Project description:we monitored the responsive changes of rice genes at 0 and 6 hours across Xoo pathotype GIV infection in Nipponbare (NIP), ostopbp1c mutant and OsTOPBP1C-overexpressor by RNA sequencing. These findings provide new insights for directly identifying iTALEs-targeted resistance gene and the regulatory roles of OsTOPBP1C in rice-Xoo interactions.
Project description:This study conducts small RNA sequencing (sRNA-seq) on panicles from wild-type rice and the ddm1a/1b double mutant to identify DDM1-regulated sRNA loci in genome-wide scale.
Project description:Cleistogamy is a useful agronomic trait to prevent gene flow in transgenic crops and to maintain genetic purity in autogamous crops including rice. Previously, we isolated a natural cleistogamous rice mutant, lodiculeless spikelet (ld). Map-based cloning approach identified about 4 kb deletion spanning two microRNAs, the entire MIR806a precursor and upstream of MIR172b precursor, in the ld locus. CRISPR/Cas9-mediated transgenic approach validated that mutations of MIR172b, not MIR806a, was responsible for the cleistogamy phenotype. Small RNA sequencing revealed that the expression of miR172b was almost completely reduced in the ld mutants. Quantitative RT-PCR analysis indicated that expression of AP2 target genes of miR172b was not changed in the ld mutants. Finally, we discussed possible regulatory mechanisms on how the defect of MIR172b causes cleistogamy in rice. This is the first report that mutation of a MIR gene causes cleistogamy in rice.
Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice.
Project description:We conducted a global genomic analysis on the top6a3 mutant leaves by using an Illumina-type RNA sequencing We firstly conducted a global transcription analysis in rice leaves after the γ-irradiation treatment.
Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
Project description:Rice grains are rich in starch but are deficient in proteins containing essential amino acids such as lysine and threonine. Therefore, efforts have been made to improve the nutritional value of rice by overexpressing the genes involved in lysine biosynthesis and/or suppression of lysine catabolism that led to the increased protein content in rice grains. Despite the economic and nutritional benefits rice, the protein accumulation mechanisms are largely elusive. Therefore, to explore the comprehensive proteome profiles, three different parts of rice grains including embryo, endosperm, bran were harvested from weedy rice cultivars (cv. Dharial) and its EMS mutant (DM) having 9.3 and 14.8% of protein content in rice grains, respectively. Here, we utilized a label-free quantitative proteomic analysis and this approach led to the identification of total 5,821 proteins. Of these, 322, 723, and 550 proteins revealed significant differences in their abundance in rice embryo, endosperm, and bran, respectively. Functional classification of identified proteins revealed that enrichment of proteins associated with nitrogen compound biosynthesis and transport, intracellular transport, localization, protein/amino acid synthesis, and photosynthesis, among others were observed in endosperm and bran of high protein mutant rice cultivar. Taken together, the current study uncovers the proteome changes and highlight the various functions of metabolic pathways associated with protein accumulation in rice.
Project description:In this study, we aim to generate genome-scale DNA methylation profiles at single-base resolution in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. Using high-throughput whole genome bisulfite Sequencing, we generated DNA methylation maps covering the vast majority of cytosines in the rice genome. More than 152 million high quality reads were obtained for each tissue sample using Illumina platform. We discovered extensive DNA methylation in rice cultivars, identified the context and level of methylation at each site.Numerous differentially methylated regions (DMRs) among different cultivars under control and stress conditions were identified and many of them were associated with differential gene expression. The high resolution methylome maps of different rice genotypes and differentially methylated regions will serve as reference for understanding the epigenetic regulation of stress responses in plants. Whole genome bisulfite sequencing of seven control/stressed samples from three rice cultivars (IR64, N22 and Pokkali)