Open Access Research article

Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Laima Antanaviciute1, Felicidad Fernández-Fernández1, Johannes Jansen2, Elisa Banchi3, Katherine M Evans4, Roberto Viola3, Riccardo Velasco3, Jim M Dunwell5, Michela Troggio3 and Daniel J Sargent3*

Author Affiliations

1 East Malling Research (EMR), New Road, East Malling, Kent, ME19 6BJ, UK

2 Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, the Netherlands

3 Istituto Agrario San Michele all’Adige, Via E. Mach 1, 38010, San Michele all'Adige, Italy

4 WSU Tree Fruit Research & Extension Center, 1100 N. Western Ave., Wenatchee, WA, 98801-1230, USA

5 School of Biological Sciences, University of Reading, Reading, RG6 6AH, UK

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BMC Genomics 2012, 13:203  doi:10.1186/1471-2164-13-203

Published: 25 May 2012



A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny.


Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence.


We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

Infinium; Golden Gate; Breeding; Selection; Genome sequence; Marker