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

Abstract

11There is substantial interest in uncovering the genetic basis of the traits underlying adaptive 12 responses in tree species, as this information will ultimately aid conservation and industrial 13 endeavors across populations, generations, and environments. Fundamentally, the 14 characterization of such genetic bases is within the context of a genetic architecture, which 15 describes the mutlidimensional relationship between genotype and phenotype through the 16 identification of causative variants, their relative location within a genome, expression, 17 pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity. 18Here, we review theory related to polygenic local adaptation and contextualize these 19 expectations with methods often used to uncover the genetic basis of traits important to tree 20 conservation and industry. A broad literature survey suggests that most tree traits generally 21 exhibit considerable heritability, that underlying quantitative genetic variation ( "# ) is structured

A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.)

“…However, synonymous SNPs could also be under direct selection and cause changes in phenotypic traits, since they can affect mRNA splicing, mRNA stability, and translation kinetics 94 – 96 or affect translation and protein synthesis due to tRNA bias 97 , 98 . This highlights the importance of considering not only non-synonymous SNPs but also synonymous and non-coding SNPs, since they could have a key role in gene expression and post-transcriptional regulation and, thus, influence important adaptive phenotypic traits 47 , 62 , 99 , 100 .…”

“…The genetic variation underlying many traits in forest trees is likely to be polygenic, controlled by a large number of loci with small and moderate effects [46][47][48] . A common approach for the identification of genetic polymorphisms underlying adaptive traits is to test for associations between phenotypes and genetic variation 49,50 .…”

Can long‐lived species keep pace with climate change? Evidence of local persistence potential in a widespread conifer

“…Heterogeneity in the distribution of abiotic and biotic factors has the potential to impede gene flow by creating geographic barriers or a matrix of unsuitable habitat across which dispersal cannot occur (Sork et al., 1999; Wang & Bradburd, 2014). On one hand, isolated populations may be able to adapt to local conditions more rapidly because non‐adapted alleles no longer flow into the population (Lind et al., 2018). Such populations may also lack the genetic variation to respond to novel environmental selection, thus increasing the risks of local extirpation (Aitken et al., 2008).…”

Modelling multilocus selection in an individual‐based, spatially‐explicit landscape genetics framework

“…These technological and methodological advances have increased our capacity to investigate the genomic basis of local adaptation in an increasingly large number of non‐model species. However, our ability to validate candidate adaptive loci that are identified through outlier‐based approaches has lagged for a number of reasons, including: the small number of well‐annotated reference genomes available; the difficulty of obtaining phenotypic data for many species (especially at the large sample sizes needed for robust genome‐wide association studies to identify small effect loci that underlie most quantitative traits); and the impracticality of experimental approaches to validation for many organisms, such as common gardens and reciprocal transplants (e.g., Cushman, ; de Villemereuil, Gaggiotti, & Till‐Bottraud, ; Lind, Menon, Bolte, Faske, & Eckert, ). In this context, simulation models may be the best option currently available for corroborating empirical findings in many species.…”