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Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network

https://doi.org/10.1101/461947

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Stepwise cis-Regulatory Changes in ZCN8 Contribute to Maize Flowering-Time Adaptation

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Maize selection passes the century mark: a unique resource for 21st century genomics

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The indeterminate Gene Encodes a Zinc Finger Protein and Regulates a Leaf-Generated Signal Required for the Transition to Flowering in Maize

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Dwarf8 polymorphisms associate with variation in flowering time

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Key questions in the genetics and genomics of eco-evolutionary dynamics

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A study of allelic diversity underlying flowering-time adaptation in maize landraces

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Erratum: Corrigendum: A study of allelic diversity underlying flowering-time adaptation in maize landraces

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The genetic basis of flowering responses to seasonal cues

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The effect of artificial selection on phenotypic plasticity in maize

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Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize

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Transcript and metabolite signature of maize source leaves suggests a link between transitory starch to sucrose balance and the autonomous floral transition

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Evolutionary divergence of phytochrome protein function inZea maysPIF3 signaling

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Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae

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First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes

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Genomics of Parallel Experimental Evolution in Drosophila

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FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana

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delayed flowering1 Encodes a Basic Leucine Zipper Protein That Mediates Floral Inductive Signals at the Shoot Apex in Maize

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Involvement of the MADS-Box GeneZMM4in Floral Induction and Inflorescence Development in Maize

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Mechanisms of Floral Induction in Grasses: Something Borrowed, Something New

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The ZmASR1 Protein Influences Branched-Chain Amino Acid Biosynthesis and Maintains Kernel Yield in Maize under Water-Limited Conditions

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Expression of a Gibberellin 2-Oxidase Gene around the Shoot Apex Is Related to Phase Transition in Rice

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Florigen-Encoding Genes of Day-Neutral and Photoperiod-Sensitive Maize Are Regulated by Different Chromatin Modifications at the Floral Transition

inferredcites →https://doi.org/10.1104/pp.16.00285openalex-snapshot

Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1

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Allele-Specific Assay Reveals Functional Variation in theChalcone SynthasePromoter ofArabidopsis thalianaThat Is Compatible with Neutral Evolution

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ramosa2 Encodes a LATERAL ORGAN BOUNDARY Domain Protein That Determines the Fate of Stem Cells in Branch Meristems of Maize

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The Maize Transcription Factor KNOTTED1 Directly Regulates the Gibberellin Catabolism Gene ga2ox1

inferredcites →https://doi.org/10.1105/tpc.110.081406openalex-snapshot

TheFT-LikeZCN8Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize

inferredcites →https://doi.org/10.1105/tpc.112.099614openalex-snapshot

Ontogeny of the Maize Shoot Apical Meristem

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PHENOTYPIC AND GENOTYPIC CONVERGENCES ARE INFLUENCED BY HISTORICAL CONTINGENCY AND ENVIRONMENT IN YEAST

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Genome‐wide atlas of transcription during maize development

inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01326.xopenalex-snapshot

RAPID EVOLUTION CAUSED BY POLLINATOR LOSS IN MIMULUS GUTTATUS

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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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The Genetic Architecture of Maize Flowering Time

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The Molecular Diversity of Adaptive Convergence

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Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds

inferredcites →https://doi.org/10.1186/s12862-015-0382-5openalex-snapshot

Dearth of polymorphism associated with a sustained response to selection for flowering time in maize

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1242/dev.112.3.891openalex-snapshot

Identification of multiple stages in the conversion of maize meristems from vegetative to floral development

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mixOmics: An R package for ‘omics feature selection and multiple data integration

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Genome-Wide Patterns of Arabidopsis Gene Expression in Nature

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Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

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Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

inferredcites →https://doi.org/10.1371/journal.pone.0043450openalex-snapshot

A Gene Regulatory Network Model for Floral Transition of the Shoot Apex in Maize and Its Dynamic Modeling

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.1534/g3.114.010686openalex-snapshot

A MITE Transposon Insertion Is Associated with Differential Methylation at the Maize Flowering Time QTLVgt1

inferredcites →https://doi.org/10.1534/genetics.103.026096openalex-snapshot

Structure and Expression of Maize Phytochrome Family HomeologsSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY234825, AY234826, AY234827, AY234828, AY234829, AY234830.

inferredcites →https://doi.org/10.1534/genetics.107.084830openalex-snapshot

Key Impact of Vgt1 on Flowering Time Adaptation in Maize: Evidence From Association Mapping and Ecogeographical Information

inferredcites →https://doi.org/10.1534/genetics.111.136903openalex-snapshot

Flowering Time in Maize: Linkage and Epistasis at a Major Effect Locus

inferredcites →https://doi.org/10.1534/genetics.114.161943openalex-snapshot

Usefulness of Multiparental Populations of Maize ( Zea mays L.) for Genome-Based Prediction

inferredcites →https://doi.org/10.1534/genetics.115.186288openalex-snapshot

Experimental Evolution withCaenorhabditisNematodes

inferredcites →https://doi.org/10.2135/cropsci1996.0011183x003600060021xopenalex-snapshot

Twenty Cycles of Biparental Mass Selection for Prolificacy in the Open‐Pollinated Maize Population Golden Glow

inferredcites →https://doi.org/10.2135/cropsci1998.0011183x003800040035xopenalex-snapshot

Twenty‐Seven Cycles of Divergent Mass Selection for Ear Length in Maize

inferredcites →https://doi.org/10.3835/plantgenome2015.04.0025openalex-snapshot

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development

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Genomics of long- and short- term adaptation in maize and teosinte

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations

inferred← citeshttps://doi.org/10.1093/genetics/iyad186openalex-snapshot

Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments

inferred← citeshttps://doi.org/10.1101/2020.12.22.423930openalex-snapshot

Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations

inferred← citeshttps://doi.org/10.1111/pce.13660openalex-snapshot

Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays

inferred← citeshttps://doi.org/10.1371/journal.pgen.1009213openalex-snapshot

Gene regulatory effects of a large chromosomal inversion in highland maize

inferred← citeshttps://doi.org/10.24072/pci.evolbiol.100071openalex-snapshot

Early and late flowering gene expression patterns in maize

inferred← citeshttps://doi.org/10.32649/ajas.2023.179766openalex-snapshot

SELECTION FOR FEMALE FLOWERING TRAIT AND ITS EFFECT ON YIELD, ITS COMPONENTS, AND POPPING SIZE OF POPCORN (ZEA MAYS AVARTA)

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How does selection for flowering in maize shapes defenses components against the European Corn Borer ?

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Composantes de la dynamique de l'interaction entre le maïs et les insectes lépidoptères foreurs de tige

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Role of phenology in plant-pest interactions : Experimental and mathematical modeling approaches applied to maize stem borers

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Modéliser l'évolution de la relation génotype-phénotypes dans des réseaux de régulation

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Approche génomique de la détection des barrières au flux de gènes

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The dynamics of the response to selection under high drift-high selection : insights from Saclay’s divergent selection experiments for flowering time in maize

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