ArticlePlant physiology2010
Digital gene expression signatures for maize development.
Article in Plant physiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 87 citations in OpenAlex.
- Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization.Planta · 2023Review
- Functional Endophytes Regulating Plant Secondary Metabolism: Current Status, Prospects and Applications.International journal of molecular sciences · 2023Review
- Effect of thermospermine on expression profiling of different gene using massive analysis of cDNA ends (MACE) and vascular maintenance in Arabidopsis.Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Comparative Transcriptomic Analysis of the Development of Sepal Morphology in Tomato (International journal of molecular sciences · 2020Article
- TheHorticulture research · 2020Article
- Combined fine mapping, genetic diversity, and transcriptome profiling reveals that the auxin transporter gene ns plays an important role in cucumber fruit spine development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- De novo sequencing, assembly and characterisation of Aloe vera transcriptome and analysis of expression profiles of genes related to saponin and anthraquinone metabolism.BMC genomics · 2018Article
- Transcriptome Profiling of Tomato Uncovers an Involvement of Cytochrome P450s and Peroxidases in Stigma Color Formation.Frontiers in plant science · 2017Article
- The quest for epigenetic regulation underlying unisexual flower development inEpigenetics & chromatin · 2017Article
- Digital Gene Expression Analysis Provides Insight into the Transcript Profile of the Genes Involved in Aporphine Alkaloid Biosynthesis in Lotus (Frontiers in plant science · 2017Article
- Transcriptomic Analysis Implies That GA Regulates Sex Expression via Ethylene-Dependent and Ethylene-Independent Pathways in Cucumber (Frontiers in plant science · 2017Article
- Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba.Molecules (Basel, Switzerland) · 2016Article
- The Quest for Molecular Regulation Underlying Unisexual Flower Development.Frontiers in plant science · 2016Review
- Transcriptome Analysis Provides Insights into the Mechanisms Underlying Wheat Plant Resistance to Stripe Rust at the Adult Plant Stage.PloS one · 2016Article
- Asymmetric transcriptomic signatures between the cob and florets in the maize ear under optimal- and low-nitrogen conditions at silking, and functional characterization of amino acid transporters ZmAAP4 and ZmVAAT3.Journal of experimental botany · 2015Article
- Genome-wide identification and analysis of drought-responsive genes and microRNAs in tobacco.International journal of molecular sciences · 2015Article
- Article
- Transcriptome profiling reveals roles of meristem regulators and polarity genes during fruit trichome development in cucumber (Cucumis sativus L.).Journal of experimental botany · 2014Article
- Article
- Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid.International journal of molecular sciences · 2014Article
Corrections and comments
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Authors and funding
8 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 the 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 profiles using Illumina's high-throughput sequencing technology and the newly assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in axillary meristem determinacy. The RA3 gene encodes a trehalose-6-phosphate phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of digital gene expression libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20- to 21-nucleotide reads with frequencies spanning 4 orders of magnitude. Unique sequence tags were anchored to 3'-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of nonredundant signature tags to the maize genome, which associated with 37,117 gene models and unannotated regions of expression. In total, 66% of genes were detected by at least nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) in functional analyses of differentially expressed maize genes. Results from this study provide a basis for the analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.