Identification of microRNAs and their targets in inflorescences of an Ogura-type cytoplasmic male-sterile line and its maintainer fertile line of turnip (Brassica rapa ssp. rapifera) via high-throughput sequencing and degradome analysis
Identification of microRNAs and their targets in inflorescences of an Ogura-type cytoplasmic male-sterile line and its maintainer fertile line of turnip (Brassica rapa ssp. rapifera) via high-throughput sequencing and degradome analysis
复制标题
DOI：
10.1371/journal.pone.0236829
复制
发表时间：
2020-07
期刊：
影响因子：
3.7
通讯作者：
Sue Lin;S. Su;Libo Jin;Renyi Peng;Da Sun;Hao Ji;Youjian Yu;Jian Xu
中科院分区：
文献类型：
--
作者：
Sue Lin;S. Su;Libo Jin;Renyi Peng;Da Sun;Hao Ji;Youjian Yu;Jian Xu
细胞质雄性不育（Cytoplasmic male sterile， CMS）是被子植物中一个被广泛应用的性状，是由于细胞核与线粒体相互作用受到干扰而抑制了功能性花粉的产生。MicroRNAs （miRNAs）是一种小的非编码rna，在植物中作为转录或转录后基因沉默的调控分子。mirna的发现及其在CMS诱导中的可能意义为这一现象的复杂性提供了线索。此前，我们对芜菁（Brassica rapa ssp）的Ogura-CMS系进行了鉴定。花药发育明显受损，伴有小孢子产生缺陷和绒毡层过早退化。在本研究中，采用高通量测序对mirna进行全基因组研究。以芜菁Ogura-CMS系及其保持可育系（MF）为材料，构建了6个花序小RNA文库。共鉴定出120个与89个成熟mirna相对应的pre- mirna，包括87个转化mirna和33个新mirna。在这些mirna中，来自12个pre- mirna的10个差异表达成熟mirna的表达在Ogura-CMS系和MF系的花序之间发生了2倍以上的变化，其中8个mirna下调，2个mirna上调。采用茎环实时荧光定量PCR验证差异表达mirna的表达谱。此外，为了鉴定鉴定的mirna的靶标，进行了降解分析。共鉴定出25个mirna中的22个靶点和28个mirna中的17个靶点分别参与了萝卜Ogura-CMS和MF系的生殖发育。部分mirna与其靶标之间的表达模式呈负相关。其中一些已确定的靶点，如鳞片启动子结合样转录因子家族蛋白、生长素反应因子和含五肽重复序列的蛋白，先前已报道与植物生殖发育有关。综上所述，我们的研究结果有助于提高对mirna介导的调控途径的理解，这些途径可能参与了萝卜CMS的发生。
Cytoplasmic male sterility (CMS) is a widely used trait in angiosperms caused by perturbations in nucleus-mitochondrion interactions that suppress the production of functional pollen. MicroRNAs (miRNAs) are small non-coding RNAs that act as regulatory molecules of transcriptional or post-transcriptional gene silencing in plants. The discovery of miRNAs and their possible implications in CMS induction provides clues for the intricacies and complexity of this phenomenon. Previously, we characterized an Ogura-CMS line of turnip (Brassica rapa ssp. rapifera) that displays distinct impaired anther development with defective microspore production and premature tapetum degeneration. In the present study, high-throughput sequencing was employed for a genome-wide investigation of miRNAs. Six small RNA libraries of inflorescences collected from the Ogura-CMS line and its maintainer fertile (MF) line of turnip were constructed. A total of 120 pre-miRNAs corresponding to 89 mature miRNAs were identified, including 87 conversed miRNAs and 33 novel miRNAs. Among these miRNAs, the expression of 10 differentially expressed mature miRNAs originating from 12 pre-miRNAs was shown to have changed by more than two-fold between inflorescences of the Ogura-CMS line and inflorescences of the MF line, including 8 down- and 2 up-regulated miRNAs. The expression profiles of the differentially expressed miRNAs were confirmed by stem-loop quantitative real-time PCR. In addition, to identify the targets of the identified miRNAs, a degradome analysis was performed. A total of 22 targets of 25 miRNAs and 17 targets of 28 miRNAs were identified as being involved in the reproductive development for Ogura-CMS and MF lines of turnip, respectively. Negative correlations of expression patterns between partial miRNAs and their targets were detected. Some of these identified targets, such as squamosa promoter-binding-like transcription factor family proteins, auxin response factors and pentatricopeptide repeat-containing proteins, were previously reported to be involved in reproductive development in plants. Taken together, our results can help improve the understanding of miRNA-mediated regulatory pathways that might be involved in CMS occurrence in turnip.