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Genetic diversity of the genus Malus and implications for linkage mapping with SNPs

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Abstract

Knowledge about the sequence-based genetic diversity of a crop species is important in order to develop highly informative genotyping assays, which will eventually positively impact breeding practice. Diversity data were obtained from two pools of 185 and 75 accessions each, representing most of the species belonging to the genus Malus, by re-sequencing 27 gene-specific amplicons and by screening 237 Malus × domestica SNPs using the multiplex genotyping technology SNPlex™. Nucleotide diversity and insertion/deletion rates in M. × domestica were estimated as π = 0.0037 and 1/333 bp, respectively. The SNP frequency was estimated as 0.0194 (1 SNP/52 bp) while within a single apple cultivar an average of one SNP in every 455 bp was found. We also investigated transferability (T SNP) of the heterozygous state of SNPs across the species M. × domestica and the genus Malus. Raw re-sequencing showed that 12–15% of M. × domestica SNPs are transferable to a second M. × domestica cultivar, however T SNP rose to ∼41% with SNPs selected for high minor allele frequency. T SNP of chosen SNPs averaged ∼27% in the two M. × domestica-related species, Malus sieversii and Malus sylvestris, but was much lower in more distantly related species. On the basis of T SNP, simulations, and empirical results, we calculated that a close-design, multiplexed genotyping array with at least 2,000 SNPs is required for building a highly saturated linkage maps within any M. × domestica cross. The same array would gradually lose informativeness in increasingly phylogenetically distant Malus species.

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Acknowledgements

We thank Giuseppina Coppola, Pierluigi Magnago and Massimo Pindo for technical support. We also thank Phil Forsline, Valerio Gallerati, Anders S. Larsen and Andreas Peil for providing germplasm accessions. We thankfully acknowledge the financial support of Provincia Autonoma di Trento, Italy.

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Authors and Affiliations

  1. Istituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy

    Diego Micheletti, Michela Troggio, Fabrizio Costa, Mickael Malnoy, Riccardo Velasco & Silvio Salvi

  2. Myriad Genetics, Salt Lake City, UT, USA

    Andrey Zharkikh

  3. Department of Agroenvironmental Sciences and Technologies, University of Bologna, Bologna, Italy

    Silvio Salvi

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  1. Diego Micheletti
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  2. Michela Troggio
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  3. Andrey Zharkikh
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  4. Fabrizio Costa
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  5. Mickael Malnoy
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  6. Riccardo Velasco
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  7. Silvio Salvi
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Correspondence to Michela Troggio.

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Communicated by E. Dirlewanger

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Suppl. Table 1

List of accessions (PDF 113 kb)

Suppl. Table 2

Details on gene sequenced (PDF 121 kb)

Suppl. Table 3

Details on T SNP (PDF 144 kb)

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Micheletti, D., Troggio, M., Zharkikh, A. et al. Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genetics & Genomes 7, 857–868 (2011). https://doi.org/10.1007/s11295-011-0380-8

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