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. For each of two biological replicates, tissue was collected from B73 and Mo17 parental controls and the IBM2 Syn10 doubled haploid mapping population at 4 weeks after germination (V5 stage). One hundred thirty-five IBM2 Syn10 lines were used in this study. The tissue sampled was the 1.5 cm tip of all crown roots that had developed at the time of harvest, representing the most metabolically active region based on whole-tissue visualization of triphenyl tetrazolium chloride staining. Tissues were flash frozen in liquid nitrogen and stored at -80º C. They were manually ground into a fine powder using a mortar and pestle on dry ice. Two-channel hybridizations were considered as single channel. Therefore, the same raw data file is linked to two Samples appended as _Cy3 and _Cy5.

ORGANISM(S): Zea mays

SUBMITTER: Kevin Hayes 

PROVIDER: E-GEOD-29964 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress