Project description:We analyzed the transcriptomic profile of EFR:XA21:GFP rice lines treated with elf18 to identify genes differentially regulated during this response. We sequenced cDNA from EFR:XA21:GFP leaves treated with 500 nM elf18 for 0.5, 1, 3, 6, and 12 h. We also included untreated EFR:XA21:GFP and Kitaake as controls. Note: All samples in SRA were assigned the same sample accession (SRS843490). This is incorrect as there are different samples, hence â??Source Nameâ?? was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:The present study quantifies the transcriptomes of wild-type and transgenic Ubi::OsYHB rice seedlings (in the genetic background of Oryza sativa ssp. japonica CV Nipponbare) grown in the dark or under continous red light (Rc, at 50 µmol m-2 s-1) conditions. Overall design: WT (Nipponbare cultivar; Nip) and Ubi::OsYHB/Nip transgenic seedlings were grown at 28°C for 5 days in darkness or under continuous red light at 50 µmol m-2 s-1 (Rc50). Seedlings were harvested in subjective morning, immediately frozen in liquid nitrogen and strored at -80°C until RNA extraction. The expression of OsYHB is driven by the maize Ubiquitin promoter. Two biological replicates for each treatment. Two independent, genetically single-insertion, homozygous Ubi::OsYHB/Nip lines (#1 and # 9, with determined 41- and 23-fold overexpression levels of OsYHB in comparison to the wild-type control, respectively) were used. GeneChip 3' IVT Express Kit (Affymetrix) was used to synthesize and label aRNA.
Project description:Drought stress is the main abiotic factor affecting rice production. Rain-fed upland rice which is grown on unbounded fields and totally dependent on rainfall for moisture is more prone to drought stress compared to rice from other ecosystems. However, upland rice has adapted to this limited water condition, thus are more drought tolerant than rice from other ecosystems. We performed the first transcriptome sequencing of drought tolerant indica upland rice cultivar Kuku Belang to identify differentially expressed genes related to drought tolerance mechanism. Raw reads for non-treated and PEG-treated Oryza sativa subspecies indica cv. Kuku Belang were deposited in the NCBI SRA database with accession number SRP074520 (https://www.ncbi.nlm.nih.gov/sra?term=SRP074520).
Project description:As higher plants are sessile organisms, they are unable to move to more favorable places; thus, they have developed the ability to survive under potentially detrimental conditions. Ubiquitination is a crucial post-translational protein modification and participates in abiotic stress responses in higher plants. In this study, we identified and characterized OsDIRP1 (Oryza sativa Drought-Induced RING Protein 1), a nuclear-localized putative RING E3 ubiquitin (Ub) ligase in rice (Oryza sativa L.). OsDIRP1 expression was induced by drought, high salinity, and abscisic acid (ABA) treatment, but not by low temperature (4°C) stress, suggesting that OsDIRP1 is differentially regulated by different abiotic stresses. To investigate its possible role in abiotic stress responses, OsDIRP1-overexpressing transgenic rice plants (Ubi:OsDIRP1-sGFP) were generated, and their phenotypes were analyzed. The T4 Ubi:OsDIRP1-sGFP lines showed decreased tolerance to drought and salt stress as compared to wild-type rice plants. Moreover, Ubi:OsDIRP1-sGFP progeny were less sensitive to ABA than the wild-type during both germination and post-germination growth. In contrast, Ubi:OsDIRP1-sGFP plants exhibited markedly higher tolerance to prolonged cold (4°C) treatment. These results suggest that OsDIRP1 acts as a negative regulator during drought and salt stress, whereas it functions as a positive factor during the cold stress response in rice.
Project description:As an extremely early flowering cultivar, rice cultivar Kitaake is a suitable model system for molecular studies. Expression analyses revealed that transcript levels of the flowering repressor Ghd7 were decreased while those of its downstream genes, Ehd1, Hd3a, and RFT1, were increased. Sequencing the known flowering-regulator genes revealed mutations in Ghd7 and OsPRR37 that cause early translation termination and amino acid substitutions, respectively. Genetic analysis of F2 progeny from a cross between cv. Kitaake and cv. Dongjin indicated that those mutations additively contribute to the early-flowering phenotype in cv. Kitaake. Because the short life cycle facilitates genetics research, this study generated 10 000 T-DNA tagging lines and deduced 6758 flanking sequence tags (FSTs), in which 3122 were genic and 3636 were intergenic. Among the genic lines, 367 (11.8%) were inserted into new genes that were not previously tagged. Because the lines were generated by T-DNA that contained the promoterless GUS reporter gene, which had an intron with triple splicing donors/acceptors in the right border region, a high efficiency of GUS expression was shown in various organs. Sequencing of the GUS-positive lines demonstrated that the third splicing donor and the first splicing acceptor of the vector were extensively used. The FST data have now been released into the public domain for seed distribution and facilitation of rice research.
Project description:Oryza meridionalis is a potential source for improving Asian cultivated rice O. sativa via direct hybridization and backcrossing. However, hybrid sterility between O. sativa and O. meridionalis is the main barrier of reproduction hindering the transfer of favorable genes from O. meridionalis to O. sativa. To investigate the nature of hybrid sterility between O. sativa and O. meridionalis, three accessions of O. meridionalis were used as male parents to cross Dianjingyou 1, an O. sativa subsp. japonica cultivar following the backcross with the recurrent parent of Dianjingyou 1. Twenty pollen sterility NILs (BC6F1) were obtained and genotyped by using simple sequence repeat (SSR) markers distributed across the 12 rice chromosomes. The heterozygous markers were employed to genotype the corresponding segregation populations for mapping sterility genes. As a result, five novel loci for pollen sterility between O. sativa and O. meridionalis were identified and designated as S51(t), S52(t), S53(t), S54(t) and S55(t), respectively. The genetic behavior of five novel loci followed one-locus allelic interaction model. The disharmonious interaction between Asian cultivated rice allele and wild relative allele led to the partial or full abortion of male gametes for one parent allele in the heterozygotes. These results will be useful for elucidating the mechanism of interspecific hybrid sterility and further utilizing favorable genes from O. meridionalis for enhancement of rice breeding.