Original Paper

Tree Genetics & Genomes

, Volume 7, Issue 4, pp 857-868

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

  • Diego MichelettiAffiliated withIstituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund Mach
  • , Michela TroggioAffiliated withIstituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund Mach Email author 
  • , Andrey ZharkikhAffiliated withMyriad Genetics
  • , Fabrizio CostaAffiliated withIstituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund Mach
  • , Mickael MalnoyAffiliated withIstituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund Mach
  • , Riccardo VelascoAffiliated withIstituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund Mach
  • , Silvio SalviAffiliated withIstituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund MachDepartment of Agroenvironmental Sciences and Technologies, University of Bologna

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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.

Keywords

Apple High-throughput genotyping SNP