The genomics of local adaptation in trees: are we out of the woods yet?

• Published in: Tree genetics & genomes Vol. 14; no. 2; pp. 1 - 30
• Main Authors: Lind, Brandon M., Menon, Mitra, Bolte, Constance E., Faske, Trevor M., Eckert, Andrew J.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.04.2018; Springer Nature B.V
• Subjects: Adaptation; Biomedical and Life Sciences; Biotechnology; Conservation; Epistasis; Forestry; Gene expression; Genetic diversity; genetic variation; genome; Genomics; genotype; Heritability; Life Sciences; Loci; phenotype; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant species; pleiotropy; Polygenic inheritance; Populations; Quantitative genetics; Review; surveys; Tree Biology; Trees; Trees; Genetic architecture; Polygenic local adaptation; GWAS
• DOI: 10.1007/s11295-017-1224-y
• ISSN: 1614-2942

There is substantial interest in uncovering the genetic basis of the traits underlying adaptive responses in tree species, as this information will ultimately aid conservation and industrial endeavors across populations, generations, and environments. Fundamentally, the characterization of such genetic bases is within the context of a genetic architecture, which describes the mutlidimensional relationship between genotype and phenotype through the identification of causative variants, their relative location within a genome, expression, pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity. Here, we review theory related to polygenic local adaptation and contextualize these expectations with methods often used to uncover the genetic basis of traits important to tree conservation and industry. A broad literature survey suggests that most tree traits generally exhibit considerable heritability, that underlying quantitative genetic variation ( Q ST ) is structured more so across populations than neutral expectations ( F ST ) in 69% of comparisons across the literature, and that single-locus associations often exhibit small estimated per-locus effects. Together, these results suggest differential selection across populations often acts on tree phenotypes underlain by polygenic architectures consisting of numerous small to moderate effect loci. Using this synthesis, we highlight the limits of using solely single-locus approaches to describe underlying genetic architectures and close by addressing hurdles and promising alternatives towards such goals, remark upon the current state of tree genomics, and identify future directions for this field. Importantly, we argue, the success of future endeavors should not be predicated on the shortcomings of past studies and will instead be dependent upon the application of theory to empiricism, standardized reporting, centralized open-access databases, and continual input and review of the community’s research.