Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-51047
PROVIDER: PRJNA219746 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR999032_1.fastq.gz | Fastqsanger.gz | |||
| SRR999032_2.fastq.gz | Fastqsanger.gz | |||
| SRR999033_1.fastq.gz | Fastqsanger.gz | |||
| SRR999033_2.fastq.gz | Fastqsanger.gz | |||
| SRR999034_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 72 |
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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:The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements and regulatory DNA revealed through chromatin accessibility maps can be harnessed for manipulating gene expression to subtle phenotypic outputs that enhance productivity in specific environments. Here, we present a genome-wide view of accessible chromatin and nucleosome occupancy at a very early stage in the development of both pollen- and grain-bearing inflorescences of the important cereal crop maize (Zea mays), using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion. Results showed that in these largely undifferentiated tissues, approximately 1.5-4 percent of the genome is accessible, with the majority of MNase hypersensitive sites marking proximal promoters but also 3’ flanks of maize genes. This approach mapped regulatory elements to footprint-level resolution, and through integration of complementary transcriptome and transcription factor occupancy data, we annotated regulatory factors such as combinatorial motifs and long non-coding RNAs that potentially contribute to organogenesis in maize inflorescence development, including tissue-specific regulation between male and female structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity, revealed new SNP-trait associations in known regulators of inflorescence development. These analyses provide a first look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
2020-06-05 | GSE136685 | 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:Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.
2018-08-17 | GSE118673 | 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.
2013-11-27 | GSE51047 | GEO
Project description:The regulatory landscape of early maize inflorescence development
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Project description:Background. Carbon allocation between vegetative and reproductive tissues impacts cereal grain production. Despite their great agricultural importance, sink-source relationships have not been fully characterized at early reproductive stages in maize. Here we quantify the accumulation of non-structural carbohydrates and patterns of gene expression in the top internode of the stem and the female inflorescence of maize at the onset of grain filling (reproductive stage R1). Methods. Top internode stem and female inflorescence tissues of the Puma maize inbred line were collected at reproductive stage R1 (without pollination). The accumulation of non-structural carbohydrates was quantified by spectrophotometry. Global gene expression was evaluated in both tissues by RNA sequencing. Results. At reproductive stage R1, the maize female inflorescence accumulates non-structural carbohydrates, notably starch, at higher levels than the top internode of the stem. Gene expression analysis identified 491 genes to be differentially expressed between the female inflorescence and the stem top internode. Gene ontology classification of differentially expressed genes showed enrichment for sucrose synthesis, the light-dependent reactions of photosynthesis, and transmembrane transporters. Our results suggest that sugar transporters play a key role in sugar partitioning in the maize stem and reveal previously uncharacterized differences between the female inflorescence and the top internode of the stem at early reproductive stages.
2021-09-11 | GSE181998 | GEO
Project description: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.
2022-06-22 | GSE179997 | GEO
Project description: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. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
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Project description:Regulatory variation controlling architectural pleiotropy in maize
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