Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.
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.
Department of Integrative Biology, University of Texas at AustinEarth Institute and Department of Ecology, Evolution and Environmental Biology, Columbia University jl3985@columbia.edu tjuenger@austin.texas.edu.
Jesse R
JR
Lasky
Department of Integrative Biology, University of Texas at Austin.
David L
DL
Des Marais
Department of Integrative Biology, University of Texas at Austin.
David B
DB
Lowry
Bioinformatics and Genomics Program, Centre for Genomic Regulation, Barcelona, Spain.
Inna
I
Povolotskaya
Bioagricultural Sciences and Pest Management, Colorado State University.
John K
JK
McKay
Land, Air and Water Resources, University of California, Davis.
James H
JH
Richards
Department of Integrative Biology, University of Texas at Austin.
Timothy H
TH
Keitt
Department of Integrative Biology, University of Texas at Austin jl3985@columbia.edu tjuenger@austin.texas.edu.
Thomas E
TE
Juenger
D000064:Acclimatization; D017360:Arabidopsis / Q000235:genetics / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000235:genetics*; D057231:Climate Change; D018506:Gene Expression Regulation, Plant; D056084:Genetic Fitness; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012641:Selection, Genetic; D013312:Stress, Physiological
D029681:Arabidopsis Proteins
abiotic stress; landscape genomics; phenotypic plasticity; regulatory evolution; transcriptome