Tree Genetics & Genomes

, Volume 10, Issue 6, pp 1645–1660 | Cite as

Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis

  • Inês S. Modesto
  • Célia Miguel
  • Francisco Pina-Martins
  • Maria Glushkova
  • Manuela Veloso
  • Octávio S. Paulo
  • Dora Batista
Original Paper


Cork oak (Quercus suber L.) is an evergreen tree species endemic to the western Mediterranean Basin with a major economical, social and ecological relevance, associated with cork extraction and exploitation. In the last years, cork oak stands have been facing a significant decline, which may be aggravated by the climate changes that are predicted to occur within cork oak distribution range during this century. Under this scenario, the assessment of adaptive genetic variation is essential to understand how cork oak may cope with these threats and to delineate strategies for the management of its genetic resources. In this study, six candidate genes possibly significant for environmental adaptation were analysed in cork oak populations from its entire distribution range. Signatures of natural selection were investigated using population genetic statistics and environmental association tests under alternative scenarios of population genetic structure. Signals of balancing selection were detected in the putative non-expressor of pathogenesis-related gene 1 (NPR1), involved in plant defence response against pathogens, in auxin response factor 16 (ARF16), a gene implicated in root development, in RAN3, also involved in developmental processes, and in glutamine synthetase nodule isozyme (GS), involved in nitrogen fixation. Furthermore, for ARF16, a class I heat shock protein (sHSP) and GS, associations were found between SNP allele and haplotype frequencies and several spatial and climatic variables, suggesting that these genes may have a role on cork oak local adaptation. In this study, the first steps were taken into gathering information on cork oak adaptation to environmental conditions.


Adaptive genetic variation Balancing selection Candidate gene Environmental association Western Mediterranean 



We thank José Conde (CISE - Centro de Interpretação da Serra da Estrela, Seia, Portugal) for the indispensable support in the exhaustive survey and sample collection at Serra da Estrela, and Maria Helena Almeida (Instituto Superior de Agronomia, UTL) for sample access and advice regarding the international provenance trial (FAIR I CT 95 0202) established at Monte Fava, Alentejo, Portugal. This work was funded by Portuguese funds through FCT - Fundação para a Ciência e Tecnologia (projects PTDC/AGR-GPL/104966/2008 and SOBREIRO/0036/2009). We thank the anonymous reviewers for their constructive comments and suggestions which helped us to improve the manuscript.

Data archiving statement

Sequence data has been submitted to GenBank (National Center for Biotechnology Information) and can be accessed through the accession numbers KF988869-KF989346. A complete list of accession numbers is provided in Online Resource 2.

Supplementary material

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Online Resource 1 (PDF 38 kb)
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Online Resource 2 (PDF 159 kb)
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Online Resource 3 (PDF 10 kb)
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Online Resource 4 (PDF 154 kb)
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Online Resource 5 (PDF 364 kb)
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Online Resource 6 (PDF 84 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Inês S. Modesto
    • 1
  • Célia Miguel
    • 2
    • 3
  • Francisco Pina-Martins
    • 1
    • 4
  • Maria Glushkova
    • 5
  • Manuela Veloso
    • 6
  • Octávio S. Paulo
    • 1
  • Dora Batista
    • 1
    • 7
  1. 1.Centro de Biologia Ambiental (CBA), Computational Biology and Population Genomics Group (CoBiG2)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
  2. 2.Instituto de Tecnologia Química e BiológicaUniversidade Nova de Lisboa (ITQB-UNL)OeirasPortugal
  3. 3.Instituto de Biologia Experimental e Tecnológica (IBET)OeirasPortugal
  4. 4.Centro de Estudos do Ambiente e do Mar (CESAM) e Departamento de BiologiaUniversidade de AveiroAveiroPortugal
  5. 5.Department of Forest Genetics, Physiology and PlantationsForest Research Institute of B.A.S.SofiaBulgaria
  6. 6.Unidade de Biotecnologia e Recursos GenéticosInstituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV)OeirasPortugal
  7. 7.Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical (CIFC-Biotrop/IICT)OeirasPortugal

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