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Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development

Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development

Published on: March 5, 2017

Dynamic transcriptome landscape of maize embryo and endosperm development.

Jian Chen¹, Biao Zeng¹, Mei Zhang¹

¹State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China.

Plant Physiology

|July 20, 2014

Summary

This study maps the maize (Zea mays) seed transcriptome across development, identifying key genes and regulatory networks. It reveals DNA methylation

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Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

Area of Science:

Plant biology
Genomics
Developmental biology

Background:

Maize (Zea mays) is a crucial cereal crop and a model for seed development research.
Comprehensive genome-wide transcriptome data for maize seed development is lacking.
Understanding seed development is vital for agricultural advancements.

Purpose of the Study:

To create a spatiotemporal transcriptome atlas of maize seed development.
To identify genes and regulatory networks governing seed development.
To explore the role of DNA methylation in seed-specific gene expression.

Main Methods:

High-throughput RNA sequencing of 53 maize seed samples from fertilization to maturity.
Analysis of embryo, endosperm, and whole seed tissues.
Coexpression analysis and integration with nonseed transcriptome data.
Correlation of gene expression with DNA methylation patterns.

Main Results:

A transcriptome atlas encompassing 26,105 genes involved in seed development, including 1,614 transcription factors.
Identification of fundamental transcriptomic reprogramming and developmental phases.
Discovery of 91 seed-specific transcription factors and 1,167 other seed-specific genes.
Evidence that gene body hypomethylation is crucial for highly expressed seed-specific genes like zeins.

Conclusions:

This study provides a valuable resource for understanding maize seed development.
Key regulatory networks and mechanisms underlying monocot seed development are elucidated.
The findings offer insights into genetic control for improving crop yield and quality.