GEO DataSets

(Submitter supplied) We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects. fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the impact of fzt mutation on miRNA abundance in seedling and tassel primordia. We also investigated the transcript abundance of potential target genes of miRNA that were impacted in fzt mutant by transcriptome profiling. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

26 Samples

Download data: TXT

(Submitter supplied) As a key member of the grass-specific subclade of argonaute proteins, AGO18b protein has been proposed to bind 24-nt meiotic phasiRNAs based on their co-expression in tapetal and meiotic cells. Here we show that expression of in maize tassels is strictly induced by developmental stages. Interestingly, reduced expression of AGO18b in both Mutator-mediated (ago18b::mum) and RNAi mutants leads to an increase in plant height and tassel length, suggesting its non-meiotic function as a negative regulator of SAM/IM maintenance. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL15463 GPL20156

18 Samples

Download data: XLSX

(Submitter supplied) S. reilianum triggered loss of organ and meristem identity, and loss of meristem determinacy in male and female inflorescences and flowers. Microarray analysis showed that these developmental changes were accompanied with transcriptional regulation of genes proposed to regulate floral organ and meristem identity, and meristem determinacy in maize.

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

6 Samples

Download data: CEL, CHP

(Submitter supplied) Here we report, that levels of the micronutrient boron are instrumental for meristem maintenance by integration into specific meristem maintenance pathways. We used RNA-seq analysis of the boron deficient maize mutant tassel-less1 to identify early molecular defects induced by boron deficiency in maize reproductive (tassel) meristems. RNA-seq results were independently verified through downstream in silico, double mutant, microscopy, proteomic, and molecular analyses.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

6 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15463 GPL9361

40 Samples

Download data: TXT

(Submitter supplied) RNA-seq was performed on 2-3mm WT and rel2-ref mutant maize tassels

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20156

6 Samples

Download data: TXT

(Submitter supplied) fasciated ear4 (fea4) is a semi-dwarfed mutant with fasciated ears and tassels, and greatly enlarged vegetative and inflorescence meristems. Chromatin Immunoprecipitation-sequencing (ChIP-seq) and expression profiling by RNA-seq suggest that fea4 is required to regulate the auxin response and leaf differentiation programs in the periphery of the meristem, suggesting a new mechanism of meristem size regulation that is spatially and mechanistically distinct from the CLV-WUS model.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15463 GPL19255

10 Samples

Download data: TXT

(Submitter supplied) RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.

Organism:

Setaria viridis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23621

5 Samples

Download data: TXT

(Submitter supplied) Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression (DGE) profiles using Illumina’s high-throughput sequencing technology and the newly-assembled B73 maize reference genome. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9141

7 Samples

Download data: GFF3, TXT

(Submitter supplied) Purpose: The goal of this study is to identify differentially expressed genes (DEGs) in immature ears between Barren inflorescence3 (Bif3) mutant and its wild-type siblings in maize. Methods: the 3-4 mm ear primordia of maize wild-type and Bif3 mutant were dissected from maize plant at the reproductive stage, and samples were snap freeze using liquid nitrogen. The total RNAs were prepared using RNeasy mini kit (Qiagen). more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

7 Samples

Download data: CSV, XLSX

(Submitter supplied) Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture. more...

Organism:

Setaria viridis

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL23621 GPL29001

26 Samples

Download data: RDATA, TXT, XLSX

(Submitter supplied) Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. more...

Organism:

Setaria viridis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23621

22 Samples

Download data: TXT

(Submitter supplied) RNA-seq was performed on 5-10mm maize tassels

Organism:

Zea mays

Type:

Other

Platform:

GPL9361

3 Samples

Download data

(Submitter supplied) RNA sequencing of the near-isogenic line mnd1.a in cv. Bowman background, compared to cv. Mesa and cv. Bowman Purpose: Expression analysis and variant calling.

Organism:

Hordeum vulgare

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22077

22 Samples

Download data: VCF, XLSX

(Submitter supplied) miRNAs play important roles in every aspect of plant development. Small RNA regulation confers sensitivity and robustness onto gene regulatory networks, and the morphogen-like readout of small RNA mobility gradients yields sharply delineated domains of target gene expression. However, how the spatiotemporal patterns of miRNA activity are attained is less well understood. We used the high-resolution maize shoot apex transcriptome atlas (Knauer et al., 2019) together with data from small RNA-Seq, PARE analysis, small RNA in-situ hybridization, and RNAseq of weak dcl1 mutant tissues to demonstrate that miRNA accumulation and function during development is regulated in a tiissue dependent manner at the transcriptional and post-transcriptional level.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17628 GPL15463

9 Samples

Download data: TXT

(Submitter supplied) This project is to generate and analyze the transcriptomes of bract primordium of maize, and to identify the genes, pathways and networks that suppress bract outgrowth in maize inflorescence.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

12 Samples

Download data: TXT