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Updated: Jan 13, 2026

Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development
Published on: March 5, 2017
Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development
Chi-Chih Wu1,2, Ludvig Larsson3, Kun-Ting Hsieh1,4
1Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
Researchers mapped gene expression in maize to understand leaf development. This spatial-temporal analysis reveals key regulators controlling transitions from stem cells to differentiated leaf structures.
Area of Science:
- Plant biology
- Developmental biology
- Genomics
Background:
- Leaf development originates from the shoot apical meristem (SAM).
- Gene expression cascades governing leaf cell specification and differentiation from the SAM are largely unknown.
- Few key regulators of this process have been identified.
Purpose of the Study:
- To optimize a spatial transcriptomics protocol for maize.
- To reconstruct 3D gene expression profiles of the SAM and developing leaves.
- To identify gene expression dynamics during leaf development.
Main Methods:
- Optimized a 10× Genomics Visium spatial transcriptomics protocol.
- Developed computational pipelines for 3D gene expression profiling.
- Performed spatial-temporal transcriptome analysis on maize seedlings.
Main Results:
- Successfully mapped positional gene expression in 3D across developmental stages.
- Identified dynamic transitions from undifferentiated stem cells to differentiated leaf structures.
- Discovered distinct transcriptional programs and key regulators for meristem maintenance, leaf initiation, vascular differentiation, and cellular heterogeneity.
Conclusions:
- The optimized spatial transcriptomics pipeline provides high resolution for mapping gene expression in 3D.
- This approach offers superior spatial-temporal context compared to single-cell profiling.
- The pipeline is applicable to studying plant developmental transitions, cell specification, and differentiation.
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