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Unravelling genetic diversity and cultivar parentage in the Danish apple gene bank collection

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Abstract

Characterization of apple germplasm is important for conservation management and breeding strategies. A set of 448 Malus domestica accessions, primarily of local Danish origin, were genotyped using 15 microsatellite markers. Ploidy levels were determined by flow cytometry. Special emphasis was given to pedigree reconstruction, cultivar fingerprinting and genetic clustering. A reference set of cultivars, mostly from other European countries, together with a private nursery collection and a small set of Malus sieversii, Malus sylvestris and small-fruited, ornamental Malus cultivars, was also included. The microsatellite markers amplified 17–30 alleles per loci with an average degree of heterozygosity at 0.78. We identified 104 (23%) duplicate genotypes including colour sports. We could infer first-degree relationships for many cultivars with previously unknown parentages. STRUCTURE analysis provided no evidence for a genetic structure but allowed us to present a putative genetic assembly that was consistent with both PCA analysis and parental affiliation. The Danish cultivar collection contains 10% duplicate genotypes including colour sports and 22% triploids. Many unique accessions and considerable genetic diversity make the collection a valuable resource within the European apple germplasm. The findings presented shed new light on the origin of Danish apple cultivars. The fingerprints can be used for cultivar identification and future management of apple genetic resources. In addition, future genome-wide association studies and breeding programmes may benefit from the findings concerning genetic clustering and diversity of cultivars.

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Acknowledgements

A generous grant from Foreningen PlanDanmark and a PhD scholarship from the Department of Plant and Environmental Sciences, University of Copenhagen made this work possible. We are thankful to Jacob Weiner for valuable comments on the manuscript, to Charles-Eric Durel for a fruitful discussion and to Stefan Morberg for skillful technical assistance on flow cytometry. We thank Prima Plant (Sabro, Denmark), Tuse Næs Gårdmosteri (Holbæk, Denmark), Karen Syberg and Louise De Bang for providing plant material.

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  1. Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 3th floor, DK-1871, Frederiksberg C, Denmark

    Bjarne Larsen, Torben Bo Toldam-Andersen, Carsten Pedersen & Marian Ørgaard

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  1. Bjarne Larsen
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  2. Torben Bo Toldam-Andersen
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  3. Carsten Pedersen
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Correspondence to Bjarne Larsen.

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Data archiving statement

A full list of accession names, numbers and origin are given in Online Resource 1.

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Communicated by M. Troggio

Electronic supplementary material

Online Resource 1

List of accessions and accession numbers. Accessions originate from the gene bank collection, “Pometet” (Taastrup, Copenhagen Region), University of Copenhagen, unless otherwise specified. (PDF 75 kb)

Online Resource 2

STRUCTURE analysis for 344 M. domestica cultivars. The graph shows delta K vs. K for K = 2–12, tested over 20 runs. (PDF 10 kb)

Online Resource 3

List of ploidy level for Malus domestica cultivars and M. sieversii, determined by flow cytometry. (PDF 60 kb)

Online Resource 4

Each horizontal row contains accessions with identical genotype profile of 15 SSR-loci. The duplicate genotypes are divided into four categories: previously (beige) and not previously reported synonyms (blue), subclones such as colour sports from an original genotype (red) and accessions from the private nursery collection Assens (green). (PDF 36 kb)

Online Resource 5

Network of first degree relationships. Arrows point from parent to offspring. Information given in each box: cultivar name, accession number, ploidy level, S-RNase alleles and approximate geographical origin and year of origin. (PDF 57 kb)

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Larsen, B., Toldam-Andersen, T.B., Pedersen, C. et al. Unravelling genetic diversity and cultivar parentage in the Danish apple gene bank collection. Tree Genetics & Genomes 13, 14 (2017). https://doi.org/10.1007/s11295-016-1087-7

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