title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: DuPont Agricultural Biotechnology, Wilmington, DE 19880, USA.
authors: Beth
authors: B
authors: Holloway
authors: Stanley
authors: S
authors: Luck
authors: Mary
authors: M
authors: Beatty
authors: J-Antoni
authors: JA
authors: Rafalski
authors: Bailin
authors: B
authors: Li
mesh_terms: D003577:Cytochrome P-450 Enzyme System / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D016678:Genome; D006238:Haploidy; D018527:Hydroponics; D010940:Plant Proteins; D018517:Plant Roots / Q000235:genetics; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D003577:Cytochrome P-450 Enzyme System; C107203:abscisic acid 8'-hydroxylase