State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
BMC Plant Biol. 2020 Jun 29;20(1):300. doi: 10.1186/s12870-020-02508-y.
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 BCF 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.
远缘杂交是在水稻中创造种间遗传变异和培育新品种的重要途径。已经构建了大量回交导入系（BIL）来解决水稻中的科学问题。然而，关于栽培稻、野生稻及其 BIL 后代中关键调控因子 lncRNA 的研究报道甚少。
本研究利用高通量 RNA 测序技术，探讨了 O. sativa、O. longistaminata及其三个 BCF 后代中 lncRNA 的功能特征和差异。共筛选出 1254 个 lncRNA，后代与 O. sativa 之间差异表达 lncRNA 的数量明显少于后代与 O. longistaminata 之间差异表达 lncRNA 的数量。一些 lncRNA 调控一个以上的 mRNA，89.5%的 lncRNA 通过顺式作用调控靶基因的表达。共鉴定到 78 个 lncRNA 和 271 个 mRNA 被 280 个 miRNA 靶向，22 个 lncRNA 被预测为 20 个 microRNA 的前体。一些 miRNA 被发现靶向其自身潜在的前体 lncRNA。在所有三个后代中，超过 50%的 lncRNA 表现出亲本表达水平优势（ELD），并且大多数 lncRNA 表现出 ELD-O. sativa 而不是 ELD-O. longistaminata。进一步分析表明，lncRNA 可能调控植物激素相关基因的表达以及 O. sativa、O. longistaminata及其后代的适应性。
综上所述，上述结果为阐明 O. sativa、O. longistaminata及其 BIL 后代中 lncRNA 的功能特征和表达差异提供了有价值的线索，并扩展了我们对 lncRNA 在水稻中生物学功能的认识。
