Dataset Information

Transcriptomic Analysis Reveals New Insights into High-Temperature-Dependent Glume-Unclosing in an Elite Rice Male Sterile Line.

ABSTRACT: Glume-unclosing after anthesis is a widespread phenomenon in hybrid rice and also a maternal hereditary trait. The character of Glume-unclosing in rice male sterile lines also seriously influences germination rate and the commercial quality of hybrid rice seeds. We validated that the type of glume-unclosing after anthesis in the elite rice thermo-sensitive genic male sterile (TGMS) line RGD-7S was caused by high temperature. Transcriptomic sequencing of rice panicles was performed to explore the change of transcript profiles under four conditions: pre- and post-anthesis under high temperature (HRGD0 and HRGD1), and pre- and post-anthesis under low temperature (LRGD0 and LRGD1). We identified a total of 14,540 differentially expressed genes (DEGs) including some heat shock factors (HSFs) across the four samples. We found that more genes were up-regulated than down-regulated in the sample pair HRGD1vsHRGD0. These up-regulated genes were significantly enriched in the three biological processes of carbohydrate metabolism, response to water and cell wall macromolecular metabolism. Simultaneously, we also found that the HSF gene OsHsfB1 was specially up-regulated in HRGD1vsHRGD0. However, the down-regulated DEGs in LRGD1vsLRGD0 were remarkably clustered in the biological process of carbohydrate metabolism. This suggests that carbohydrate metabolism may play a key role in regulation of glume-unclosing under high temperature in RGD-7S. We also analyzed the expression pattern of genes enriched in carbohydrate metabolism and several HSF genes under different conditions and provide new insights into the cause of rice glume-unclosing.

SUBMITTER: Fu C

PROVIDER: S-EPMC5306291 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptomic Analysis Reveals New Insights into High-Temperature-Dependent Glume-Unclosing in an Elite Rice Male Sterile Line.

Fu Chongyun C Wang Feng F Liu Wuge W Liu Dilin D Li Jinhua J Zhu Manshan M Liao Yilong Y Liu Zhenrong Z Huang Huijun H Zeng Xueqin X Ma Xiaozhi X

Frontiers in plant science 20170214

Glume-unclosing after anthesis is a widespread phenomenon in hybrid rice and also a maternal hereditary trait. The character of Glume-unclosing in rice male sterile lines also seriously influences germination rate and the commercial quality of hybrid rice seeds. We validated that the type of glume-unclosing after anthesis in the elite rice thermo-sensitive genic male sterile (TGMS) line RGD-7S was caused by high temperature. Transcriptomic sequencing of rice panicles was performed to explore the ...[more]

PMID: 28261226

Similar Datasets

Project description:BackgroundPhoto-thermo-sensitive genic male sterile (PTGMS) rice (Oryza sativa L.) is usually considered two-line male sterile rice because of its dual-purpose in two-line hybrid rice system: under short days and low temperatures, it is fertile and used for self-propagation, but under long days and high temperatures, it is sterile and used for hybrid seed production. Therefore, photoperiod and temperature conditions are extremely important for the fertility transition of two-line male sterile rice. In recent years, there have been frequent occurrences of abnormally low-temperature (ALT) resulting in failure of two-line hybrid rice seed production. The daily average temperature (DAT) during ALT events is sometimes higher than the critical sterility-inducing temperature (CSIT) of two-line male sterile rice, of which the night temperature is lower than the CSIT. DAT has been traditionally used as the single indicator of pollen fertility transition, but it is unknown why the fertility of two-line male sterile rice in seed production restored fertility under ALT conditions.ResultsFor Hang93S (H93S), a newly released PTGMS line, we hypothesized fertility transition is determined mainly by the cumulative effective low temperature (ELT) and only a certain duration of low temperature is required every day during the fertility-sensitive period. This study simulated ALTs where the DAT was higher than the CSIT while some segments of night temperature were lower than the CSIT. The results showed H93S exhibited a fertility transition to varying degrees. Moreover, fertility was restored under simulated ALT conditions and pollen fertility increased with increasing cumulative ELT, indicating that the fertility transition was affected primarily by the cumulative ELT. Results also indicated that pollen fertility increased as the number of treatment days increased.ConclusionsThe fertility transition is caused mainly by the cumulative ELT. In two-line male sterile rice breeding, the effects of day length, ALT at night, and continuous response days should be considered together. The present study provides new insight into fertility transition so breeders can more effectively utilize the two-line male sterile rice, H93S, in breeding programs.

Project description:BackgroundCircular 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.ResultsIn 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.ConclusionIn 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.

Project description:Background: Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B.Results: We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background.Conclusion: We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching.

Dataset Information

Transcriptomic Analysis Reveals New Insights into High-Temperature-Dependent Glume-Unclosing in an Elite Rice Male Sterile Line.

Publications

Transcriptomic Analysis Reveals New Insights into High-Temperature-Dependent Glume-Unclosing in an Elite Rice Male Sterile Line.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets