Genomic Studies of Local Adaptation in Natural Plant Populations

Abstract

Local adaptation arises as a result of selection by the local environment favoring phenotypes that enhance fitness. Geographic patterns of phenotypic variation are in part due to this selective process. Classically, the genetic basis of those phenotypes has been studied in plant populations using a quantitative genetic approach in which plants from different source populations are grown in common environments, in reciprocal transplant experiments, or in studies across a wide geographic and environmentally heterogeneous area. Limitations of these approaches to understanding the genetic basis of phenotypic variation can now be addressed with next generation sequencing, gene expression profiles, and epigenetic analysis. In this paper, I summarize contemporary genomic research on local adaptation by comparing findings from the Arabidopsis annual plant model system with long-lived tree species in four kinds of local adaptation studies: 1) genomic studies of transplant experiments; 2) landscape genomic studies; 3) gene expression studies; 4) epigenetic studies of local adaptation. Although the basic study designs of common garden, reciprocal transplants, and geographic variation have remained constant, the inclusion of contemporary genomic approaches has provided substantive advances in our understanding of the genetic underpinnings of local adaptation, including the impact of climate, the identification of candidate genes involved in genotype-by-environment interactions, and evidence for the potential role of epigenetic modification. Despite these advances, new questions are arising and key areas for future research include more exploration of gene networks in response to biotic and abiotic stressors and improved statistical tools for traits with polygenic inheritance.

Keywords: Arabidopsis; DNA methylation; Quercus; climate change; epigenetic; gene expression.