Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n = 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trai...

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Bibliographic Details
Published in:Genetics (Austin) 2007-03, Vol.175 (3), p.1441-1450
Main Authors: West, M.A, Kim, K, Kliebenstein, D.J, Van Leeuwen, H, Michelmore, R.W, Doerge, R.W, St. Clair, D.A
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis thaliana
Chromosome Mapping
Circadian rhythm
expression quantitative trait loci
expression traits
gene expression
gene expression regulation
Genetic Variation
Genomics
Genotype & phenotype
heritability
Inheritance Patterns - genetics
Investigations
messenger RNA
Microarray Analysis
microarray technology
molecular sequence data
nucleotide sequences
Population
Quantitative Trait Loci
RNA Precursors - genetics
Signal transduction
Studies
transgressive segregation
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Summary:The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n = 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R(2) < 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.106.064972