The cultivated apple, Malus pumila Mill. (2n = 2x = 34), is a member of the Spireaoideae subfamily of Rosaceae, and is the fourth most economically-important fruit crop worldwide. As a consequence of the long juvenility phase of apple trees and of relatively high husbandry costs, the breeding and selection of novel apple rootstocks and scions is a time-consuming and costly procedure. Marker assisted selection (MAS) has the potential to increase the precision of apple breeding and an essential prerequisite to MAS is the production of high quality saturated genetic linkage maps to enable marker-trait associations to be made.
The genome of the apple scion cultivar ‘Golden Delicious’ was recently sequenced and assembled into 17 pseudo-chromosomes by an international consortium  using predominantly second generation 454 sequencing technology. Despite the inherent difficulties associated with contig assembly and gene-prediction in complex heterozygous genomes , the ‘Golden Delicious’ genome covers 598.3 Mbp, an estimated 71.2% of the Malus genome and almost complete coverage of the gene-space of the variety , with an average depth of sequencing 16.9×. Thus, the sequence provides a solid foundation for a wealth of downstream research activities including marker development, linkage map construction and marker-trait association.
The availability of data relating to single nucleotide polymorphisms (SNPs) from early in the development of the ‘Golden Delicious’ genome sequence meant that assays have been developed for screening segregating SNPs in apple mapping populations at relatively high throughput using the SNPlex and Golden Gate genotyping platforms [3, 4], permitting not only the rapid development of linkage maps for Malus progenies, but the high resolution anchoring orientation of the scaffolded sequence data to a reference linkage map . The degree of transferability of heterozygous SNPs between Malus varieties and species, and between Malus and Pyrus has recently been assessed , and estimates have been made about the number of SNPs required to allow the construction of a saturated linkage map in any given Malus progeny. In the study of Micheletti et al. , SNPs identified from the ‘Golden Delicious’ genome sequence were validated and tested for heterozygous transferability (TSNP) in a diverse selection of Malus germplasm. The investigation showed that SNPs identified within the ‘Golden Delicious’ sequence had an average transferability rate of 40.9% to Malus cultivars, with the lowest TSNP to the cultivar ‘Wagner’ (25.7%) from those tested. The transferability rate in rootstock germplasm was between 29.9% and 39.7%, whilst to an accession of Pyrus pyrifolia, the TSNP value was just 1.8%, demonstrating low cross-genera SNP transferability of the SNPs tested .
Through international collaboration, led by the RosBREED initiative in the USA , the Malus research community has developed an Infinium® II WGG genotyping array (referred to hereafter as the International RosBREED SNP Consortium array; IRSC array) for Malus and Pyrus using data from the re-sequencing of 27 Malus genotypes along with data from the ‘Golden Delicious’ genome sequence. The IRSC array contains a total of 7,867 Malus SNPs  in addition to 921 Pyrus SNPs. The development of this array represents a milestone in the development of molecular genetics and genomics resources for Malus and offers the promise of rapid, low-cost, high-throughput genotyping for the purposes of linkage map construction and the genotyping of germplasm collections, that will facilitate future QTL and genome-wide association studies. However, reports are yet to emerge of the efficacy of such arrays for genotyping germplasm and mapping populations from divergent sources or from species related to those for which they were originally designed.
The M432 mapping progeny [8, 9] has been raised for the study of genes controlling traits of relevance to rootstock breeding, with the long-term aim of developing robust markers for MAS. Since the progeny is derived from parental rootstock varieties, the genetic basis of the seedlings that comprise the population represents a departure from the well-characterised scion genotypes that were used to identify SNPs for the construction of the IRSC array . The progeny has been previously characterised with S-locus-specific markers, and 323 (306 co-dominant, and 17 dominant) SSR markers  distributed throughout the Malus genome. A comprehensive consensus linkage map of the progeny has been developed spanning 17 linkage groups (LGs), with an average marker density of one marker every 3.79 cM. The linkage map was partially anchored to the ‘Golden Delicious’ genome sequence, and a total of 47% of the sequence that was contained in metacontigs could be assigned positions on the M432 map.
The aim of this investigation was to test the IRSC array in the M432 rootstock mapping progeny to determine its utility to genome-wide saturated map construction. Additionally, we aimed to increase the percentage of the Malus genome sequence that could be directly related to regions of the M432 linkage map for the purposes of candidate gene identification and marker development following QTL analysis. We evaluated the SNP-based linkage map produced against the previously-published SSR-based linkage map of the population developed by Fernández-Fernández et al. . We compared the positions of SNP markers on the M432 linkage map with their predicted positions on the ‘Golden Delicious’ genome sequence and assessed the accuracy of the genomic placement of the heterozygous SNP markers in relation to the genetic positions of the markers on the M432 map. An evaluation was made of the ease at which the IRSC array could be implemented in the mapping progeny in relation to previous SSR assays performed for linkage map construction in this progeny.