Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression

Zoe Lye, Jae Young Choi, Michael D. Purugganan

Research output: Contribution to journalArticlepeer-review


Deleterious genetic variation is maintained in populations at low frequencies. Under a model of stabilizing selection, rare (and presumably deleterious) genetic variants are associated with increase or decrease in gene expression from some intermediate optimum. We investigate this phenomenon in a population of largely Oryza sativa ssp. indica rice landraces under normal unstressed wet and stressful drought field conditions. We include single nucleotide polymorphisms, insertion/deletion mutations, and structural variants in our analysis and find a stronger association between rare variants and gene expression outliers under the stress condition. We also show an association of the strength of this rare variant effect with linkage, gene expression levels, network connectivity, local recombination rate, and fitness consequence scores, consistent with the stabilizing selection model of gene expression.

Original languageEnglish (US)
Article numbermsac193
JournalMolecular Biology and Evolution
Issue number9
StatePublished - Sep 1 2022


  • crop
  • gene dysregulation
  • rare variant
  • stabilizing selection

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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