAs. Over 50% of lncRNAs showed parental expression level dominance (ELD) in all three progenies, and most lncRNAs showed ELD-O. sativa rather than ELD-O. longistaminata. Further analysis showed that lncRNAs might regulate the expression of plant hormone-related genes and the adaptability of O. sativa, O. longistaminata and their progenies. Taken together, the above results provided valuable clues for elucidating the functional features and expression differences of lncRNAs between O. sativa, O. longistaminata and their BIL progenies, and expanded our understanding about the biological functions of lncRNAs in rice.

中文翻译：

---

水稻回交渗入系（BC2F12）中lncRNA的全基因组鉴定和综合分析。

远距离杂交是在水稻中产生种间遗传变异和育种新品种的重要途径。针对水稻中的科学问题，已经构建了许多回交渗入系（BIL）。然而，关于栽培稻，野生稻及其BIL后代中关键调控因子lncRNA的研究报道较少。在这里，高通量RNA测序技术被用来探讨功能性特征和lncRNAs在O. sativa，O. longistaminata及其三个BC2F12后代中的差异。总共筛选出1254个lncRNA，子代和水稻之间差异表达的lncRNA的数量显着少于子代和长稻之间的差异。一些lncRNA调节不止一种mRNA，即89种。5％的lncRNA通过顺式作用调节靶基因的表达。280个miRNA靶向总共78个lncRNA和271个mRNA，并且预测22个lncRNA是20个microRNA的前体。发现一些miRNA靶向其自身潜在的前体lncRNA。在所有三个后代中，超过50％的lncRNA均显示出亲本表达水平优势（ELD），而大多数lncRNA均显示出ELD-0。苜蓿而不是ELD-O。longistaminata。进一步的分析表明，lncRNAs可能调控植物激素相关基因的表达以及稻，长叶稻及其后代的适应性。综上所述，以上结果为阐明O. sativa，O。longistaminata及其BIL后代之间lncRNAs的功能特征和表达差异提供了有价值的线索。