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Updated: May 31, 2026

06:41
Imaging and Analysis for Quantifying Maize (Zea mays) Abiotic Stress Phenotypes
Published on: March 28, 2025
Genome-wide expression quantitative trait loci (eQTL) analysis in maize.
Beth Holloway1, Stanley Luck, Mary Beatty
1DuPont Agricultural Biotechnology, Wilmington, DE 19880, USA.
BMC Genomics
|July 2, 2011
Summary
Expression quantitative trait loci (eQTL) analysis in maize identified thousands of cis- and trans-acting eQTL. A novel regulatory gene controlling ABA 8'-hydroxylase pseudogene expression was discovered, validating eQTL cloning feasibility.
Area of Science:
- Plant genetics
- Genomics
- Molecular biology
Background:
- Expression quantitative trait loci (eQTL) analyses are crucial for understanding transcriptional regulation in various species.
- Microarray-based studies identify cis-acting (proximal gene regulation) and trans-acting (unlinked gene regulation) factors.
Purpose of the Study:
- To identify cis- and trans-acting eQTL in maize roots.
- To identify candidate genes underlying trans-acting eQTL.
- To demonstrate the feasibility of eQTL cloning in maize.
Main Methods:
- Hydroponics-based genetical genomics study.
- Analysis of a Zea mays IBM2 Syn10 double haploid population.
- Positional cloning for candidate gene identification.
Main Results:
- Tens of thousands of cis- and trans-acting eQTL were identified in maize roots.
- False-positive eQTL were observed due to incomplete parental genome sequences.
- A class I glutamine amidotransferase was identified as a candidate trans-acting factor regulating an ABA 8'-hydroxylase pseudogene.
Conclusions:
- eQTL cloning is feasible in maize, aiding the understanding of gene expression regulation.
- Incomplete genome sequences can lead to false-positive eQTL identification.
- A novel regulatory mechanism involving glutamine amidotransferase was uncovered.

