Gene expression divergence between locally adapted inland annual and coastal perennial ecotypes of Mimulus guttatus across developmental stages
The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants. Overall design: To identify patterns of gene expression divergence between the ecotypes, we compared gene expression for leaves and floral buds collected from one coastal perennial (SWB-4) and one inland annual (LMC-17) accession. Developmentally equivalent leaf pairs and floral buds were collected in a time series manner. Only one tissue was collected per plant to avoid induced responses and repeated measures. For the inland annual plants, we sampled at the two-leaf, four-leaf, and floral bud stages because plants often flowered after producing four true leaves. Because the coastal perennial plants flowered at a later developmental stage, we sampled at the two-leaf, four-leaf, six-leaf, eight-leaf, and floral bud stages. All tissue samples were collected before anthesis. Overall, we collected 10 biological replicates for each developmental stage x ecotype combination (N = 80 total tissue samples).