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Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers


A set of 493 old and local Spanish accessions of apple (Malus x domestica Borkh) maintained at three collections in Northeastern Spain was studied using 16 simple sequence repeats in order to estimate their genetic diversity and to identify the genetic structure and relationships among their accessions. An additional diverse set of 45 apple cultivars, including old Spanish and international cultivars, was added as reference. Genetic analyses performed by Bayesian model-based clustering revealed a very strong differentiation of two major groups. The first one clustered 159 individuals (52 % of unique genotypes) including local accessions and six old Spanish cultivars. The second major group was formed by 145 individuals, including 38 international reference cultivars and one old Spanish cultivar. Nested Bayesian clustering was applied to those two groups and two and four sub-groups were found at each one, respectively. The identification of private and unique alleles, and the remarkable differences in allelic richness among groups and sub-groups constitute further evidence of a clear genetic structure. The results obtained through the factorial correspondence and analyses of molecular variance confirmed those obtained by Bayesian analyses, revealing moderate but significant differentiation among the two major groups (F ST = 0.076) and the six sub-groups (F ST = 0.111). Our results highlight that the genetic diversity encompassed by currently cultivated apple accounts only for a small fraction of that existing within the species, and that an important part (≈60 %) of the local material analyzed constitutes a good example of genetic distinctness with respect to the main cultivars used in European orchards.

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This study was partially funded by INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (project grant no RF2004-008-C03-00). The authors want to thank Dr. Valero Urbina, director of the UdL Germplasm Bank and Dr. Alvaro Blanco, director of the EEAD-CSIC Germplasm Bank for their support.

Author information

Correspondence to Jorge Urrestarazu.

Additional information

Communicated by E. Dirlewanger

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online resource 1

Apple accessions maintained by the Universidad Pública de Navarra (UPNA), Escuela Técnica Superior de Ingeniería Agraria de la Universidad de Lleida (ETSIA-UDL) and Estación Experimental Aula Dei-CSIC (EEAD-CSIC) Germplasm Banks. Collection information includes accession name and bank code, site of collection, specific latitude and longitude, approximate elevation and collecting source code according to Food and Agriculture Organization of the United Nations/International Plant Genetic Resources Institute (FAO/IPGRI, 2001) multicrop passport descriptors (PDF 58 kb)

Online resource 2

Number of accessions evaluated in this study according to their origin, indicated by latitude (°N) and altitude (meter above sea level; PDF 5 kb)

Online resource 3

Groups of genotypes that shared alleles (in bold and italics) at each of the 16 SSR loci analyzed. Underline indicates reference cultivars (PDF 15 kb)

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Urrestarazu, J., Miranda, C., Santesteban, L.G. et al. Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers. Tree Genetics & Genomes 8, 1163–1180 (2012).

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  • Malus x domestica
  • SSR
  • diversity
  • genetic structure
  • Northeastern Spain