The geographic mosaic theory of coevolution explicitly states that species with broad distributions must have the capacity to interact with a range of environmental factors, both abiotic and biotic. For plant species this variability might include tolerances to drought or cold, and different cocktails of alkaloids may be better suited to fend off local communities of herbivores. While phenotypic plasticity likely accounts for much of the variation among populations it is also clear that local adaptation is extremely important. We have explored the role that transcribed microsatellites might play in facilitating local adaptation of common sunflower populations across a well-established cline. A common garden experiment focusing on accessions collected from Kansas and Oklahoma provided material for a large-scale RNA-seq experiment. It was designed to test the “tuning knob” hypothesis that implies incremental changes in microsatellite allele lengths result in incremental changes in phenotypes. The RNA-seq data allowed for both microsatellite genotyping and estimation of gene expression level, the phenotype. The molecular ecology at transcribed microsatellite loci of interest was then compared to that of anonymous microsatellites to test for evidence of local adaptation, and additional gene expression analyses were conducted by means of qPCR.
Results/Conclusions
Seed for the common garden experiment came from three populations Kansas and three in Oklahoma. Differentially expressed genes between the two latitudes were assessed. Mononucleotide repeats and standardized AG repeats were significantly enriched within differentially expressed genes. Further, of 3325 microsatellite-encoding transcripts genotyped using the RNA-Seq data, microsatellite allele length for 14.4% of them showed significant correlation with gene expression levels. These findings suggest that a substantial number of microsatellites across the sunflower transcriptome may function as “tuning knobs” for gene expression. A subset of these transcribed microsatellite loci were used in a population genetic study involving populations across a wider latitudinal range from Manitoba to Oklahoma. Allele frequency differences at transcribed microsatellite loci across this geographic range were consistent with signatures of local adaptation when compared to the genetic structure inferred from anonymous microsatellites. These results suggest that shorter or longer allele lengths may be favored in even more extreme environments. Further, qPCR revealed patterns of gene expression in this broader geographic sample that were consistent with those seen in the RNA-seq experiment. Our study provides compelling evidence that transcribed microsatellites have the capacity to facilitate local adaptation.