Tree Genetics & Genomes

, Volume 7, Issue 4, pp 857–868

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

  • Diego Micheletti
  • Michela Troggio
  • Andrey Zharkikh
  • Fabrizio Costa
  • Mickael Malnoy
  • Riccardo Velasco
  • Silvio Salvi
Original Paper

DOI: 10.1007/s11295-011-0380-8

Cite this article as:
Micheletti, D., Troggio, M., Zharkikh, A. et al. Tree Genetics & Genomes (2011) 7: 857. doi:10.1007/s11295-011-0380-8

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 (TSNP) 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 TSNP rose to ∼41% with SNPs selected for high minor allele frequency. TSNP 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 TSNP, 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

AppleHigh-throughput genotypingSNP

Supplementary material

11295_2011_380_MOESM1_ESM.pdf (113 kb)
Suppl. Table 1List of accessions (PDF 113 kb)
11295_2011_380_MOESM2_ESM.pdf (121 kb)
Suppl. Table 2Details on gene sequenced (PDF 121 kb)
11295_2011_380_MOESM3_ESM.pdf (145 kb)
Suppl. Table 3Details on TSNP (PDF 144 kb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Diego Micheletti
    • 1
  • Michela Troggio
    • 1
  • Andrey Zharkikh
    • 2
  • Fabrizio Costa
    • 1
  • Mickael Malnoy
    • 1
  • Riccardo Velasco
    • 1
  • Silvio Salvi
    • 1
    • 3
  1. 1.Istituto Agrario San Michele all’Adige, Research and Innovation Centre, Foundation Edmund MachTrentoItaly
  2. 2.Myriad GeneticsSalt Lake CityUSA
  3. 3.Department of Agroenvironmental Sciences and TechnologiesUniversity of BolognaBolognaItaly