Lodgepole pine linkage map reveals patterns of genomic clustering of locally adaptive loci
Date
2023-03-17
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Abstract
Adaptation to heterogeneous local conditions is near ubiquitous throughout the tree of life. Climate adaption requires a complex system of trade-offs and multifaceted responses, and while the evolutionary theory is reasonably well developed and empirical evidence abundant, the genetic basis of local adaptation is poorly understood for complex traits outside of model organisms. Conifers demonstrate an immense capacity for local adaptation over a wide range of climatic and ecological conditions, and although they are ecologically and economically important, the size and complexities of conifer genomes have limited our ability to study the genetic basis of such adaptation as reference resources are scarce. Here, I have constructed a linkage map for lodgepole pine to examine the patterns of linkage disequilibrium and physical linkage amongst putative adaptive loci identified by Genotype-Environment Associations (GEAs) to 19 climate related variables. We find the high amounts of linkage disequilibrium (LD) observed amongst top-candidate genes are largely attributable to physical linkage, yet are generally distinct loci with some cases potentially indicative of neutral genetic hitchhikers. The context provided by the linkage map to signals of adaptation reveals an intriguing pattern of clustering of loci and reuse of genomic regions in response to distinct, but related, environment factors. These patterns suggest evolution of both clustered and diffuse architectures underlying climate adaptation in lodgepole pine.
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Evolutionary Genetics, Local Adaptation, Forestry, Linkage Mapping
Citation
McDonald, T. K. (2023). Lodgepole pine linkage map reveals patterns of genomic clustering of locally adaptive loci (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.