Project description:Setaria viridis (A10.1) circadian expression after light or temperature entrainment Overall design: Plants were grown under either 12 hour photocycles (12h light/12h dark) or 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C) then sampled every 2 hours for 48 hours under constant light and constant temperature conditions (32 deg C). Photocycle entrained samples are labeled LDHH-F, and thermocycle entrained samples are entrained LLHC-F.
Project description:Setaria viridis (green millet) is gaining popularity as a model C4 monocot due to its small size, rapid life cycle, and compact, sequenced genome. To analyze the structure and regulation of genes throughout development, the transcriptomes of 13 tissues at different stages of development were determined by RNA sequencing, and transcription start sites were mapped. Genes were identified that are differentially expressed in different developmental stages within the leaf, as well as in the apical meristem before and after the transition from vegetative to reproductive growth, and in panicles before and after anthesis. In a majority of genes, transcription initiated at the sequence YR within a narrow peak 20 – 40 nt downstream of a TATA box. Genes expressed in multiple tissues generally use the same transcription start site across all tissue types. Several introns were identified that increase gene expression. These results will increase understanding of plant development, improve the annotation of the Setaria genome, and provide tissue-specific or constitutive promoters for use in transgenic applications. Overall design: RNA was isolated from wild-type Setaria viridis and sequenced from a total of 13 different samples at various stages during development, with three biological replicates per sample. Some replicates were sequenced more than once (a/b/…) to generate sufficient reads.
Project description:RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence. Overall design: Inflorescence primordia were hand-dissected from bsl1 mutant and wild-type control Setaria plants at 15 Days After Sowing (DAS). Plants were grown together in a controlled growth chamber. Inflorescence primordia were pooled (~10 representative primordia per pool) into biological replicates (3 for wild-type and 2 for mutant). Transcriptomes were sequenced and compared for differentially expressed genes.
Project description:Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare in gene expression in the S. viridis crown between drought vs watered treatments. RNA from Lower region (crown) or Upper region (stem) of watered (W) or drought (D) treated Setaria plants were harvested at 6 or 9 days after sowing; there are 8 samples per biological repeat, 3 biological repeats.