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Open Access Highly Accessed Research article

Genome-wide expression quantitative trait loci (eQTL) analysis in maize

Beth Holloway13, Stanley Luck1, Mary Beatty2, J-Antoni Rafalski1 and Bailin Li1*

Author Affiliations

1 DuPont Agricultural Biotechnology, Wilmington, DE 19880, USA

2 Pioneer Hi-Bred International, Johnston, IA 50131, USA

3 United Stated Department of Agriculture Honey Bee Breeding, Genetics, and Physiology Laboratory, Baton Rouge, LA 70820, USA

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BMC Genomics 2011, 12:336  doi:10.1186/1471-2164-12-336

Published: 30 June 2011



Expression QTL analyses have shed light on transcriptional regulation in numerous species of plants, animals, and yeasts. These microarray-based analyses identify regulators of gene expression as either cis-acting factors that regulate proximal genes, or trans-acting factors that function through a variety of mechanisms to affect transcript abundance of unlinked genes.


A hydroponics-based genetical genomics study in roots of a Zea mays IBM2 Syn10 double haploid population identified tens of thousands of cis-acting and trans-acting eQTL. Cases of false-positive eQTL, which results from the lack of complete genomic sequences from both parental genomes, were described. A candidate gene for a trans-acting regulatory factor was identified through positional cloning. The unexpected regulatory function of a class I glutamine amidotransferase controls the expression of an ABA 8'-hydroxylase pseudogene.


Identification of a candidate gene underlying a trans-eQTL demonstrated the feasibility of eQTL cloning in maize and could help to understand the mechanism of gene expression regulation. Lack of complete genome sequences from both parents could cause the identification of false-positive cis- and trans-acting eQTL.