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Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study.

ABSTRACT: We evaluate genomic data, relative to phenotypic and climatic data, as a basis for assisted gene flow and genetic conservation. Using a seedling common garden trial of 281 lodgepole pine (Pinus contorta) populations from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that phenotype-associated loci are equivalent or slightly superior to climate data for describing local adaptation in seedling traits, but that climate data are superior to genomic data that have not been selected for phenotypic associations. We also find agreement between the climate variables associated with genomic variation and with 20-year heights from a long-term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with the experimental traits occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than those indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.

SUBMITTER: Mahony CR

PROVIDER: S-EPMC6935591 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study.

Mahony Colin R CR MacLachlan Ian R IR Lind Brandon M BM Yoder Jeremy B JB Wang Tongli T Aitken Sally N SN

Evolutionary applications 20190930 1

We evaluate genomic data, relative to phenotypic and climatic data, as a basis for assisted gene flow and genetic conservation. Using a seedling common garden trial of 281 lodgepole pine (<i>Pinus contorta</i>) populations from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that phenotype-associated loci are equivalent or slightly sup ...[more]

PMID: 31892947

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Project description:BACKGROUND:Lodgepole pine (Pinus contorta) and interior spruce (Picea glauca, Picea engelmannii, and their hybrids) are distantly related conifer species. Previous studies identified 47 genes containing variants associated with environmental variables in both species, providing evidence of convergent local adaptation. However, if the intensity of purifying selection varies with the environment, clines in nucleotide diversity could evolve through linked (background) selection that would yield allele frequency-environment signatures resembling local adaptation. If similar geographic patterns in the strength of purifying selection occur in these species, this could result in the convergent signatures of local adaptation, especially if the landscape of recombination is conserved. In the present study, we investigated whether spatially/environmentally varying purifying selection could give rise to the convergent signatures of local adaptation that had previously reported. RESULTS:We analyzed 86 lodgepole pine and 50 interior spruce natural populations spanning heterogeneous environments in western Canada where previous analyses had found signatures of convergent local adaptation. We estimated nucleotide diversity and Tajima's D for each gene within each population and calculated the strength of correlations between nucleotide diversity and environmental variables. Overall, these estimates in the genes with previously identified convergent local adaptation signatures had no similar pattern between pine and spruce. Clines in nucleotide diversity along environmental variables were found for interior spruce, but not for lodgepole pine. In spruce, genes with convergent adaption signatures showed a higher strength of correlations than genes without convergent adaption signatures, but there was no such disparity in pine, which suggests the pattern in spruce may have arisen due to a combination of selection and hybridization. CONCLUSIONS:The results rule out purifying/background selection as a driver of convergent local adaption signatures in lodgepole pine and interior spruce.

Project description:BackgroundGenomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias.ResultsMT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP.ConclusionsThe power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.

Dataset Information

Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study.

Publications

Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study.

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