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Signatures of adaptation and genetic structure among the mainland populations of Pinus radiata (D. Don) inferred from SNP loci

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Abstract

Insights into the relative contributions of locus specific and genome-wide effects on population genetic diversity can be gained through separation of their resulting genetic signals. Here we explore patterns of adaptive and neutral genetic diversity in the disjunct natural populations of Pinus radiata (D. Don) from mainland California. A first-generation common garden of 447 individuals revealed significant differentiation of wood phenotypes among populations (P ST), possibly reflecting local adaptation in response to environment. We subsequently screened all trees for genetic diversity at 149 candidate gene single nucleotide polymorphism (SNP) loci for signatures of adaptation. Ten loci were identified as being possible targets of diversifying selection following F ST outlier tests. Multivariate canonical correlation performed on a data set of 444 individuals identified significant covariance between environment, adaptive phenotypes and outlier SNP diversity, lending support to the case for local adaptation suggested from F ST and P ST tests. Covariation among discrete sets of outlier SNPs and adaptive phenotypes (inferred from multivariate loadings) with environment are supported by existing studies of candidate gene function and genotype–phenotype association. Canonical analyses failed to detect significant correlations between environment and 139 non-outlier SNP loci, which were applied to estimate neutral patterns of genetic differentiation among populations (F ST 4.3 %). Using this data set, significant hierarchical structure was detected, indicating three populations on the mainland. The hierarchical relationships based on neutral SNP markers (and SSR) were in contrast with those inferred from putatively adaptive loci, potentially highlighting the independent action of selection and demography in shaping genetic structure in this species.

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Acknowledgments

The authors would like to extend gratitude to the late Dr Ken Eldridge, whose efforts towards conservation of radiata pine genetic resources have underpinned so much of the work achieved in this species. We sincerely thank Ken and Charlie Bell for their insightful discussions; David Neale, Gavin Moran and Colin Matheson for helpful comments on the manuscript and Wei Li for laboratory support. We would also like to thank several anonymous reviewers for constructive suggestions and advice in early versions of the manuscript. The SSR data set of Karhu et al. (2006) was used with permission from the authors. This research was funded by the Commonwealth Scientific and Industrial Research Organisation, ArborGen LLC, Forest and Wood Products Australia and the Southern Tree Breeding Association.

Data Archiving Statement

SNP genotype data, phenotypic traits and environmental parameters on individual trees applied in this study will be made available as supplemental text files which can be downloaded with the manuscript.

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Dillon, S.K., Nolan, M.F., Matter, P. et al. Signatures of adaptation and genetic structure among the mainland populations of Pinus radiata (D. Don) inferred from SNP loci. Tree Genetics & Genomes 9, 1447–1463 (2013). https://doi.org/10.1007/s11295-013-0650-8

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