RNA-seq of Oryza sativa L. Dongjin and Iksan 526 seeds at 20 days after heading
Ontology highlight
ABSTRACT: The resveratrol-producing rice (Oryza sativa L.) inbred line, Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in leaves and seeds. Especially, ultra-performance liquid chromatography (UPLC) analysis revealed that the biosynthesis of piceid reached peak levels at 20 days after heading (DAH) seeds. To investigate endogenous piceid biosynthesis genes (UGTs), total RNA samples of 20 DAH seeds was used for RNA-seq.
Project description:For gene expression analysis, RNA-seq was performed in seeds of Dongjin (white rice), Heukseol (black rice) and Jeokjinju (red rice) at 20 days after heading
Project description:The gene expression profiling analyses by DNA chip showed that the gene expression pattern of mice fed resveratrol-enriched rice DJ526 was very different from mice fed either resveratrol or Dongjin rice alone, respectively, modifying expression of genes related to aging regulation, cell differentiation, extracellular matrix, neurogenesis, or secretion. (1) Ctrl (The control mice fed a NFD in which the carbohydrate source was corn starch and sucrose), (2) RS (resveratrol mice fed a NFD in which the carbohydrate source was corn starch and sucrose except containing resveratrol), (3) DJ (Dongjin mice fed a NFD in which the corn starch and sucrose were replaced with Dongjin rice), and (4) DJ526 (DJ526 mice fed a NFD in which the corn starch and sucrose were replaced with the resveratrol-enriched rice DJ526)
Project description:Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight disease, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 protein groups. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase-1 in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type (WT). In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to WT. Mitochondrial localization of the selected arginase was further confirmed by fluorescent microscopy using GFP-tagged arginase. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of arginase in plant defense against Xoo.
Project description:Responses to drought in rice are regulated by transcription factor OsbZIP46 via ABA signaling. This work characterizes a protein MODD that negatively regulates OsbZIP46 activity and stability through HDAC-related chromatin remodeling and OsPUB70-mediated ubiquitination, respectively, to fine tune ABA signaling and drought resistance. Examination of mRNA levels in modd mutants and wild type plants under normal condition.
Project description:We created a triple loss-of-function/knockout mutant targeting three rice genes simultaneously. The three selected genes are as follows: OsADF1 (LOC_Os02g44470), OsADF6 (LOC_Os04g46910), and OsADF9 (LOC_Os07g30090). These three ADFs are strongly transcriptional expressed in the rice mature anthers (stages 13) and bi-/tricelluler pollen. The triple mutant of these OsADFs does not produce self-fertilizing seeds due to the short length of the pollen tube (male-sterile). This data is about mature anther transcriptome data about the triple mutant of OsADFs (ADFmT). We sampled mature anther for the analysis.
Project description:Seed germination is a complicated physiological process, during which structures of mitochondria and plastids are recovered, and metabolisms are re-activated (Han and Yang, 2015). It has been shown that metabolism reactivation is very important for rice germination (He et al., 2011b;Han et al., 2014a). It is still unknown if protein acetylation involved in and regulate these metabolisms during rice seed germination. To answer this question, we globally profiled the acetylome in rice embryos from the germinating seeds. A number of acetylated enzymes were identified. The results provide more information about the metabolism regulation in germinating seeds.
Project description:As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment. Whole plants of two rice cultivars Zhonghua11 (low temperature sensitive) and Hanfeng (low temperature tolerance) were treated at 14°C for 2 days during seed development stage. The plants without treatment serve as controls. Rice seeds were harvested for RNA extraction.
Project description:Gene expression profoling of developping endosperm at 3 and 6 days after flowering (DAH): Nipponbare vs NIL(TGW6) We used two rice varieties, NIL(TGW6) and Nipponbare.NIL(TGW6) is a nearly isogenic line containing the thousand grain weight qTGW6. For samples used three stages: 3 and 6 DAH endosperm in both Nipponbare and NIL(TGW6). Two dye swapped experiments were performed.
Project description:Carbon (C) and nitrogen (N) contents of grain-filling stage are keys item that determined the growth of rice, and also the quality of seed. Therefore, to elucidating the mechanism of C/N signaling in a seed is an important problem for crops whose seed is used as food like rice. The DNA microarray analysis with the rice seed which was performed the additional fertilizer at the time of heading, in order to clarify how C/N signal change of the rhizosphere in seed production stage affects a seed component on a gene expression level. Fertilization was supplied at the same time of plantation and performed middle fertilizing 37 days after germination. 400 mg of ammonium chloride (NH4 Cl) was supplied at the time of heading to the “ + NH4 Cl ” group. Rice seeds were selected from 6 plants for RNA extraction, and hybridization on Affymetrix microarrays. We sought to understand the change of gene expression by the additional fertilization.
Project description:To summarize the impact of high temperature on rice grain filling, we performed the rice 44k oligo microarray analysis. Total RNA was extracted from developing caryopses ripened under 33ËC/28ËC (high temperature) and 25ËC/20ËC (Control), and subjected to 44k oligo-DNA microarray with 3 biological replicates.