Project description:Oryza sativa Indica group IR29 (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 24 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.
Project description:Dissecting Molecular Mechanisms Underlying Salt Tolerance in Rice: A Comparative Transcriptional Profiling of the Contrasting Genotypes (IR29 vs. FL478)
Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.
Project description:The impact of global warming on weather patterns raises concerns for agriculture management. Using NGS technologies, we identified the miRNA profile that is expressed in rice cultivar grown at two different temperatures. We observed 118 and 100 miRNAs uniquely expressed at 35°C and 25°C respectively. Potential targets of these miRNAs have been identified. An interesting example, would be mir1863b which targets Os07g46670.3; a homologue of the ERD15 gene in Arabidopsis which is involved in dehydration stress response.
