Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis

Marilyn A L West, Kyunga Kim, Daniel J. Kliebenstein, Hans Van Leeuwen, Richard W Michelmore, R. W. Doerge, Dina A. St. Clair

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Abstract

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 1/4 211) 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 (R2 < 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.

Original languageEnglish (US)
Pages (from-to)1441-1450
Number of pages10
JournalGenetics
Volume175
Issue number3
DOIs
StatePublished - Mar 2007

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Quantitative Trait Loci
Arabidopsis
Genetic Transcription
Microarray Analysis
Eukaryota
Population
Genome

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

West, M. A. L., Kim, K., Kliebenstein, D. J., Van Leeuwen, H., Michelmore, R. W., Doerge, R. W., & St. Clair, D. A. (2007). Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics, 175(3), 1441-1450. https://doi.org/10.1534/genetics.106.064972

Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. / West, Marilyn A L; Kim, Kyunga; Kliebenstein, Daniel J.; Van Leeuwen, Hans; Michelmore, Richard W; Doerge, R. W.; St. Clair, Dina A.

In: Genetics, Vol. 175, No. 3, 03.2007, p. 1441-1450.

Research output: Contribution to journalArticle

West, MAL, Kim, K, Kliebenstein, DJ, Van Leeuwen, H, Michelmore, RW, Doerge, RW & St. Clair, DA 2007, 'Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis', Genetics, vol. 175, no. 3, pp. 1441-1450. https://doi.org/10.1534/genetics.106.064972
West MAL, Kim K, Kliebenstein DJ, Van Leeuwen H, Michelmore RW, Doerge RW et al. Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. Genetics. 2007 Mar;175(3):1441-1450. https://doi.org/10.1534/genetics.106.064972
West, Marilyn A L ; Kim, Kyunga ; Kliebenstein, Daniel J. ; Van Leeuwen, Hans ; Michelmore, Richard W ; Doerge, R. W. ; St. Clair, Dina A. / Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis. In: Genetics. 2007 ; Vol. 175, No. 3. pp. 1441-1450.
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