Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes.

Authors:
Benjamin Hornoy
Benjamin Hornoy
Université de Rennes 1
Nathalie Pavy
Nathalie Pavy
Université Laval
Ville de Québec | Canada
Jean Beaulieu
Jean Beaulieu
Natural Resources Canada
Jean Bousquet
Jean Bousquet
Université Laval
Canada

Genome Biol Evol 2015 Nov 11;7(12):3269-85. Epub 2015 Nov 11.

Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada

Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome.Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs.Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources.

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http://dx.doi.org/10.1093/gbe/evv218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700950PMC

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November 2015
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Cold Spring Harb Perspect Biol. 2014
Controlling the false discovery rate: a practical and powerful approach to multiple testing
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