Comparative Small RNA Analysis of Pollen Development in Autotetraploid and Diploid Rice

Abstract

MicroRNAs (miRNAs) play key roles in plant reproduction. However, knowledge on microRNAome analysis in autotetraploid rice is rather limited. Here, high-throughput sequencing technology was employed to analyze miRNAomes during pollen development in diploid and polyploid rice. A total of 172 differentially expressed miRNAs (DEM) were detected in autotetraploid rice compared to its diploid counterpart, and 57 miRNAs were specifically expressed in autotetraploid rice. Of the 172 DEM, 115 and 61 miRNAs exhibited up- and down-regulation, respectively. Gene Ontology analysis on the targets of up-regulated DEM showed that they were enriched in transport and membrane in pre-meiotic interphase, reproduction in meiosis, and nucleotide binding in single microspore stage. osa-miR5788 and osa-miR1432-5p_R+1 were up-regulated in meiosis and their targets revealed interaction with the meiosis-related genes, suggesting that they may involve in the genes regulation associated with the chromosome behavior. Abundant 24 nt siRNAs associated with transposable elements were found in autotetraploid rice during pollen development; however, they significantly declined in diploid rice, suggesting that 24 nt siRNAs may play a role in pollen development. These findings provide a foundation for understanding the effect of polyploidy on small RNA expression patterns during pollen development that cause pollen sterility in autotetraploid rice.

Combined Analysis of mRNAs and miRNAs to Identify Genes Related to Biological Characteristics of Autotetraploid Paulownia

“…In this study, we compared the length distribution of the sRNAs at the level of the reference genome and the previously reported transcriptome, and identified that the majority of sRNAs in these four libraries were 24 nt in length, followed by 21-nt sRNAs, and, at the previous transcriptome level, the majority of sRNAs were also 21-24 nt in length with a peak at 24 nt, followed by 21 nt, but the proportion of 21-nt sRNAs was lower in PF4 compared with PF2 [28,40]. Similar results have also been reported in other polyploid plants, such as raphanobrassica and rice [54,55]. It has been reported that 24-nt sRNAs can not only promote plant cell division and morphogenesis, but also target DNA methylation to regulate gene expression [56], suggesting that DNA methylation might be related to tetraploid Paulownia phenotypic variations.…”

Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis

“…Then we compared 38 DERs uniquely belonging to F 1 compared to its parents with previously identified differentially expressed miRNAs. We detected one miRNA, osa-miR5072_L-2_1ss3AG , which was down-regulated in meiosis between Taichung65-2x and Taichung65-4x during pollen development, and predicted a target, LOC_Os02g24960 , which was annotated as retrotransposon protein22.…”

“…miRNA, an important epigenetic factor, regulates the changes in transcriptomes associated with heterosis and fertility2122. Here, 38 miRNAs, uniquely belonging to F 1 compared to its parents, were identified, and they predicted 397 target genes.…”

“…Moreover, one miRNA, osa-miR5072_L-2_1ss3AG , which predicted a target, LOC_Os02g24960 , and annotated as retrotransposon protein, was detected in anther meiosis. Since DNA methylation variation of transposable elements are widespread and had a remarkable effect on gene expression in autotetraploid rice2232, the changes in rich retrotransposon, transposon and transposable elements may act as a “super-genome shock” response factor for creating adaptability and to produce high fertility and heterosis in neo-tetraploid hybrids.…”

“…miRNAs with P-value  < 0.05 and log 2 (fold change ratio) >1 were considered as differentially expressed miRNAs. Targeted genes of differentially expressed miRNAs were predicted by using psRNATarget (http://plantgrn.noble.org/psRNATarget/)2239.…”