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

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Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. Centro de Biologia Ambiental (CBA), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1759-016, Lisboa, Portugal

    Inês S. Modesto, Francisco Pina-Martins, Octávio S. Paulo & Dora Batista

  2. Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB-UNL), Av. da República, 2780-157, Oeiras, Portugal

    Célia Miguel

  3. Instituto de Biologia Experimental e Tecnológica (IBET), Apartado 12, 2781-901, Oeiras, Portugal

    Célia Miguel

  4. Centro de Estudos do Ambiente e do Mar (CESAM) e Departamento de Biologia, Universidade de Aveiro, 3810-193, Aveiro, Portugal

    Francisco Pina-Martins

  5. Department of Forest Genetics, Physiology and Plantations, Forest Research Institute of B.A.S., 132 “St. Kliment Ohridski” blvd., 1756, Sofia, Bulgaria

    Maria Glushkova

  6. Unidade de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Quinta do Marquês, 2784-505, Oeiras, Portugal

    Manuela Veloso

  7. Centro de Investigação das Ferrugens do Cafeeiro/Instituto de Investigação Científica Tropical (CIFC-Biotrop/IICT), Quinta do Marquês, 2784-505, Oeiras, Portugal

    Dora Batista

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  1. Inês S. Modesto
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  2. Célia Miguel
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  3. Francisco Pina-Martins
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  4. Maria Glushkova
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Correspondence to Inês S. Modesto.

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Communicated by A. Kremer

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Modesto, I.S., Miguel, C., Pina-Martins, F. et al. Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis. Tree Genetics & Genomes 10, 1645–1660 (2014). https://doi.org/10.1007/s11295-014-0786-1

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