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Genetic pool structure of local apple cultivars from Portugal assessed by microsatellites

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Abstract

A set of 87 apple accessions, located in three Portuguese apple germplasm collections, plus eight reference cultivars, were analyzed using 16 SSRs with the aim of assessing their genetic diversity and structure and evaluating relationships among them. Among the accessions studied, 64 unique genotypes were identified, 51 diploids and 13 putative triploids, revealing 19 groups of synonyms and 4 of homonyms. The genetic analyses performed by Bayesian model-based clustering (Structure) revealed a clear differentiation of two major groups (RPP1 and RPP2), one of them (RPP1) corresponding to old local Portuguese accessions, some of them putatively derived from ancient hybridization with Reineta, and the second one (RPP2) including all reference accessions and local Portuguese accessions considered to be of more recent origin. These results were confirmed by factorial correspondence analysis (FCA) and molecular variance analysis (AMOVA) and are in accordance with the Jaccard coefficients. Results indicate that the Portuguese apple germplasm includes an important and distinct gene pool of cultivars with respect to reference international cultivars, being a relevant source of genetic diversity for present and future breeding programs, originated at least 200 years ago, when some of these cultivars were firstly named. Moreover, this study will be useful to improve the apple germplasm management and in the definition of a preservation strategy concerning the Portuguese apple landraces.

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Acknowledgments

This work was supported by European Investment Funds by FEDER/COMPETE/POCI–Competitiveness and Internationalization Operational Programme, under the Project POCI-01-0145-FEDER-006958, National Funds by FCT–Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013 and the scholarship SFRH/BD/96400/2013 and Galicia Norte Portugal European Grouping of Territorial Cooperation (GNP-EGTC) funds supporting an internship at University of Santiago de Compostela, under the IACOBUS program. The authors acknowledge the “Research Institute of Horticulture and Seeds” INRA, Agrocampus Ouest, University of Angers, for providing the eight reference DNA samples.

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Authors and Affiliations

  1. Centro de Investigação e de Tecnologias Agro-Ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro, 5000-801, Vila Real, Portugal

    V. Ferreira, V. Carnide, O. Pinto-Carnide & I. Castro

  2. Departamento de Producción Vexetal, Escola Politécnica Superior, Universidade de Santiago de Compostela, Campus de Lugo, 27002, Lugo, Spain

    A. M. Ramos-Cabrer & S. Pereira-Lorenzo

  3. Divisão de Apoio ao Setor Agroalimentar, Direção Regional de Agricultura e Pescas do Norte, Quinta de S. José, S. Pedro de Merelim, 4700-859, Braga, Portugal

    A. Assunção

  4. Direção de Serviços de Desenvolvimento Agroalimentar e Rural, Direção Regional de Agricultura e Pescas do Algarve, Apartado 282, Patacão, 8001-904, Faro, Portugal

    A. Marreiros

  5. Centro de Investigação de Montanha (CIMO), Escola Superior Agrária de Ponte de Lima, Instituto Politécnico de Viana do Castelo (ESAPL/IPVC), 4990-706, Refóios, Portugal

    R. Rodrigues

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  1. V. Ferreira
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Correspondence to I. Castro.

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Data Archiving Statement

The authors declare that all the work described in this manuscript followed the standard Tree Genetics and Genomes policy. Our results are based on an original database of genetic profiles not submitted to a public database. Moreover, genetic profiles of our manuscript have been included as supplemental file.

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Communicated by E. Dirlewanger

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ESM 1

Fig. 1—Dendrogram of genetic similarity generated using the Jaccard coefficient and the UPGMA method for the 141 accessions and 13 SSR loci. International reference cultivars are shown in italic and underlined; Spanish reference cultivars are shown in italic. (PDF 1232 kb)

ESM 2

Table 1—List of the 95 apple accessions studied, 87 Portuguese and 8 references, and allele sizes in base pairs at each of 16 microsatellite loci analyzed. (XLSX 38 kb)

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Ferreira, V., Ramos-Cabrer, A.M., Carnide, V. et al. Genetic pool structure of local apple cultivars from Portugal assessed by microsatellites. Tree Genetics & Genomes 12, 36 (2016). https://doi.org/10.1007/s11295-016-0997-8

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