Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing.
Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing.
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通过转录组和小 RNA 测序的关联分析深入了解棉花花药发育
DOI：
10.1186/s12870-018-1376-4
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发表时间：
2018-08-03
影响因子：
5.3
通讯作者：
Liu Z
中科院分区：
文献类型：
--
作者：
Chen J;Su P;Chen P;Li Q;Yuan X;Liu Z
研究背景植物花药发育是一个受基因精确控制的系统复杂的过程。这一过程的调控基因及其调控机制仍然难以捉摸。与许多作物中mRNA或miRNA的花药发育研究相比，针对棉花花药结合两种组学的关联分析尚未见报道。 结果本研究通过转录组关联分析和小RNA测序，研究了棉花花药发育的四个阶段：产孢细胞增殖期（SCP）、减数分裂期（MP）、小孢子释放期（MRP）和花粉成熟期（PM）的棉花花药发育的分子机制。分析表明，随着发育的进展，差异表达基因越来越多地被招募。功能基因的表达在不同发育阶段存在显着差异。与细胞周期、孕酮介导的卵母细胞成熟和减数分裂相关的基因主要在花药发育早期（SCP和MP）表达，与能量代谢、黄酮类生物合成、轴突引导和磷脂酶D信号通路相关的基因主要在花药发育后期（MRP和PM）表达富集。表达模式分析显示，MP中差异表达基因数量最多，且差异表达基因的表达谱显着增加，这表明MP在整个花药发育周期中的重要性。此外，miRNA靶向基因的预测和分析表明miRNA在花药发育中发挥着重要作用。 miRNAghr-miR393、Dt_chr12_6065和At_chr9_3080分别通过靶基因参与细胞周期、碳水化合物代谢和生长素合成代谢，从而实现对花药发育的调控。结论通过mRNA和miRNA的关联分析，我们的工作更好地了解了棉花花药不同发育阶段的优先表达基因和调控以及减数分裂期的重要性，并miRNA参与这一过程的精确调控，这对于阐明植物花药发育响应内外部环境的机制具有重要意义。
BackgroundPlant anther development is a systematic and complex process precisely controlled by genes. Regulation genes and their regulatory mechanisms for this process remain elusive. In contrast to numerous researches on anther development with respect to mRNAs or miRNAs in many crops, the association analysis combining both omics has not been reported on cotton anther.ResultsIn this study, the molecular mechanism of cotton anther development was investigated with the employment of association analysis of transcriptome and small RNA sequencing during the predefined four stages of cotton anther development, sporogenuous cell proliferation (SCP), meiotic phase (MP), microspore release period (MRP) and pollen maturity (PM). Analysis revealed that the differentially expressed genes are increasingly recruited along with the developmental progress. Expression of functional genes differed significantly among developmental stages. The genes related with cell cycle, progesterone-mediated oocyte maturation, and meiosis are predominantly expressed at the early stage of anther development (SCP and MP), and the expression of genes involved in energy metabolism, flavonoid biosynthesis, axon guidance and phospholipase D signaling pathways is mainly enriched at the late stage of anther development (MRP and PM). Analysis of expression patterns revealed that there was the largest number of differentially expressed genes in the MP and the expression profiles of differentially expressed genes were significantly increased, which implied the importance of MP in the entire anther development cycle. In addition, prediction and analysis of miRNA targeted genes suggested that miRNAs play important roles in anther development. The miRNAs ghr-miR393, Dt_chr12_6065 and At_chr9_3080 participated in cell cycle, carbohydrate metabolism and auxin anabolism through the target genes, respectively, to achieve the regulation of anther development.ConclusionsThrough the association analysis of mRNA and miRNA, our work gives a better understanding of the preferentially expressed genes and regulation in different developmental stages of cotton anther and the importance of meiotic phase, and also the involvement of miRNAs in precise regulation for this process, which would be valuable for clarifying the mechanism of plant anther development in response to internal and external environments.