Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 31, Issue 9, Pages 2283-2296Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msu170
Keywords
abiotic stress; landscape genomics; phenotypic plasticity; regulatory evolution; transcriptome
Funding
- National Science Foundation [IOS-0922457, DEB-0618347, DEB-0618294, DEB-0618302]
- United States Department of Agriculture NIFA-AFRI postdoctoral fellowships [2011-67012-30696, 2011-67012-30663]
- Direct For Biological Sciences
- Division Of Environmental Biology [1022196] Funding Source: National Science Foundation
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [0922457] Funding Source: National Science Foundation
- NIFA [2011-67012-30663, 579307, 2011-67012-30696, 687448] Funding Source: Federal RePORTER
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Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, eSR) to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, eGEI). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients.
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