Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana

PLoS Genet. 2012;8(8):e1002839. doi: 10.1371/journal.pgen.1002839. Epub 2012 Aug 2.


The phenotypic effect of a gene is normally described by the mean-difference between alternative genotypes. A gene may, however, also influence the phenotype by causing a difference in variance between genotypes. Here, we reanalyze a publicly available Arabidopsis thaliana dataset [1] and show that genetic variance heterogeneity appears to be as common as normal additive effects on a genomewide scale. The study also develops theory to estimate the contributions of variance differences between genotypes to the phenotypic variance, and this is used to show that individual loci can explain more than 20% of the phenotypic variance. Two well-studied systems, cellular control of molybdenum level by the ion-transporter MOT1 and flowering-time regulation by the FRI-FLC expression network, and a novel association for Leaf serration are used to illustrate the contribution of major individual loci, expression pathways, and gene-by-environment interactions to the genetic variance heterogeneity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anion Transport Proteins / genetics
  • Anion Transport Proteins / metabolism
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Base Sequence
  • Databases, Genetic
  • Flowers / genetics*
  • Flowers / metabolism
  • Gene Expression Regulation, Plant*
  • Genes, Plant*
  • Genetic Association Studies
  • Genetic Loci
  • Genetic Variation
  • Genotype
  • MADS Domain Proteins / genetics
  • MADS Domain Proteins / metabolism
  • Molecular Sequence Data
  • Molybdenum / metabolism
  • Phenotype
  • Plant Leaves / genetics*
  • Plant Leaves / metabolism
  • Quantitative Trait, Heritable
  • Systems Biology


  • Anion Transport Proteins
  • Arabidopsis Proteins
  • FLF protein, Arabidopsis
  • FRI protein, Arabidopsis
  • MADS Domain Proteins
  • MOT1 protein, Arabidopsis
  • Molybdenum

Grant support

This work was supported by the Swedish Foundation for Strategic Research (F2006-0029:1); the Swedish Research Council for Environment, Agricultural Sciences, and Spatial Planning (FORMAS 2010-643); and a European Young Investigators (EURYI) Award to ÖC (Swedish Research Council 349-2005-8628). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.