Expression data of young panicles from microspore mother cell to meiosis of rice
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PROVIDER: PRJNA181190 | ENA |
REPOSITORIES: ENA
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Project description:The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homolog of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and to identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq, bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast. We sequenced the transcriptome of young panicles of Osam1 mutant and wild-type rice.
2015-07-01 | E-GEOD-66469 | biostudies-arrayexpress
Project description:The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homolog of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and to identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq, bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast.
2015-07-01 | GSE66469 | GEO
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 71% (2.3 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops. To address whether RNase ZS1 involves in mRNA metabolism, whole-genome microarray was performed using RNA from young panicles of wild type (AnN and ZH11) and tms5 (AnS-1 and Os02g12290iL1) plants grown at permissive and restrictive temperatures.
2016-08-01 | E-GEOD-42367 | biostudies-arrayexpress
Project description:In order to systematically identify the possible regulatory roles of (long nocoding RNAs) lncRNAs and (circular RNAs) cirRNAs in the rice photo-thermosensitive genic male sterile (PTGMS) line that were involved in fertility transition, 18 RNA libraries from rice young panicles of the Wuxiang S sterile line rice (WXS (S)) and its fertile line rice (WXS (F)) at the pollen mother cell (PMC) formation stage (P2), the meiosis stage (P3), and the microspore formation stage (P4) were constructed, with three biological replicates for each condition. These libraries were sequenced using an Illumina Hiseq 2500 platform, and approximately 214.54 Gb clean reads were generated. we performed genome-wide identification and characterization of lncRNAs circRNAs using high-throughput strand-specific RNA sequencing (ssRNA-seq) technology and bioinformatics tools to investigate the expression profiles of circRNAs in the PTGMS rice line WXS and their potential roles in the fertility transition.A total of 3948 lncRNAs and 9994 circRNAs were indentifiled in WXS rice, and our findings clearly revealed that lnRNAs and circRNAs might be endogenous noncoding regulators of flower and pollen development in the PTGMS rice line.
2021-05-30 | GSE125608 | GEO
Project description:Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improving rice yields. The molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear, but in the recently developed TGMS-Co27 lines which is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1). UGPase protein accumulates in TGMS-Co27 florets at low temperatures and temperature-sensitive splicing is involved in its sterility transitions.However, details of the molecular mechanisms involved are unknown. we use microarrays to compare transcriptomic profiles during the meiosis-stage of flower development in TGMS-Co27 and wild-type (H1493) plants grown at high and low temperatures. The detected differences in expression profiles provide further understanding of the regulatory networks underlying flower development generally, identify genes involved in the TGMS process in TGMS-Co27 and may provide reference data for analyses of molecular mechanisms underlying sterility transitions in other PGMS/TGMS rice lines. Meiosis-stage inflorescences were used for this study because pollen mother cells (PMCs) of TGMS-Co27 plants begin to degenerate at this stage. Samples from H1493 grown at high temperature, TGMS-Co27 grown at high temperature, H1493 grown at low temperature and TGMS-Co27 grown at low temperature were harvested to compare the difference between fertile and sterile rice lines.
2015-04-28 | E-GEOD-56779 | biostudies-arrayexpress
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 71% (2.3 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops.
2016-08-01 | GSE42367 | GEO
Project description:Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improving rice yields. The molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear, but in the recently developed TGMS-Co27 lines which is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1). UGPase protein accumulates in TGMS-Co27 florets at low temperatures and temperature-sensitive splicing is involved in its sterility transitions.However, details of the molecular mechanisms involved are unknown. we use microarrays to compare transcriptomic profiles during the meiosis-stage of flower development in TGMS-Co27 and wild-type (H1493) plants grown at high and low temperatures. The detected differences in expression profiles provide further understanding of the regulatory networks underlying flower development generally, identify genes involved in the TGMS process in TGMS-Co27 and may provide reference data for analyses of molecular mechanisms underlying sterility transitions in other PGMS/TGMS rice lines.
2015-04-28 | GSE56779 | GEO
Project description:miRNAs can regulate target gene expression by mRNA cleavage. Rice degradome sequencing was employed to validate mRNA targets of rice miRNAs. Two rice samples, 3-week-old seedling and young panicles were included in the study.
2009-11-23 | E-GEOD-18248 | biostudies-arrayexpress
Project description:Transfer of genetic traits from wild or related species into cultivated rice is nowadays an important aim in rice breeding. Breeders use genetic crosses to introduce desirable genes from exotic germplasms into cultivated rice varieties. However, in many hybrids there is only a low level of pairing (if existing) and recombination at early meiosis between cultivated rice and wild relative chromosomes. With the objective of getting deeper into the knowledge of the proteins involved in early meiosis, when chromosomes associate correctly in pairs and recombine, the proteome of isolated rice meiocytes has been characterized by nLC-MS/MS at every stage of early meiosis (prophase I). Up to 1316 different proteins have been identified in rice isolated meiocytes in early meiosis, being 422 exclusively identified in early prophase I (leptotene, zygotene or pachytene). The classification of proteins in functional groups showed that 167 were related to chromatin structure and remodelling, nucleic acid binding, cell-cycle regulation and cytoskeleton. Moreover, the putative roles of sixteen proteins which have not been previously associated to meiosis or were not identified in rice before, are also discussed namely: seven proteins involved in chromosome structure and remodeling, five regulatory proteins (such as SKP1 (OSK), a putative CDK2 like efector), a protein with RNA recognition motifs, a neddylation-related protein, and two microtubule-related proteins. Revealing the proteins involved in early meiotic processes could provide a valuable tool kit to manipulate chromosome associations during meiosis in rice breeding programs.
2014-08-13 | PXD001058 | Pride
Project description:Sequencing of sRNA and PARE libraries was performed for tissues collected from developmentally staged young panicles and anthers in rice variety Nongken 58
2018-05-09 | GSE108238 | GEO