Cytometric and genetic analysis of Slovenian local apple genotypes

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Abstract
Background: The genetic diversity and ploidy of apple varieties in Slovenia is not well known so far. In this study, a total of 233 genotypes and 8 reference varieties were analysed with a set of 15 SSR markers in order to estimate the genetic diversity and to determine the genetic structure and relationships among the apple germplasm studied. Results: A total of 228 different alleles were successfully amplified, with an average of 15.2 alleles per locus. All markers were highly discriminating and powerful for varietal identification, with an average power of discrimination of 0.94. The results showed that the germplasm is highly diverse with a mean expected heterozygosity of 0.83 and a mean observed heterozygosity of 0.86. Of the 233 genotypes, 51 were recognised as synonyms and duplicates (22% redundancy), and a total of 182 unique genotypes were identified in the collections. An amount of 23% of the genotypes were identified as triploids by flow cytometry. The UPGMA clustering revealed three main groups. The genetic analysis, which was performed using the Bayesian model, revealed a very strong differentiation into two main groups. The first group comprised 85 genotypes (72% with qI > 0.80), including four reference varieties and seven local varieties. The second group comprised 105 genotypes (65% with qI > 0.80), including 4 reference varieties and two local varieties. In addition, nested Bayesian clustering was applied to these two groups, and four and two sub-groups were found, respectively. Conclusions: Altogether, this study of apple germplasm in the Slovenian landscape indicate a high diversity of apple varieties present and underline the importance of preserving these varieties. The SSR markers used, helped to identify duplicates, synonyms and homonyms within and between collections, which will help us to establish a core collection.
Funding Information
  • the Slovenian Research and Innovation Agency (P4-0077, P4-0077)
  • European Agricultural Fund for Rural Development

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