Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice.
Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice.
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小RNA分析揭示同源四倍体水稻花粉和胚囊发育过程中的差异表达
DOI：
10.1186/s12864-017-3526-8
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发表时间：
2017-02-06
期刊：
影响因子：
4.4
通讯作者：
Liu X
中科院分区：
文献类型：
--
作者：
Li X;Shahid MQ;Xia J;Lu Z;Fang N;Wang L;Wu J;Chen Z;Liu X
花粉和胚囊部分不育是同源四倍体水稻育性低下的两个主要原因。我们之前的研究表明，小 RNA 的变化可能与同源四倍体水稻的花粉育性有关。然而，关于同源四倍体水稻中小RNA对花粉和胚囊发育的比较分析的知识仍然未知。在本研究中，采用WE-CLSM（整体伊红B染色共聚焦激光扫描显微镜）和高通量测序技术来检查细胞学变异，并分析同源四倍体水稻与二倍体水稻相比花粉和胚囊发育过程中小RNA的变化。在同源四倍体水稻花粉和胚囊发育过程中，分别检测到 321 个和 368 个差异表达 miRNA（DEM）。对与胚囊和花粉发育相关的 DEM 靶点进行 Gene Ontology 富集分析，揭示了胚囊发育过程中细胞分化和信号转导等 30 个突出功能基因类，而同源四倍体水稻花粉发育过程中仅检测到花发育和转录因子活性等 7 个突出功能基因类。 39 DEM 的表达水平揭示了与减数分裂相关基因的相互作用，但在花粉和胚囊发育过程中却表现出相反的表达模式。其中，osa-miR1436_L + 3_1ss5CT和osa-miR167h-3p与雌性减数分裂相关，osa-miR159a.1和osa-MIR159a-p5与雄性减数分裂相关。 21 nt-phasiRNA 在花粉和胚囊发育过程中均被检测到，而 24 nt-phasiRNA 仅在花粉发育过程中被发现，与二倍体水稻相比，其在同源四倍体中表现出下调，且其时空表达模式与 osa-miR2275d 相似。 24 nt TEs-siRNA 在胚囊中上调，但在花粉发育中下调。上述结果不仅提供了同源四倍体水稻花粉和胚囊发育的四个标志性阶段中小RNA的变化，而且还鉴定了同源四倍体水稻中特异性表达的miRNA，特别是减数分裂相关的miRNA、花粉特异性24nt-phasiRNA和TEs-siRNA。总之，这些发现为理解花粉和胚囊发育过程中多倍体对小RNA表达模式的影响奠定了基础，这可能导致同源四倍体水稻的不同异常。本文的在线版本 (doi:10.1186/s12864-017-3526-8) 包含补充材料，可供授权用户使用。
Partial pollen and embryo sac sterilities are the two main reasons for low fertility in autotetraploid rice. Our previous study revealed that small RNAs changes may associate with pollen fertility in autotetraploid rice. However, knowledge on comparative analysis between the development of pollen and embryo sac by small RNAs in autotetraploid rice is still unknown. In the present study, WE-CLSM (whole-mount eosin B-staining confocal laser scanning microscopy) and high-throughput sequencing technology was employed to examine the cytological variations and to analyze small RNAs changes during pollen and embryo sac development in autotetraploid rice compared with its diploid counterpart. A total of 321 and 368 differentially expressed miRNAs (DEM) were detected during pollen and embryo sac development in autotetraploid rice, respectively. Gene Ontology enrichment analysis on the targets of DEM associated with embryo sac and pollen development revealed 30 prominent functional gene classes, such as cell differentiation and signal transduction during embryo sac development, while only 7 prominent functional gene classes, such as flower development and transcription factor activity, were detected during pollen development in autotetraploid rice. The expression levels of 39 DEM, which revealed interaction with meiosis-related genes, showed opposite expression patterns during pollen and embryo sac development. Of these DEM, osa-miR1436_L + 3_1ss5CT and osa-miR167h-3p were associated with the female meiosis, while osa-miR159a.1 and osa-MIR159a-p5 were related with the male meiosis. 21 nt-phasiRNAs were detected during both pollen and embryo sac development, while 24 nt-phasiRNAs were found only in pollen development, which displayed down-regulation in autotetraploid compared to diploid rice and their spatial-temporal expression patterns were similar to osa-miR2275d. 24 nt TEs-siRNAs were found to be up-regulated in embryo sac but down-regulated in pollen development. The above results not only provide the small RNAs changes during four landmark stages of pollen and embryo sac development in autotetraploid rice but also have identified specifically expressed miRNAs, especially meiosis-related miRNAs, pollen-specific-24 nt-phasiRNAs and TEs-siRNAs in autotetraploid rice. Together, these findings provide a foundation for understanding the effect of polyploidy on small RNAs expression patterns during pollen and embryo sac development that may lead to different abnormalities in autotetraploid rice. The online version of this article (doi:10.1186/s12864-017-3526-8) contains supplementary material, which is available to authorized users.