Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs

Annu Rev Plant Biol. 2009;60:93-114. doi: 10.1146/annurev.arplant.043008.092114.


Scientific inquiries in fields ranging from ecology to plant breeding assess phenotypic variation within a plant species either to explain its presence or utilize its consequences. Frequently this natural genetic variation is studied via mapping quantitative trait loci (QTLs); however, elucidation of the underlying molecular mechanisms is a continuing bottleneck. The genomic analysis of transcripts as individual phenotypes has led to the emerging field of expression QTL analysis. This field has begun both to delve into the ecological/evolutionary significance of this transcript variation as well as to use specific eQTLs to speed up our analysis of the molecular basis of quantitative traits. This review introduces eQTL analysis and begins to illustrate how these data can be applied to multiple research fields.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • 14-3-3 Proteins / chemistry
  • 14-3-3 Proteins / metabolism
  • Arabidopsis / genetics
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / chemistry
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Gene Expression Regulation, Plant*
  • Oryza / genetics
  • Oryza / metabolism
  • Phosphoproteins / chemistry
  • Phosphoproteins / genetics
  • Phosphoproteins / metabolism
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Polymorphism, Genetic
  • Protein Interaction Domains and Motifs
  • Quantitative Trait Loci*


  • 14-3-3 Proteins
  • Arabidopsis Proteins
  • Phosphoproteins
  • Plant Proteins