Decoding the gene regulatory network of endosperm differentiation in maize

Yue Yuan, Qiang Huo, Ziru Zhang, Qun Wang, Juanxia Wang, Shuaikang Chang, Peng Cai, Karen M. Song, David W. Galbraith, Weixiao Zhang, Long Huang, Rentao Song () and Zeyang Ma ()
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Yue Yuan: China Agricultural University
Qiang Huo: China Agricultural University
Ziru Zhang: China Agricultural University
Qun Wang: China Agricultural University
Juanxia Wang: China Agricultural University
Shuaikang Chang: China Agricultural University
Peng Cai: China Agricultural University
Karen M. Song: Duke University
David W. Galbraith: University of Arizona
Weixiao Zhang: China Agricultural University
Long Huang: China Agricultural University
Rentao Song: China Agricultural University
Zeyang Ma: China Agricultural University

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: Abstract The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene-expression pattern from 6 to 7 days after pollination. We profile the genomic DNA-binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.

Date: 2024
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DOI: 10.1038/s41467-023-44369-7

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