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Open AccessArticle

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

1
School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA
2
Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA
3
USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331, USA
4
Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
5
Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2021, 12(1), 110; https://doi.org/10.3390/genes12010110
Received: 31 December 2020 / Revised: 14 January 2021 / Accepted: 15 January 2021 / Published: 18 January 2021
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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. View Full-Text
Keywords: cold adaptation; growth; phenology; cold hardiness; GWAS; GEA; Douglas-fir cold adaptation; growth; phenology; cold hardiness; GWAS; GEA; Douglas-fir
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MDPI and ACS Style

De La Torre, A.R.; Wilhite, B.; Puiu, D.; St. Clair, J.B.; Crepeau, M.W.; Salzberg, S.L.; Langley, C.H.; Allen, B.; Neale, D.B. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes 2021, 12, 110. https://doi.org/10.3390/genes12010110

AMA Style

De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes. 2021; 12(1):110. https://doi.org/10.3390/genes12010110

Chicago/Turabian Style

De La Torre, Amanda R.; Wilhite, Benjamin; Puiu, Daniela; St. Clair, John B.; Crepeau, Marc W.; Salzberg, Steven L.; Langley, Charles H.; Allen, Brian; Neale, David B. 2021. "Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir" Genes 12, no. 1: 110. https://doi.org/10.3390/genes12010110

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