ABSTRACT: A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).
Project description:Oryza sativa VIN3-LIKE2 (OsVIL2) acts as an epigenetic regulator together with Polycomb Repressive Complex2 (PRC2), which mediates trimethylation of histone H3 lysine 27 (H3K27me3) on target chromatin. T-DNA mutants of OsVIL2 displayed abnormal spikelet development. To understand function of OsVIL2 during spikelet development, RNA-sequencing was conducted in developing panicles of wild-type (WT) and osvil2 mutants.
Project description:In rice (Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops.The identification of different yield related QTLs facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. In the present study, We cloned and characterized a large-panicle QTL, and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an average of 37.62% increase in total grain yield per plant. trait loci (QTLs) and are derived from variation inherent in crops.
Project description:In rice (Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops.The identification of different yield related QTLs facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. In the present study, We cloned and characterized a large-panicle QTL, and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an average of 37.62% increase in total grain yield per plant. trait loci (QTLs) and are derived from variation inherent in crops. OsEBS-transgenic rice B10201 and B10301 and control Guichao2
Project description:To identify genes that are regulated by MeJA and drought, global expression profilings were performed on panicles from Ubi1:AtJMT, drought-treated NT, and untreated NT plants. The underlying assumption of this approach was that high levels of MeJA produced either by overexpression of AtJMT in the transgenic panicles or by drought treatment in the NT panicles regulates genes that are involved in spikelet and/or panicle development. Profiling was conducted using the Rice 3’-Tiling Microarray (GreenGene Biotech, Yongin, Korea). RNA samples from S1 panicles of Ubi1:AtJMT, drought-treated NT and untreated NT plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats.
Project description:Rice reproductive development is highly sensitive to high temperature stress. In rice flowering occurs over a period of at least 5 days. Heat stress alters the global gene expression dynamics in panicle especially during pollen development, anthesis and grain filling. Some of the rice genotypes like Nagina 22 show better spikelet fertility and grain filling compared to high yielding and popular rice cultivars like IR 64. We carried out microarray analysis of 8 days heat stressed panicles of Nagina22, heat and drought tolerant aus rice cultivar and IR64, a heat susceptible indica genotype along with unstressed samples of Nagina22 and IR64 so as to understand the transcriptome dynamics in these two genotypes under heat stress and to identify the genes important for governing heat stress tolerance in rice.
Project description:The biochemistry of C4 photosynthesis relies on a specific suite of leaf functional properties, often referred to as Kranz anatomy, where there is increased vein density and the proportion of bundle sheath cells surrounding the veins compared to C3 photosynthesizing species. From a suite of putative Kranz anatomy regulators, TML was identified. Loss of function tml mutations lead to the development of large lateral veins in positions normally occupied by smaller intermediate veins in both C3 and C4 species tested. In order to elucidate the role of TML in vein patterning, we set out to profile transcriptional changes that happen in the leaf primordia upon tml knock-out in the C4 species Zea mays.
Project description:Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia. In this study, we analysed the transcriptome associated with ligule formation using laser microdissection RNA-sequencing (LM-RNAseq). We quantified transcript accumulation in the PLB and adjacent pre-blade and pre-sheath regions of wild-type leaf primordia in order to identify candidate genes involved in proximal-distal patterning at the blade-sheath boundary. We also compared transcript accumulation in lg1-R mutants and wild-type siblings to identity genes acting downstream of LG1.
Project description:Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialised ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally-derived fringe. Recessive liguleless1 mutants lack ligules and auricles, and have upright leaves. We utilized laser-microdissection RNAseq to identify genes that are differentially expressed along discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation, and compared transcript accumulation in wild type and liguleless1 mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these ligule genes are also implicated to function during leaf initiation or lateral branching, and intersect multiple hormonal signalling pathways. We propose that genetic modules utilised in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.
Project description:Sequencing of sRNA and PARE libraries was performed for tissues collected from developmentally staged young panicles and anthers in rice variety Nongken 58
Project description:To gain mechanistic insights on OsMADS2 functions in rice spikelet development, we have employed global expression profilling to identify the genes regulated by OsMADS2. Transgenic rice panicle RNAs were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional OsMADS2 whereas upregulated genes will need OsMADS2 for their repression. Experiment Overall Design: Two independent biological RNA pools of dsRNAiOsMADS2 transgenic panicles were compared with a single wild type RNA pool in two different hybridizations. A third hybridization was performed with reciprocally dye-lebeled wild type RNA and one of the mutant RNA.