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Updated: Jun 25, 2025
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Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development
Published on: March 5, 2017
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Population-level gene expression can repeatedly link genes to functions in maize
J Vladimir Torres-Rodríguez1,2,3, Delin Li4, Jonathan Turkus1,2,3
1Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
The Plant Journal : for Cell and Molecular Biology
|May 30, 2024
Summary
Transcriptome-wide association studies (TWAS) in maize identified 10 times more flowering time genes than genome-wide association studies (GWAS). This gene expression resource links genes to plant functions across tissues and experiments.
Area of Science:
- Plant genetics
- Genomics
- Molecular biology
Background:
- Genome-wide association studies (GWAS) have limitations in pinpointing specific genes.
- Transcriptome-wide association studies (TWAS) offer higher resolution but have had mixed success in plants.
- Maize (Zea mays) is a crucial crop with complex traits like flowering time.
Purpose of the Study:
- To develop and apply a robust TWAS method for maize gene discovery.
- To identify genes regulating flowering time in maize.
- To create a valuable gene expression resource for plant science.
Main Methods:
- Generated full-length RNA-seq data from 693 diverse maize genotypes.
- Conducted TWAS and GWAS on flowering time traits from field experiments.
- Performed expression quantitative trait loci (eQTL) analysis.
Main Results:
- TWAS identified approximately 10 times more candidate genes for flowering time than GWAS.
- TWAS successfully identified known flowering time genes acting in the shoot apical meristem.
- Trait data from a new environment identified additional flowering time genes without new expression data.
- Trans-eQTL analysis revealed further known maize flowering time genes.
Conclusions:
- The generated maize gene expression resource is effective for linking genes to functions.
- TWAS is a powerful tool for gene discovery in plants, complementing GWAS.
- This resource facilitates understanding of plant phenotypes across various conditions and tissues.
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