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Genome-wide gene expression of rice cultivar Gui-630 (Indica) X Taiwanjing (Japonica) and mutant lemmata (lem) panicle

ABSTRACT: The lem mutant was discovered in a doubled haploid (DH) line derived from the F1 of Gui-630 (Indica)xTaiwanjing (Japonica) by anther culture. The lem mutant did not affect other traits but caused all other floral organs (including palea, lodicule, stamen and carpel) to homeotically transform into lemma or lemma-like structures and caused floral meristem to be indeterminate, thus resulting in the mutant floret consisting of whorls of lemma and lemma-like organs. To identify the global gene expression changes mediated by LEM, we used 57K Affymetrix rice whole genome array to investigate the differences of genome-wide transcriptome between the young panicles of mutant lem versus WT samples during flower development stage. Keywords: rice (Oryza sativa L.),wild-type and lemmata mutant

ORGANISM(S): Oryza sativa

PROVIDER: GSE20522 | GEO | 2010/03/12

SECONDARY ACCESSION(S): PRJNA125251

REPOSITORIES: GEO

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Genome-wide gene expression of rice cultivar Gui-630 (Indica) X Taiwanjing (Japonica) and mutant lemmata (lem) panicle

Project description:The lem mutant was discovered in a doubled haploid (DH) line derived from the F1 of Gui-630 (Indica)xTaiwanjing (Japonica) by anther culture. The lem mutant did not affect other traits but caused all other floral organs (including palea, lodicule, stamen and carpel) to homeotically transform into lemma or lemma-like structures and caused floral meristem to be indeterminate, thus resulting in the mutant floret consisting of whorls of lemma and lemma-like organs. To identify the global gene expression changes mediated by LEM, we used 57K Affymetrix rice whole genome array to investigate the differences of genome-wide transcriptome between the young panicles of mutant lem versus WT samples during flower development stage. Keywords: rice (Oryza sativa L.),wild-type and lemmata mutant We generate gene expression profiles of rice cultivar Gui-630 (indica)x Taiwanjing (japonica) and mutant lemmata by using 57K Affymetrix rice whole genome array.

2010-03-23 | E-GEOD-20522 | biostudies-arrayexpress

Comparative transcriptional profiling of organs of the barley spike

2009-09-16 | GSE16754 | GEO

Gene expression in the barley spike during drought stress

2009-09-30 | GSE17669 | GEO

Transcription profiling of barley lemma, palea, awn and developing seed

Project description:The lemma, the palea and the awn of a barley spike are photosynthetic organs and supply the developing seed with carbohydrates. In addition, the lemma and the palea cover the seed and protect it from pathogens and insects. In this study, we compared gene expression among the lemma, the palea, the awn and the developing seed of barley at the grain-filling stage (Zadok scale 83) using the Barley1 Genome Array in order to identify genes that determine the primary function of these organs. Experiment Overall Design: Lemma, palea, awn and seed were collected at grain-filling stage (Zadok scale 83) to compare differences in gene expression. For each organ three biological replications were collected on three different dates. On each of the three dates, one replication of each organ was collected from plants grown in separate pots using a randomized complete block design (RCBD). In ths design, organ type was the treatment effect and date of sample collection (replication) was the block. To get enough tissue for RNA extraction, each replication for each organ was collected from four plants in the same pot. RNA from each replicate sample was hybridized to individual Barley1 GeneChips. Thus, for four organs with three replications (blocks), a total of 12 Barley1 GeneChips were used.

2009-09-25 | E-GEOD-16754 | biostudies-arrayexpress

Spatio-temporal gene expression of various tissues/organs throughout entire growth in rice

Project description:An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting. A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.

2011-01-13 | E-GEOD-21396 | biostudies-arrayexpress

Transcription profiling of barley lemma, palea, awn and seed from drought-stressed plants

Project description:The photosynthetic organs of the barley spike (lemma, palea and awn) are resistant to drought. This is a beneficial trait because they can sustain grain-filling when drought occurs at the reproductive stage. There is little information about gene expression in the spike organs under drought conditions. In this study, we compared gene expression in drought-stressed lemma, palea, awn and seed at the grain-filling stage using the Barley1 Genome Array in order to identify drought-regulated organ-specific genes. Experiment Overall Design: Barley plants were drough-stressed for 4 days at the grain-filling stage by withholding water. Lemma, palea, awn and seed were collected to determine gene expression during drought in each organ. For each organ three biological replications were collected on three different dates. On each of the three dates, one replication of each organ was collected from plants grown in separate pots using a randomized complete block design (RCBD). In ths design, organ type and drought treatment were treatment effects and date of sample collection (replication) was the block. To get enough tissue for RNA extraction, each replication for each organ was collected from four plants in the same pot. RNA from each replicate sample was hybridized to individual Barley1 GeneChips. Thus, for four organs with three replications (blocks) and two treatment levels, a total of 24 Barley1 GeneChips were used.

2009-10-10 | E-GEOD-17669 | biostudies-arrayexpress

MADS1-regulated lemma and awn development benefits barley yield

Project description:Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthates to promote grain fill. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, leading to increased grain size and weight. Cytological data indicated that MADS1 promotes grain growth by promoting cell proliferation, while multi-omics data revealed MADS1 target genes associated with cell cycle, phytohormone signaling, and developmental processes. We defined two direct targets of MADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants; and demonstrated that MADS1 interacts APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development. Notably, we found that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development to inform strategies for Triticeae crop improvement. Three replicates of barley tissues were collected for RNA extraction: lemma and awn from the central part of lemma and awn from WT and mads1 mutants for RNA-seq and RT-qPCR

2023-09-01 | GSE228410 | GEO

Analysis of representative organ specific genes and promoters of rice using 3â ORF oriented long oligomer microarray

Project description:The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3â² ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters. A total of 14 chips were used for microarray. Total RNAs were extracted from rice 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination. Experiments were duplicated.

2016-07-28 | E-GEOD-84903 | biostudies-arrayexpress

Analysis of representative organ specific genes and promoters of rice using 3’ ORF oriented long oligomer microarray

Project description:The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3′ ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters.

2016-07-28 | GSE84903 | GEO

Wheat spikelet LC-MSMS - iTRAQ-based quantitative proteome analysis reveals metabolic changes between a cleistogamous wheat mutant and its wild-type wheat counterpart

Project description:A novel wheat mutant, ZK001, characterized as cleistogamic and presumed to provide structural barriers for Fusarium head blight during the flowering stage, was created through static magnetic fields mutagenesis from YM18. The atrophied, thin and ineffective lodicules of ZK001 lost the ability to push the lemma and palea apart during the flowering stage. Compared to YM18, ZK001 exhibited lower Fusarium infection. comparative studies at the proteome level were employed between YM18 and ZK001. isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) were employed to characterize protein expression differences between YM18 and ZK001.

2019-05-14 | PXD010188 | Pride

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