Analysis of small RNAs revealed differential expressions during pollen and embryo sac development in autotetraploid rice

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 an...

Full description

Saved in:
Bibliographic Details
Published in:BMC genomics 2017-02, Vol.18 (1), p.129-129, Article 129
Main Authors: Li, Xiang, Shahid, Muhammad Qasim, Xia, Juan, Lu, Zijun, Fang, Na, Wang, Lan, Wu, Jinwen, Chen, Zhixiong, Liu, Xiangdong
Format: Article
Language:English
Subjects:
Abnormalities
Analysis
Autotetraploid
Cell differentiation
Chromosomes
Comparative analysis
Confocal microscopy
Differentiation (biology)
Diploids
DNA methylation
Embryonic development
Embryos
Fertility
Gene expression
Gene Expression Profiling
Genetic aspects
Genetic transcription
Genomics
Meiosis
Meiosis - genetics
MicroRNA
MicroRNAs
MicroRNAs - genetics
Next-generation sequencing
Oryza - cytology
Oryza - genetics
Oryza - growth & development
Physiological aspects
Pollen
Pollen - genetics
Pollen - growth & development
Polyploidy
Principal components analysis
Rice
RNA, Small Interfering - genetics
RNA, Small Untranslated - genetics
Scanning microscopy
Seeds - genetics
Seeds - growth & development
Signal transduction
siRNA
Tetraploidy
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 abnormali
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-017-3526-8