Tree Genetics & Genomes

, Volume 9, Issue 6, pp 1447–1463

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

  • Shannon K. Dillon
  • Maureen F. Nolan
  • Philippe Matter
  • Washington J. Gapare
  • Jason G. Bragg
  • Simon G. Southerton
Original Paper

DOI: 10.1007/s11295-013-0650-8

Cite this article as:
Dillon, S.K., Nolan, M.F., Matter, P. et al. Tree Genetics & Genomes (2013) 9: 1447. doi:10.1007/s11295-013-0650-8

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 (PST), 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 FST 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 FST and PST 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 (FST 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.

Keywords

Radiata pineSNPDifferentiationLocal adaptationPopulation structure

Supplementary material

11295_2013_650_MOESM1_ESM.doc (982 kb)
ESM 1(DOC 982 kb).
11295_2013_650_MOESM2_ESM.doc (360 kb)
ESM 2(DOC 360 kb).

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Shannon K. Dillon
    • 1
  • Maureen F. Nolan
    • 1
  • Philippe Matter
    • 1
  • Washington J. Gapare
    • 1
  • Jason G. Bragg
    • 1
    • 2
  • Simon G. Southerton
    • 1
  1. 1.CSIRO Plant IndustryKingstonAustralia
  2. 2.Research School of Biology and Centre for Biodiversity AnalysisThe Australian National UniversityCanberraAustralia