Ontology highlight
ABSTRACT:
PROVIDER: PRJNA937430 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23581318_1.fastq.gz | Fastqsanger.gz | |||
| SRR23581318_2.fastq.gz | Fastqsanger.gz | |||
| SRR23581319.fastq.gz | Fastqsanger.gz | |||
| SRR23581320_1.fastq.gz | Fastqsanger.gz | |||
| SRR23581320_2.fastq.gz | Fastqsanger.gz |
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Project description: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.
2022-08-31 | GSE169600 | GEO
Project description:Plant architecture is central to yield and has been at the core of crop domestication and improvement. In cereals, inflorescence branching and leaf angle are important traits that contribute to planting density and yield potential. Several classical maize mutants show disruptions in both traits, suggesting a core regulatory network underlies pleiotropy between them. Here, we investigate regulatory modules that contribute to architectural pleiotropy between tassel branch number (TBN) and leaf angle (LA) in maize by defining transcriptional networks that function in lateral organ boundaries to promote development of these morphologically distinct organs. Using a set of nine mutants with specific developmental defects in one or both traits, we generated dynamic, context-specific gene regulatory maps that describe ligule and tassel branch development at the molecular level. Mutants introgressed into B73 and control plants were grown in environmentally controlled chambers and precisely-staged tassel primordia were hand-dissected at two stages: right before and after first primary branches initiated. Two stages capturing early development of the ligular region, including the shoot apical meristem, were also collected from mutants with LA defects. RNA-seq was performed on 140 samples and integrated into gene regulatory and co-expression networks, which were extended to include publicly available transcription factor occupancy maps for important developmental regulators, chromatin accessibility maps and natural variation to help prioritize novel genes and regulatory elements underlying diversity in LA and tassel branching phenotypes. We also used these transcriptional networks to guide multi-trait genome-wide association studies (GWAS) based on three years of field phenotyping TBN and LA traits in over 500 diverse maize lines. Various network-assisted GWAS approaches were used to identify polymorphisms in candidate genes that associate with these architecture traits and the pleiotropy between them. Our data provide novel insight into regulatory mechanisms controlling architectural pleiotropy that can be used for targeted crop improvement.
2025-02-03 | GSE180593 | GEO
Project description: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. The result provides an avenue for future research to link specific miRNAs and their targets to discrete phenotypes and developmental roles.
2015-02-20 | GSE52879 | 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:Maize develops separate ear and tassel inflorescences with initially similar morphology but finally different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely clear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. Our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation to identify new regulators and pathways for maize hybrid breeding and improvement.
2024-06-07 | GSE247571 | GEO
Project description: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. The result provides an avenue for future research to link specific miRNAs and their targets to discrete phenotypes and developmental roles. Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.
2015-02-20 | E-GEOD-52879 | biostudies-arrayexpress
Project description:Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize. meDIP-chip analysis of four maize tissues identifed few tissue-specific DNA methylation variable regions (tDMRs), whereas hundreds of genotype-specific DMRs were identified that were conserved across tissues. Methylation profiles for tassel, embryo, endosperm, and leaf of the maize inbred lines B73 and Mo17. Three biological replications for each tissue of each genotype were performed. A custom 2.1M NimbleGen array (GPL13499) was used for embryo, endosperm, and leaf, and a custom 3x1.4M NimbleGen array containing a subset of probes from the 2.1M NimbleGen array (GPL15621) was used for tassel. All of the processed data is based on the largest number of comparable probes (~1.4M) between the two arrays.
2012-08-27 | E-GEOD-38503 | biostudies-arrayexpress
Project description:QTG-Miner aides the rapid cloning of quantitative trait gene and dissection of co-directional selection of tassel branch number in maize
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