Small RNA from W23 maize anthers at 1mm, 1.5mm, and 2mm
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE30986 | GEO | 2011/07/28
SECONDARY ACCESSION(S): PRJNA146199
REPOSITORIES: GEO
Similar Datasets
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
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 Compared wild-type and male-sterile anthers from 2 ameiotic1 alleles at 2 stages of anther growth (1mm and 1.5mm)
2011-07-14 | E-GEOD-30149 | biostudies-arrayexpress
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
Project description:Small RNA from W23 maize anthers at 1mm, 1.5mm, and 2mm
| PRJNA146199 | ENA
Project description:Two-organism transcriptome profiling of infected maize anthers demonstrated that there are anther-specific gene expression programs for both the pathogen and the host. Two-dye, competitive microarray hybridizations were performed on Agilent oligo arrays. Confocal microscopy on other anthers demonstrated that U. maydis was in contact with all anther lobe cell types by 3 days post-infection and that the pathogen disrupted both host cell division and cell expansion patterns.
2013-03-21 | GSE43544 | GEO
Project description:Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed. Microarray transcript profiling demonstrates a more severe developmental disruption in ms23-ref than in ms32 anthers, which possess a different bHLH defect. RNA-seq and proteomics data together with yeast two-hybrid assays suggest that MS23 along with MS32, bHLH122, and bHLH51 act sequentially as either homo- or heterodimers to choreograph tapetal development. Among them, MS23 is the earliest-acting factor, upstream of bHLH51 and bHLH122, controlling tapetal specification and maturation. In contrast, MS32 is constitutive and independently regulated and is required later than MS23 in tapetal differentiation. We characterized a maize (Zea mays) mutant line, ms23-ref, which the tapetal cells lack a dense cytoplasm and are not Binucleate -- the two characteristics of normal TP during meiosis. The meiocytes in ms23-ref fail to progress beyond meiotic prophase I. By profiling the small RNA population in ms23 mutants, we investigated the impact of ms23 mutation on small RNAs abundance in 0.4 mm, 0.7 mm, 1.0 mm, 1.5 mm and 2.0 mm anther. We also investigated the transcript abundance that were impacted in ms23 mutant by transcriptome profiling. The result provides an avenue for future research to understand the genetic networks and protein interactions among ms23, important for tapetal development in maize anther.
2016-12-05 | GSE90849 | GEO
Project description:In this study we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. These are the RNA-seq datasets used in this study. We profiled changes in gene expression during normal maize ear and tassel development and in developing maize ear primordia upon genetic perturbation of the RAMOSA branching pathway. For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used. 10mm ears were collected and sectioned as follows from tip to base along the developmental gradient: tip 1mm sampled (tip; Inflorescence Meristem/Spikelet Pair Meristem), next 1mm discarded, next 1mm sampled (mid; Spikelet Meristem), next 2mm discarded, next 2 mm sampled (base; Floral Meristem), and immediately frozen in liquid nitrogen. Sections from ~30 sampled ears were pooled for each of 2 biological replicates to represent tip, mid, and base stages. Tassels were hand-dissected, measured, separated by stage: 1-2mm (stg1), 3-4mm (stg2), and 5-7mm (stg3), and immediately frozen in liquid N. For each stage, ~20-30 tassels were pooled for each of 2 biological replicates. For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm. Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage). First and second ear primordia were immediately hand-dissected, measured, and frozen in liquid nitrogen. For ra1, ra2 and ra3 mutants and wild-type controls, ears were pooled into two size classes: 1) 1mm class included a range of 0.7-1.5mm sized ears and nine ears were pooled for each of 2 biological replicates; 2) 2mm class included a range of 1.8-2.5mm sized ears and six ears were pooled for each of three biological replicates. Wild-type samples were proportional mixtures of heterozygote siblings segregating in ra1, ra2, and ra3 populations. Variability factors (e.g. ear size within class, ear rank on the plant, and time of collection) were distributed evenly across pooled samples.
2013-11-27 | E-GEOD-51047 | biostudies-arrayexpress
Project description:The maize spikelet contains two florets, each of which contains three anthers. Morphologically, the anthers in the upper and lower florets proceed through the same developmental program. To test for global differences in gene expression between these anthers and to identify genes that are coordinately regulated during development, RNA isolated from upper and lower floret anthers at six developmental stages was used to hybridize cDNA microarrays. Approximately 9% of the tested genes exhibited statistically significant differences in gene expression between anthers in the upper and lower florets. This suggests that several basic biological processes are differentially regulated between upper and lower floret anthers, including photosynthesis, translation, and metabolism. To identify genes that are coordinately regulated during anther development, cluster analyses were performed. A variety of patterns of gene expression were observed. Five genes involved in programmed cell death were up-regulated at the time the tapetum begins to degenerate (i.e., the early microspore stage). This finding strongly supports the hypothesis that tapetal degeneration occurs via programmed cell death. In addition, many genes involved in protein synthesis exhibited differential expression patterns during anther development. Each microarray slide was scanned multiple times. This approach led to the identification an additional 30 to 40% of statistically significant differences in gene expression as compared to a single-scan strategy. Keywords: time course
2006-07-21 | GSE3017 | GEO
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
Project description:The maize ocl4 mutants showed differing levels of male sterility, which seems correlating with the quantity of 21-nt phasiRNA remaining during pre-meiotic stage. In this case, sRNA and transcriptome was profiled and compared in this study, showed that OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers.
2021-09-09 | GSE150446 | GEO