Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir.

Amanda R De La Torre,Benjamin Wilhite,Charles H Langley,Daniela Puiu,Marc W Crepeau,Brian Allen,Steven L Salzberg,John Bradley St Clair,David B Neale

doi:10.3390/genes12010110

Amanda R De La Torre, Benjamin Wilhite + Show 7 more

Open Access

https://doi.org/10.3390/genes12010110

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Abstract

Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species’ predictions under climate change.

Highlights

Variables are phenotypic trait (Trait), proportion of variance explained (PVE), proportion of variance explained by sparse effects (PGE), posterior estimate of number of SNPs with major effect and the standard deviation across runs after burn-in (SNPs), number of SNPs with significant associations identified by GEMMA, and number of SNPs with significant associations identified by TASSEL
Our results showed the complex relationships between genotypes, growth (DIAM, HT1, HT2, HTINC), emergence (EMEAN, EMSTD), phenology (BS1, BS2, BB2), cold hardiness, and environmental variables such as degree days below 0c, precipitation as snow, and continentality (TD) (Figure 3)
Climate prediction models suggest current climate change could reduce the resilience of coastal Douglas-fir on the warmer margins of its range [21], which will translate in a reduction in fitness and lower wood productivity

Summary

Introduction

In natural populations of widely distributed species, the challenge is to identify genes underlying traits that increase the species’ ability to survive, thrive and reproduce [1,2]. Species that encounter diverse ecological and environmental natural conditions may be subject to strong differential selection pressures across heterogeneous environments that counteract the homogenizing effects of gene flow and drift in the evolution of local adaptation [3,4,5]. A comprehensive understanding of the species’ potential for evolutionary change and adaptation to changing environments will require the study of genome-wide genetic variation across the species’ natural range and its association with ecologically important traits

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