Project description:Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens [2011].
Project description:Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing).
Project description:A continuous gene expression profiling of roots was performed at regular interval during a 48-hr period in 2 different growth stages to characterize the diurnal and circadian gene expression profile of rice growth under natural field conditions. Root was collected at 2-hr intervals during a 48-hr period at 2 different growth stages corresponding to early and late vegetative stages. All samples were obtained from rice plants grown in the field during the 2008 cultivation season.
Project description:Purpose: The chloroplast DNA has not been primiarly analyzed in rice plants before. Hence, the objective of this study is to analyze and compare the differential methylation of chloroplast DNA in MR219 indica rice across different tissues and different developmental stages. Methods: We prepared a total of nine sodium bisulfite treated DNA libraries from three developing grain tissues, three leaf tissues at ripening stage and three leaf tissues at vegetative stage and sequenced them in Illumina Miseq platform. We performed quality trimming, alignment followed by methylation calling and differential methylation analysis using Trimmomatic v36, Bismark v16.3 and SeqMonk v40.0 on the sequencing data obtained. Statistical analysis was carried out in SeqMonk software and further validated in SPSS statistical software v22.2. Results: With an optimized data analysis workflow, we mapped around average of 26000 reads to chloroplast genome. Differential CpG and CHG methylation in SeqMonk v40.0 revealed that MR219 chloroplast DNA is differentially methylated in grain and leaf tissues and across vegetative stage and ripening stage in the leaf tissues. Chloroplast DNA from leaf at ripening stage was most methylated, followed by grain tissue and lastly leaf tissue from vegetative stage. Conclusions: Overall, it can be concluded that the organellar DNA in MR219 rice are differentially methylated at different tissues and across different developmental stages. The chloroplast DNA was most methylated in the leaf at ripening stage, followed by grain at ripening stage and leaf at vegetative stage. The functional significance of the differential methylation observed in this study needs to be investigated.
