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Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition
BACKGROUND: Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6683460/ https://www.ncbi.nlm.nih.gov/pubmed/31382873 http://dx.doi.org/10.1186/s12870-019-1944-2 |
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author | Wang, Ying Xiong, Zeyang Li, Qian Sun, Yueyang Jin, Jing Chen, Hao Zou, Yu Huang, Xingguo Ding, Yi |
author_facet | Wang, Ying Xiong, Zeyang Li, Qian Sun, Yueyang Jin, Jing Chen, Hao Zou, Yu Huang, Xingguo Ding, Yi |
author_sort | Wang, Ying |
collection | PubMed |
description | BACKGROUND: Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (Oryza sativa L.), little is known about the biological roles of circRNAs in the fertility transition of the PTGMS rice line. RESULTS: In the present study, RNA-sequencing libraries were constructed from the young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at three development stages with three biological replicates. A total of 9994 circRNAs were obtained in WXS rice based on high-throughput strand-specific RNA sequencing and bioinformatic approaches, of which 5305 were known circRNAs and 4689 were novel in rice. And 14 of 16 randomly selected circRNAs were experimentally validated with divergent primers. Our results showed that 186 circRNAs were significantly differentially expressed in WXS (F) compared with WXS (S), of which 97, 87 and 60 circRNAs were differentially expressed at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3) and the microspore formation stage (P4), respectively. Fertility specific expression patterns of eight circRNAs were analysis by qRT-PCR. Gene ontology (GO) and KEGG pathway analysis of the parental genes of differentially expressed circRNAs (DECs) revealed that they mainly participated in various biological processes such as development, response to stimulation, hormonal regulation, and reproduction. Furthermore, 15 DECs were found to act as putative miRNA sponges to involved in fertility transition in PTGMS rice line. CONCLUSION: In the present study, the abundance and characteristics of circRNAs were investigated in the PTGMS rice line using bioinformatic approaches. Moreover, the expression patterns of circRNAs were different between WXS (F) and WXS (S). Our findings primarily revealed that circRNAs might be endogenous noncoding regulators of flower and pollen development, and were involved in the fertility transition in the PTGMS rice line, and guide the production and application of two-line hybrid rice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1944-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6683460 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-66834602019-08-09 Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition Wang, Ying Xiong, Zeyang Li, Qian Sun, Yueyang Jin, Jing Chen, Hao Zou, Yu Huang, Xingguo Ding, Yi BMC Plant Biol Research Article BACKGROUND: Circular RNAs (circRNAs) are known to play an important role in the regulation of gene expression in eukaryotes. Photo-thermosensitive genic male sterile (PTGMS) is a very important germplasm resource in two-line hybrid rice breeding. Although many circRNAs have been identified in rice (Oryza sativa L.), little is known about the biological roles of circRNAs in the fertility transition of the PTGMS rice line. RESULTS: In the present study, RNA-sequencing libraries were constructed from the young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at three development stages with three biological replicates. A total of 9994 circRNAs were obtained in WXS rice based on high-throughput strand-specific RNA sequencing and bioinformatic approaches, of which 5305 were known circRNAs and 4689 were novel in rice. And 14 of 16 randomly selected circRNAs were experimentally validated with divergent primers. Our results showed that 186 circRNAs were significantly differentially expressed in WXS (F) compared with WXS (S), of which 97, 87 and 60 circRNAs were differentially expressed at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3) and the microspore formation stage (P4), respectively. Fertility specific expression patterns of eight circRNAs were analysis by qRT-PCR. Gene ontology (GO) and KEGG pathway analysis of the parental genes of differentially expressed circRNAs (DECs) revealed that they mainly participated in various biological processes such as development, response to stimulation, hormonal regulation, and reproduction. Furthermore, 15 DECs were found to act as putative miRNA sponges to involved in fertility transition in PTGMS rice line. CONCLUSION: In the present study, the abundance and characteristics of circRNAs were investigated in the PTGMS rice line using bioinformatic approaches. Moreover, the expression patterns of circRNAs were different between WXS (F) and WXS (S). Our findings primarily revealed that circRNAs might be endogenous noncoding regulators of flower and pollen development, and were involved in the fertility transition in the PTGMS rice line, and guide the production and application of two-line hybrid rice. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1944-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-08-05 /pmc/articles/PMC6683460/ /pubmed/31382873 http://dx.doi.org/10.1186/s12870-019-1944-2 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Wang, Ying Xiong, Zeyang Li, Qian Sun, Yueyang Jin, Jing Chen, Hao Zou, Yu Huang, Xingguo Ding, Yi Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition |
title | Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition |
title_full | Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition |
title_fullStr | Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition |
title_full_unstemmed | Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition |
title_short | Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition |
title_sort | circular rna profiling of the rice photo-thermosensitive genic male sterile line wuxiang s reveals circrna involved in the fertility transition |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6683460/ https://www.ncbi.nlm.nih.gov/pubmed/31382873 http://dx.doi.org/10.1186/s12870-019-1944-2 |
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