Project description:We performed microarray analysis of WT and ago2-1 spikelets tissue before stage 5 to identify target genes We used microarrays to detail the global gene expression in tissues from normal rice young panicles .
Project description:OsMADS1 in rice is an important transcription factor in controlling flower development, not only in flower organs development, but also in floral meristem determinacy. Early flower panicle we used is a high expression stage for OsMADS1. We used microarrays to detail the global gene expression underlying functions of OsMADS1 in rice flower development. Rice panicles in length of 2 mm and 5-7 mm were collectecd for RNA extraction and hybridization on Affymetrix microarrays.Rice panicles in length of 2 mm is the stage for the initiation of inner floral organ development and in length of 5-7 mm is the late stages for floral organ development.Though comparing the microarray data of osmads1 and wild-type (control) at these two stages, we can find the functions of OsMADS1 in the early and late flower development stages. Three biological repeats were used. And totally 12 samples were analyzed.
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 71% (2.3 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops. To address whether RNase ZS1 involves in mRNA metabolism, whole-genome microarray was performed using RNA from young panicles of wild type (AnN and ZH11) and tms5 (AnS-1 and Os02g12290iL1) plants grown at permissive and restrictive temperatures.
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:miRNAs can regulate target gene expression by mRNA cleavage. Rice degradome sequencing was employed to validate mRNA targets of rice miRNAs. Two rice samples, 3-week-old seedling and young panicles were included in the study.
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:The young panicles 2 cm length were used for expression analysis in well watered control and drought stressed treatment. The panicle samples from biological replicates of six rice varieties were obtained in three independent experiments. The expression profiles were generated using Affymetrix rice genome arrays.
Project description:The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homolog of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and to identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq, bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast. We sequenced the transcriptome of young panicles of Osam1 mutant and wild-type rice.
Project description:The Polycomb Repressive Complex 2 (PRC2) represses the transcriptional activity of target genes through trimethylation of Lysine 27 of Histone H3. The functions of the plant PRC2 have been chiefly described in Arabidopsis but specific PRC2 functions in other plant species, especially the cereals, are still largely unknown. Here we utilize ChIP-seq data in the analysis of protein coding and non-coding RNAs in early WT panicles of rice.