Coherent synthesis of genomic associations with phenotypes and home environments

Abstract

Local adaptation is often studied via 1) multiple common garden experiments comparing 30 performance of genotypes in different environments and 2) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated into a modeling framework. Here, we develop a genome-wide association model of genotype 35 interactions with continuous environmental gradients (G×E), i.e. reaction norms. We employ an imputation approach to synthesize evidence from common garden and genome-environment associations, allowing us to identify loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case 40 study on Arabidopsis thaliana, our approach reveals candidate genes for local adaptation based on known involvement in environmental stress response. Most identified SNPs exhibited home allele advantage and fitness tradeoffs along climate gradients, suggesting selective gradients maintain allelic clines. SNPs exhibiting G×E associations with fitness were enriched in genic regions, putative partial selective sweeps, and G×E associations 45 with an adaptive phenotype (flowering time). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point toward the loci underlying G×E and local adaptation; coherent models of diverse data provide a principled basis for synthesis. Adrion JR, Hahn MW, Cooper BS (2015) Revisiting classic clines in Drosophila melanogaster in the age of genomics. Trends in Genetics. Ågren J, Oakley CG, McKay JK, Lovell JT, Schemske DW (2013) Genetic mapping of 690 adaptation reveals fitness tradeoffs in Arabidopsis thaliana.

On the post-glacial spread of human commensal Arabidopsis thaliana

“…All scans identified the same strong candidate ( Supplementary Fig. 3a–c ): a SNP (chr4:10999188) located <2 kb from the flowering-time gene TWIN SISTER OF FT ( TSF , AT4G20370) and 6 kb from a defence and drought associated gene LESION SIMULATING DISEASE 1 ( LSD1 , AT4G20380), around which other studies have also identified GWAS peaks for plant phenology as well as local adaptation 25 26 27 . The non-reference allele is mostly found in the hot and dry Mediterranean environments ( Fig.…”

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

“…In this case, meta‐analysis of multiple crop progenitors and landraces in the same geographical space could provide comparative insights into mechanisms of natural and human adaptation. Statistical approaches are now available that combine the results of multi‐common garden genome‐wide association studies, which explore the genetic basis of phenotype–trial site interactions, with wild and/or landrace sample environment–genomic correlations (Lasky et al ., ). This can further facilitate an understanding of causal loci for adaptation and help to define appropriate strategies for range expansions of new and orphan crops.…”

“…Along with advances in ‘speed breeding’ (Watson et al ., ), in participatory improvement methods (Weltzien & Christinck, ) and in statistical approaches that support crop development (e.g. Meuwissen et al ., ; Lasky et al ., ), the landscape for the genetic study of new and orphan crops has therefore recently been transformed.…”

Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits

“…Some published data suggest the potential for competition 9 climate interaction effects on performance (Baron et al, 2015;Campitelli et al, 2016), though the physiological basis of these interactions is largely unknown. Third, previous research has yielded insight into genetic and physiological mechanisms of drought adaptation, providing a basis for specific hypotheses about how moisture and competitive gradients interact to select for different traits (McKay et al, 2003;Juenger et al, 2010;Des Marais et al, 2012;Lovell et al, 2013;Kenney et al, 2014;Lasky et al, 2014Lasky et al, , 2018El-Soda et al, 2015;Bac-Molenaar et al, 2016;Dittberner et al, 2018;Exposito-Alonso et al, 2018DeLeo et al, 2020).…”