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S-genotype identification, genetic diversity and structure analysis of Italian sweet cherry germplasm

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Abstract

In this study, 186 local sweet cherry accessions from 12 Italian regions, plus eight reference accessions, were analysed for the first time, using 13 microsatellite markers. Moreover, their S-incompatibility genotypes were identified with consensus primers for the S-RNase and SFB genes. A total of 161 unique genotypes were found; 18 groups of synonyms, along with the discovery of cases of misidentification. The average number of alleles per locus was 9.7, the mean expected heterozygosity (He) was 0.63, the mean observed heterozygosity (Ho) was 0.65 and the mean polymorphic information content (PIC) was 0.58. The structure analysis revealed the presence of six populations, which reflected in some cases geographical areas, the exchange of material among regions and introduction of material from abroad. A total of 17 different S-alleles were found, combined in 24 incompatibility groups of the 47 reported so far. Furthermore, 10 new incompatibility groups, from XLVII to LVI, were identified. Seven genotypes with unique S-allele combinations were included in the pollen donor group 0. The mutant allele of the pollen SFB 5 ′ was found in early ripening genotypes from Sicily and Sardinia. The variability of SSRs present in both introns of the allele S 13 was also explored; new combinations of variants were found and some accessions presented SSR variants typical of wild cherry. It is evident that the Italian sweet cherry germplasm collection represents a relevant source of genetic diversity that needs to be preserved for future breeding programmes.

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Acknowledgments

We thank Dr. Daniel J. Sargent and the PhD student Bipin Balan for helpful comments and for the English revision.

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Authors and Affiliations

  1. Dipartimento Scienze Agrarie, Alimentari e Forestali (SAAF), Università degli Studi di Palermo, Palermo, Italy

    A. Marchese, T. Caruso & F. P. Marra

  2. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA-OFA) - Sede Forlì, Forlì, Italy

    D. Giovannini & A. Leone

  3. Dipartimento di Gestione dei Sistemi Agrari e Forestali, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy

    R. Mafrica

  4. Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari, Bari, Italy

    M. Palasciano

  5. Istituto per la Valorizzazione del Legno e delle Specie Arboree del Consiglio Nazionale delle Ricerche (IVALSA-CNR), Follonica, Italy

    C. Cantini

  6. Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Napoli, Italy

    C. Di Vaio

  7. Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA-OFA) - Sede Roma, Roma, Italy

    F. R. De Salvador

  8. Dipartimento Scienze Agrarie, Forestali e Alimentari (DISAFA), Università di Torino, Torino, Italy

    G. Giacalone

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  1. A. Marchese
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Correspondence to A. Marchese.

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Data archiving statement

Sweet cherry SSR data are available in the Genome Database for Rosaceae.

Additional information

Communicated by E. Dirlewanger

Electronic supplementary material

Supplementary Figure S1

UPGMA dendrogram depicting genetic relationships among 186 Italian sweet cherry accessions, from 12 regions, based on 13 SSRs and the S-locus. (JPEG 512 kb)

Supplementary Figure S2

Most likely number of groups in the structure analysis resulted from the log likelihood related with each K-value calculated by using the ∆K method developed by Evanno et al. (2005). (JPEG 285 kb)

Table S1

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Marchese, A., Giovannini, D., Leone, A. et al. S-genotype identification, genetic diversity and structure analysis of Italian sweet cherry germplasm. Tree Genetics & Genomes 13, 93 (2017). https://doi.org/10.1007/s11295-017-1176-2

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