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Related Experiment Video

Updated: Mar 23, 2026

Measuring Gene Expression in Bombarded Barley Aleurone Layers with Increased Throughput

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Published on: March 30, 2018

Regulatory modules controlling early shade avoidance response in maize seedlings.

Hai Wang¹, Guangxia Wu¹, Binbin Zhao¹

¹Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.

|April 1, 2016

Summary

Maize seedlings

Keywords:

Maize Phytochrome Regulatory module Shade Transcriptome

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Area of Science:

Plant molecular biology
Plant physiology
Genomics

Background:

Shade avoidance response (SAR) is critical for crop yield in high-density planting.
Comprehensive regulatory network studies for SAR are lacking in monocot crops.
Understanding SAR is key to improving agricultural productivity.

Purpose of the Study:

To transcriptionally profile early genome-wide responses in maize seedlings to simulated shade and far-red light.
To identify key regulators and biological processes involved in maize SAR.
To compare SAR regulatory circuits between maize and Arabidopsis.

Main Methods:

Genome-wide transcriptional profiling of maize seedlings under simulated shade and far-red light.
Phytochrome-mediated signaling analysis (phytochrome B and phytochrome A).
Clustering of differentially transcribed genes (DTGs) and functional enrichment analysis.
Co-expression network analysis to identify transcription factor modules.
Cross-species comparison of orthologous DTGs with Arabidopsis.

Main Results:

Identified early transcriptional responses mediated by phytochrome B (shade) and phytochrome A (far-red light).
Discovered key biological processes regulated by SAR and de-etiolation.
Uncovered transcription factor modules potentially regulating SAR and de-etiolation.
Found bias in DTG distribution toward the maize1 subgenome, linked to cis-element retention.
Highlighted conserved and divergent SAR regulatory circuits between maize and Arabidopsis.

Conclusions:

Provided the first transcriptional overview of early maize phytochrome signaling dynamics.
Identified candidate regulatory genes for maize SAR, crucial for adaptation to shaded conditions.
Established a foundation for future functional genomics research in maize shade adaptation.