Multimodal single cell analysis reveals a link between flowering and leaf initiation
- 1University of Georgia
Abstract
Zea mays (maize) flowering time is genetically determined and a critical yield determinant. Yet mechanistic understanding of maize flowering remains poor. Indeterminate1 (Id1), a zinc-finger transcription factor (TF), is a monocot-conserved master regulator of maize flowering. Epistasis between Id1 and the ZeaCentroradialis-Delayed Flowering1 (Zcn-Dlf1) inductive pathway partly explains ID1 floral control; however, the strong mutant id1- floral delay is not explained by this pathway alone. To better characterize Id1 actions, we performed single-cell assay for transposase-accessible chromatin and single nucleus RNA sequencing (scATAC-seq and snRNA-seq) comparing Id1+ and id1- developing leaves. These analyses reveal id1- chromatin remodeling via TEOSINTE BRANCHED1 CYCLOIDEA PROLIFERATING CELL FACTOR (TCP) and APETALA2/ETHYLENE RESPONSEFACTOR (AP2/ERF) transcription factors and provide candidate direct targets that include AP2/ERF genes. These candidate direct targets include the family of {beta}-glucosidase genes that lose expression in id1-. Unexpectedly, CRISPR/Cas9 {beta}-glucosidase edits produced plants that phenocopied terminal ear1- (te1-) mutants. This phenocopy prompted an investigation into the genetic relationship between id1-, te1- and flowering. Surprisingly, id1- te1- plants exhibited a synergistic floral delay, producing ~90 leaves before inflorescence production. Beyond highlighting hitherto unappreciated Te1 autonomous flowering roles, this genetic synergy raises the hypothesis that meristem leaf primordia cessation underpins maize flowering.
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BibTeX
@misc{minow2026multimodal,
title = {{Multimodal single cell analysis reveals a link between flowering and leaf initiation}},
author = {M. A. A. Minow and Z. Ali and A. Sangra and N. J. Behrendt and L. Lukens and J. Colasanti and R. J. Schmitz},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.23.753879},
url = {https://www.biorxiv.org/content/10.64898/2026.09.23.753879v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Multimodal single cell analysis reveals a link between flowering and leaf initiation
AU - M. A. A. Minow
AU - Z. Ali
AU - A. Sangra
AU - N. J. Behrendt
AU - L. Lukens
AU - J. Colasanti
AU - R. J. Schmitz
PY - 2026
DA - 2026/09/23
PB - bioRxiv
DO - 10.64898/2026.09.23.753879
UR - https://www.biorxiv.org/content/10.64898/2026.09.23.753879v1
AB - Zea mays (maize) flowering time is genetically determined and a critical yield determinant. Yet mechanistic understanding of maize flowering remains poor. Indeterminate1 (Id1), a zinc-finger transcription factor (TF), is a monocot-conserved master regulator of maize flowering. Epistasis between Id1 and the ZeaCentroradialis-Delayed Flowering1 (Zcn-Dlf1) inductive pathway partly explains ID1 floral control; however, the strong mutant id1- floral delay is not explained by this pathway alone. To better characterize Id1 actions, we performed single-cell assay for transposase-accessible chromatin and single nucleus RNA sequencing (scATAC-seq and snRNA-seq) comparing Id1+ and id1- developing leaves. These analyses reveal id1- chromatin remodeling via TEOSINTE BRANCHED1 CYCLOIDEA PROLIFERATING CELL FACTOR (TCP) and APETALA2/ETHYLENE RESPONSEFACTOR (AP2/ERF) transcription factors and provide candidate direct targets that include AP2/ERF genes. These candidate direct targets include the family of {beta}-glucosidase genes that lose expression in id1-. Unexpectedly, CRISPR/Cas9 {beta}-glucosidase edits produced plants that phenocopied terminal ear1- (te1-) mutants. This phenocopy prompted an investigation into the genetic relationship between id1-, te1- and flowering. Surprisingly, id1- te1- plants exhibited a synergistic floral delay, producing ~90 leaves before inflorescence production. Beyond highlighting hitherto unappreciated Te1 autonomous flowering roles, this genetic synergy raises the hypothesis that meristem leaf primordia cessation underpins maize flowering.
ER -