Ghd7 is a central regulator for growth, development, adaptation and responses to biotic and abiotic stresses
ABSTRACT: Ghd7 regulates a range of functions in growth and development in response to environmental cues to maximize the reproductive success of the rice plant. We used microarrays to detail the regulated genes in OX-Ghd7HJ19 transgenic plants. To gain clues to downstream genes regulated by Ghd7, we performed a microarray analysis using Affimetrix rice gene chips. Young leaves in vegetative stage (35-days old) and developing panicles (0.1cm) from field-grown OX-Ghd7HJ19 transgenic and wild-type plants with two biological replicates were used to isolate RNA for chip analysis.
Project description:Illumina sequencing was employed to examine the expression profiles of rice anther miRNAs from the a non-pollen male sterile line Wuxiang S (WXS), one of photo-thermo sensitive genical male sterile (PTGMS) line rice, during in the fertility transition stage. A total of 493 known miRNAs and 273 novel miRNAs were identified during rice anther development. Based on the number of sequencing reads, a total of 26 miRNAs were discovered to be significant difference expression between WXS(S, Sterility) and WXS(F, Fertility), and the results were partially validated by qRT-PCR. Among these, 11 miRNAs were decreased and 15 miRNAs were increased in WXS(S) compared with WXS(F). The expression patterns for targets of osa-miR156a-j, osa-miR3879, osa-miR159c/d/e, osa-miR171a/c/e/i, osa-miR398b, osa-miR164d, osa-miR528 and osa-miR408 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. These targets have previously been reported to be related with pollen development and male sterility, suggesting that miRNAs might act as regulators of rice anthers. Furthermore, miRNA editing events were observed. The U-to-C and U-to-A editing phenomenon was validated by molecular cloning and sequencing. Examine small RNA profiles change of four tissues of the rice non-pollen male sterile line Wuxiang S under two different environments.
Project description:Transcriptional programs are important for the development of complex eukaryotic organisms. Suites of genes expressed with temporal and spatial controls by regulatory networks in response to environmental cues are the cornerstone for achieving the specification of morphology and physiology of the tissue or organ systems. Thus, an important issue of developmental biology is to define the subsets of expressed genes and their expression patterns that are related to the organ or tissue system. Rice is a model plant for cereal genome research. Although large amounts of data of whole genome expression have been generated in recent years in rice, the majority of the studies were designed to identify differentially expressed genes between controls and treatments with certain experimental conditions such as biotic, abiotic or light, or to investigate the comparative expression patterns between wild type and mutants of certain genes. Only in a few cases were the datasets designed for studying the transcriptomes of a limited number of organs and cell types. Thus, there is still insufficiency in the available datasets that would allow for the establishment of expression patterns for suits of genes during the developmental processes of rice. In this study, we collected 39 tissues/organs covering the life cycle of the rice from two indica varieties Minghui 63 and Zhenshan 97, and the Affymetrix GeneChip Rice Genome Array was used to investigate the transcriptomes of these organs. The objective was to develop a genomic resource of genome-wide dynamic transcriptome of the rice plant, which could be used as the reference gene expression map for rice and other cereals. Also, the dataset is used to identify the candidates of genes with potential functions in regulating the development of rice or breeding practice. Keywords: rice, expression profiling, life cycle, development, inflorescence To dissect the developmental transcriptomes of rice, a total of 39 tissues covering the entire tissue culture process and life cycle were sampled from two indica varieties Minghui 63 and Zhenshan 97. And the Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcriptomes. Two independent biological replicates were sampled from most tissues, except two seedling and three panicle tissues, for which three independent biological replicates each with two technical replicates were sampled, resulting in a dataset of 190 microarrays.
Project description:The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 31,439 rice genes was used to elucidate gene expression in leaf and panicles of non-transgenic and HMB4 over-expression line. The analyses show that transgenic rice induces early flowering due to an enhancement of stress response. A total of 20 chips were used for microarray. Total RNAs were extracted from rice leaf and panicle. Experiments were duplicated.
Project description:Analyses of QTLs for expression levels (eQTLs) of the genes reveal genetic relationship between expression variation and the regulator, thus unlocking the information for identifying the regulatory network. In this study, we used Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice flag leaf at heading date from 210 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In the study, we attempted to construct the regulatory network by identifying putative regulators and the respective targets using an eQTL guided co-expression analysis with a recombinant inbred line population of rice. The ability to reveal the regulatory architecture of the genes at the whole genome level by constructing the regulatory network is critical for understanding the biological processes and developmental programs of the organism. Here we conducted an eQTL guided function-related co-expression analysis for identifying the putative regulators and constructing gene regulatory network. The Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcript levels. one replicates were sampled from each RIL, three for parents, and three replicates for each parent resulting in a dataset of 216 microarrays.
Project description:Thermosensitive genic male sterile (TGMS) lines and photoperiod-sensitive genic male sterile (PGMS) lines have been successfully used in hybridization to improving rice yields. The molecular mechanisms underlying male sterility transitions in most PGMS/TGMS rice lines are unclear, but in the recently developed TGMS-Co27 lines which is based on co-suppression of a UDP-glucose pyrophosphorylase gene (Ugp1). UGPase protein accumulates in TGMS-Co27 florets at low temperatures and temperature-sensitive splicing is involved in its sterility transitions.However, details of the molecular mechanisms involved are unknown. we use microarrays to compare transcriptomic profiles during the meiosis-stage of flower development in TGMS-Co27 and wild-type (H1493) plants grown at high and low temperatures. The detected differences in expression profiles provide further understanding of the regulatory networks underlying flower development generally, identify genes involved in the TGMS process in TGMS-Co27 and may provide reference data for analyses of molecular mechanisms underlying sterility transitions in other PGMS/TGMS rice lines. Meiosis-stage inflorescences were used for this study because pollen mother cells (PMCs) of TGMS-Co27 plants begin to degenerate at this stage. Samples from H1493 grown at high temperature, TGMS-Co27 grown at high temperature, H1493 grown at low temperature and TGMS-Co27 grown at low temperature were harvested to compare the difference between fertile and sterile rice lines.
Project description:Purpose: The goal of this study is to identify small non-conding RNAs which are involved in rice resistance to Xoo. Methods: Rice leaves were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). And then, total RNA was extracted to be sequenced using Illumina GAIIx. Results: Using an optimized data analysis workflow to count the expression level of small ncRNA, we found several differentially expressed small ncRNA which may be participated in the interaction between rice and Xoo. Conclusions: Small ncRNA have be found to function in a variety of biological processes. Our study here has showed that several candidate miRNA or siRNA may play a significant role in rice immunity. Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). Samples were collected before inoculation (ck) and at 2, 4, and 24 hours after PXO61 or mock inoculation from Rb49 and MDJ8. Leaf fragments approximately 2 cm in length that were immediately next to the inoculation site were collected.
Project description:Over expression of a transcription factor OsEREBP1 results in attenuation of disease symptoms upon infection with bacterial pathogen Xanthomonas oryzae pv. oryzae and tolerance to drought stress in transgenic rice plants. Microarray analysis was performed to identify genes regulated by the rice transcription factor OsERBP1. Four independent replicates of the experimental OsEREBP1-ox transgenic plants and the control non-transgenic Kitaake plants were grown under normal conditions.
Project description:OsSLAC7 in Oryza sativa L. is a homolog of Arabidopsis thaliana AtSLAC1, which contains conserved C4-Dicarboxylate transporter domain. Loss of its function caused cell membrane instability and serious leaf damage. We used Affymetrix Rice Genome Array to detail the differences in global gene expression between wildtype and the OsSLAC7 T-DNA insertion mutants, and to make clear the bioprocesses affected by the mutation. OsSLAC7(Os01g0385400) T-DNA insertion mutant and wildtype japonica rice cultivar Zhonghua11 were used for RNA extraction and hybridization on Affymetrix Rice Genome Array.