Shi Wan, Quan Mingyang, Du Qingzhang, Zhang Deqiang
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China.
National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China.
Front Plant Sci. 2017 Jun 15;8:1035. doi: 10.3389/fpls.2017.01035. eCollection 2017.
Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) gene with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and ( = 0.62), suggesting that the interaction of NERDL with its putative target might be involved in wood formation. We conducted association mapping in a natural population of (435 unrelated individuals) to evaluate genetic variation and the interaction of the lncRNA NERDL with . Using additive and dominant models, we identified 30 SNPs ( < 0.01) associated with five tree growth and wood property traits. Each SNP explained 3.90-8.57% of phenotypic variance, suggesting that NERDL and its putative target play a common role in wood formation. Epistasis analysis uncovered nine SNP-SNP association pairs between and , with an information gain of -7.55 to 2.16%, reflecting the strong interactions between NERDL and its putative target. This analysis provides a powerful method for deciphering the genetic interactions of lncRNAs with mRNA and dissecting the complex genetic network of quantitative traits in trees.
长链非编码RNA（lncRNAs）是植物生长发育的重要调控因子，但在多年生植物中，lncRNAs与mRNA的等位基因相互作用却鲜为人知。在此，我们分析了NERD（RDR2非依赖型DNA甲基化所需）基因与其假定调控因子lncRNA NERDL（NERD相关lncRNA）之间的相互作用，该lncRNA与该基因的启动子区域部分重叠。在八个组织中的表达分析表明，NERDL与[此处原文缺失相关基因名称]呈正相关（r = 0.62），这表明NERDL与其假定靶标的相互作用可能参与木材形成。我们在[此处原文缺失相关植物名称]（435个无亲缘关系的个体）的自然群体中进行关联作图，以评估lncRNA NERDL的遗传变异及其与[此处原文缺失相关基因名称]的相互作用。使用加性和显性模型，我们鉴定出30个与五个树木生长和木材性质性状相关的单核苷酸多态性（SNPs，P < 0.01）。每个SNP解释了3.90 - 8.57%的表型变异，这表明NERDL及其假定靶标在木材形成中发挥共同作用。上位性分析揭示了[此处原文缺失相关基因名称]之间九个SNP - SNP关联对，信息增益为 - 7.55%至2.16%，反映了NERDL与其假定靶标之间的强相互作用。该分析为破译lncRNAs与mRNA的遗传相互作用以及剖析树木数量性状的复杂遗传网络提供了一种有力方法。
