A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer1,2,8,
- Marie Javelle2,8,9,
- Lin Li3,
- Xianran Li4,
- Xiaoli Ma1,
- Kokulapalan Wimalanathan5,10,
- Sunita Kumari2,
- Robyn Johnston6,
- Samuel Leiboff6,
- Robert Meeley7,
- Patrick S. Schnable4,
- Doreen Ware2,
- Carolyn Lawrence-Dill4,5,
- Jianming Yu4,
- Gary J. Muehlbauer3,
- Michael J. Scanlon6 and
- Marja C.P. Timmermans1,2
- 1Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany;
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 3Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108, USA;
- 4Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA;
- 5Interdepartmental Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA;
- 6Plant Biology Section, School of Intergrated Plant Science, Cornell University, Ithaca, New York 14853, USA;
- 7DuPont Pioneer, Agricultural Biotechnology, Johnston, Iowa 50131, USA
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↵8 These authors contributed equally to this work.
Abstract
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.250878.119.
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Freely available online through the Genome Research Open Access option.
- Received March 26, 2019.
- Accepted October 2, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
