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

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.

Genome‐wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

“…Our results suggest a polygenic basis of drought tolerance, consistent with previous GWAS in other complex traits in conifer species, with candidate genes distributed in different chromosomes or scaffolds, and small to moderate effect sizes (Baison et al, 2020;De La Torre et al, 2021a;Weiss et al, 2020). The exact location of candidate genes in the SESE genome could only be determined at the scaffold level, as the current assembly of the reference genome is not chromosome-scale (Neale et al, 2021).…”

“…A mixed linear model (MLM) method (Yu et al, 2006) was proposed to control for population structure and the imbalanced kinships among various individuals (Pritchard et al, 2000). Until recently, determining the molecular basis of heritable trait variation has been challenging in conifer species, and genome-wide association studies (GWAS) have been limited to a few species and traits (Baison et al, 2020;Chen et al, 2021;De La Torre et al, 2021a;Elfstrand et al, 2020;Lu et al, 2017;Weiss et al, 2020). For example, association studies of drought tolerance have only been performed with pre-selected candidate genes (Cumbie et al, 2011;Depardieu et al, 2021;Eckert et al, 2010;Gonzalez-Martinez et al, 2008;Trujillo-Moya et al, 2018) and no large-scale, genome-wide studies have been reported to date.…”

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

“…Our results suggest a polygenic basis of drought tolerance, consistent with previous genome-wide association studies in other complex traits in conifer species, with candidate genes distributed in different chromosomes or scaffolds, and small to moderate effect sizes (Baison et al, 2020;Weiss et al, 2020;De La Torre et al, 2021a). The exact location of candidate genes in the genome of coast redwood could only be determined at the scaffold level since the current assembly of the reference genome is not chromosome-scale (Neale et al, 2021).…”

“…A mixed linear model (MLM) method (Yu et al, 2006) was proposed to better control for population structure and the imbalanced kinships among various individuals (Pritchard et al, 2000). Until recently, determining the molecular basis of heritable trait variation has been challenging in conifer species, and genome-wide association studies have been limited to a few species and traits (Lu et al, 2017;Baison et al, 2020;Elfstrand et al, 2020;Weiss et al, 2020;Chen et al, 2021;De La Torre et al, 2021a). For example, association studies of drought tolerance have only been performed with pre-selected candidate genes (Gonzalez-Martinez et al, 2008;Eckert et al, 2010;Cumbie et al, 2011;Trujillo-Moya et al, 2018;Depardieu et al, 2021) and no large-scale, genome-wide studies have been reported to date.…”

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

“…Non-model species attributes, such as long-generation times, large population sizes, and highly outcrossing rates, together with large genome sizes (10-30 Gb) have limited the development of genome-wide studies [26]. Genome-wide environmental association studies have been mostly based on pre-selected candidate genes in conifers [27][28][29], with just a few exceptions [19,[30][31][32][33]. In all recent genome-wide studies in conifer species, adaptation to the environment occurred through many genes of small effect, characteristic of polygenic adaptation.…”