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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase

ABSTRACT: This study compared the transcriptomes of maize anthers at both 1mm and 1.5mm lengths from male sterile mutants with either the am1-489 or am1-pra alleles as well as from fertile siblings of the mutant plants. Comparisons were done varying just the stage (1mm vs 1.5 mm), just the allele (am1-pra vs am1-489 at the same stage), and wild-type vs mutant (same stage and allele). Genes were categorized as On (expressed) or Off (not detected) and if both channels produced an intensity, the differential expression was determined. AM1 seems to be involved in establishing or stabilizing meiotic chromosomes and it had a profound impact on gene expression in the pollen mother cells during the maturation phase from 1.0 to 1.5 mm anther length. The two alleles shared some transcript changes but am1-489 showed a more dramatic loss (>3400) at 1.5mm than am1-pra. Most differentially expressed transcripts were allele-specific. KEYWORDS: male sterility, maize, microarray, meiosis Compared wild-type and male-sterile anthers from 2 ameiotic1 alleles at 2 stages of anther growth (1mm and 1.5mm)

ORGANISM(S): Zea mays

SUBMITTER: John Fernandes

PROVIDER: E-GEOD-30149 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase

Project description:This study compared the transcriptomes of maize anthers at both 1mm and 1.5mm lengths from male sterile mutants with either the am1-489 or am1-pra alleles as well as from fertile siblings of the mutant plants. Comparisons were done varying just the stage (1mm vs 1.5 mm), just the allele (am1-pra vs am1-489 at the same stage), and wild-type vs mutant (same stage and allele). Genes were categorized as On (expressed) or Off (not detected) and if both channels produced an intensity, the differential expression was determined. AM1 seems to be involved in establishing or stabilizing meiotic chromosomes and it had a profound impact on gene expression in the pollen mother cells during the maturation phase from 1.0 to 1.5 mm anther length. The two alleles shared some transcript changes but am1-489 showed a more dramatic loss (>3400) at 1.5mm than am1-pra. Most differentially expressed transcripts were allele-specific. KEYWORDS: male sterility, maize, microarray, meiosis

2011-07-15 | GSE30149 | GEO

Small RNA from W23 maize anthers at 1mm, 1.5mm, and 2mm

Project description:Illumina small RNA sequence data from maize anthers at 3 stages - 1mm, 1.5mm, and 2mm.

2011-07-28 | GSE30986 | GEO

Small RNA from W23 maize anthers at 1mm, 1.5mm, and 2mm

Project description:Illumina small RNA sequence data from maize anthers at 3 stages - 1mm, 1.5mm, and 2mm. Plants were field-grown and then anthers dissected and grouped according to length. RNA was extracted using TriReagent protocol. Each of the 3 sample types were sequenced separately.

2011-07-28 | E-GEOD-30986 | biostudies-arrayexpress

Transcriptome profiling of maize anthers using genetic ablation to analyze pre-meiotic and tapetal cell types

Project description:Agilent oligonucleotide arrays were used to profile gene expression in dissected maize anthers of 3 types of male-sterile plants and their fertile siblings at four stages of development: after anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I. The male-sterile mutants (ms23, msca, and mac1) lack a range of normal cell types resulting from a temporal progression of anther failure. By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types. Keywords: anther development, maize, male sterility

2008-09-16 | GSE12756 | GEO

Transcriptome profiling of maize anthers using genetic ablation to analyze pre-meiotic and tapetal cell types

2008-09-16 | E-GEOD-12756 | biostudies-arrayexpress

Zea mays

Project description:Small RNA from W23 maize anthers at 1mm, 1.5mm, and 2mm

| PRJNA146199 | ENA

Allele-specific RNA-seq of single pollen precursors

Project description:Single pollen precursors were isolated from maize anthers, covering 3 weeks of development from before meiosis through mature pollen. Starting material was staged by anther length and microscopy, and anther stages were densely sampled throughout pollen development. All samples were from an F1 hybrid between A188 and B73 inbred lines, and transcripts were associated with a specific parental allele when possible. In the "transcript_counts.csv" file, each sample is given 4 columns to separate the allele calls: '_g1' contains counts matching the B73 allele, '_g2' contains counts matching the A188 allele, 'ua' means unassigned (no SNPs were present in the transcript), and '_cf' means conflicting (the transcript had SNPs matching both alleles -- this is most likely sequencing error). Code to reproduce all figures from the main text of Nelms and Walbot (2022) can be found at https://doi.org/10.5281/zenodo.6620997

2021-10-26 | GSE175505 | GEO

Transcriptome analysis of multiple pre-meiotic anther stages and laser microdissected cell types in maize

2013-05-01 | GSE43982 | GEO

Transcriptome analysis of multiple pre-meiotic anther stages and laser microdissected cell types in maize

Project description:Transcriptomes from multiple pre-meiotic stages of wild type, mac1, and msca1 maize anthers were characterized by microarray hybridization. The goal was to characterize the developmental progression as the anther specifies five cell types and grows rapidly precedeing meiotic entry. The stages characterized were immature anther primordia (0.15 mm long in maize) containing just stem cells, through somatic and germinal cell fate specification (0.20 and 0.25 mm), mitotic proliferation (0.4 mm), and finally the birth of the middle layer and tapetum (0.7 mm). To obtain cell-type specific markers, at 0.7 mm we also compared whole anthers to collections of laser-microdissected anther cell types including the archesporial cells (pre-meiotic germinal cells), nutritive layers (middle layer and tapetum) and structural layers (endothecium and epidemis) of the anther lobe. keyword: anther development, maize, male-sterile Three loop designs covered the early stages (up to 0.7 mm) with two replicates for each comparison. The first loop had 0.2 mm long anthers and compared wild type versus mac1 mutant versus msca1 mutant in a three vertex loop design. The second loop had four vertices and compared 0.15 mm WT anther primordia, 0.25 mm WT anthers, 0.4 mm WT anthers and finally 0.4 mm mac1 mutant anthers. The third had 0.7 mm anthers in a three vertex loop with the nutritive layers (middle layer and tapetum) at one vertex, the germinal pre-meiotic cells at another vertex, and whole anthers at a third vertex. The whole anther samples were also, separately and outside of the loop, compared in four replicates to the structural layers (endothecium and epidermis).

2013-05-01 | E-GEOD-43982 | biostudies-arrayexpress

Hypoxia triggers meiotic fate acquisition in maize

Project description:Evidence from confocal microscopic reconstruction of maize anther development in fertile, mac1 (excess germ cells) and msca1 (no germ cells) flowers indicates that the male germ line is multiclonal and uses the MAC1 protein to organize the somatic niche. Furthermore, we identified redox status as a determinant of germ cell fate, defining a mechanism distinct from the animal germ cell lineage. Decreasing oxygen or H2O2 increases germ cell numbers, stimulates superficial germ cell formation, and rescues germinal differentiation in msca1 flowers. Conversly, oxidizing environments inhibit germ cell specification and cause ectopic differentiation in deeper tissues. We propose that hypoxia, arising naturally within growing anther tissue, acts as a positional cue to set germ cell fate. key words: anther development, maize, male-sterile Two replicates of laser microdissected pre-meiotic cells were compared to two replicates of whole anthers, which contains pre-meiotic cells and somatic cells, from the same developmental stage and individual wild type plants. In another experiment, laser microdissected pre-meiotic cells from wild type (mac1-heterozygous) anthers were compared to laser microdissected pre-meiotic cells from mac1 (mutant) anthers.

2012-07-04 | E-GEOD-39101 | biostudies-arrayexpress

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