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Genetic Diversity, Population Structure and Construction of a Core Collection of Apple Cultivars from Italian Germplasm

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Abstract

Apple germplasm collections are increasingly appreciated as a repository for the genetic improvement of species, and their evaluation is an essential prerequisite for their utilization in apple breeding. A set of 418 apple genotypes, including 383 accessions from the Italian germplasm and 35 International cultivars as reference, was analyzed using 15 SSRs with the aim of assessing the genetic diversity within this panel of varieties, evaluating relationships among them and determining their genetic structure. Genetic analyses performed by Bayesian model-based clustering revealed a clear differentiation of two major groups (G1 and G2). Local Italian accessions were grouped mainly in G2 while all except one of the reference cultivars were found in G1. Each of these two clusters has been further divided into two subgroups by a nested approach. These results were confirmed by factorial correspondence (FCA) and molecular variance (AMOVA) analyses. A core collection of 55 accessions, representative of the Italian apple germplasm and capable of retaining all the 238 SSR alleles detected on 192 unique genotypes, was established by the M-strategy method. The Italian apple germplasm represents an important source of genetic diversity which can be used, in addition to other characterized European germplasm collections, to optimize the efficiency of genome-wide association studies aimed at identifying the genomic regions controlling major horticultural traits.

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Acknowledgments

This research was financially supported through grants from the Italian Ministry of Education, University and Research (FIRB project no. RBNE01SFXY) and partly funded under the EU seventh Framework Programme by the FruitBreedomics project no. 265582 “Integrated approach for increasing breeding efficiency in fruit tree crop”. The views expressed in this work are the sole responsibility of the authors and do not necessary reflect the views of the European Commission. The authors are grateful to Dr. Carlos Miranda from the Departamento de Produccion Agraria, Universidad Publica de Navarra, Spain, for kindly providing the instruction and help of using the MSTRAT software for statistic analysis of core collection calculation. Wei Liang’s PhD fellowship was funded by European Commission of Erasmus Mundus External Cooperation Windows.

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  1. Roberta Paris

    Present address: Centro di Ricerca per le Colture Industriali, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Bologna, Italy

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  1. Department of Agricultural Sciences, University of Bologna, Bologna, Italy

    Wei Liang, Luca Dondini, Paolo De Franceschi, Roberta Paris, Silviero Sansavini & Stefano Tartarini

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Liang, W., Dondini, L., De Franceschi, P. et al. Genetic Diversity, Population Structure and Construction of a Core Collection of Apple Cultivars from Italian Germplasm. Plant Mol Biol Rep 33, 458–473 (2015). https://doi.org/10.1007/s11105-014-0754-9

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