Genetic linkage maps permit the elucidation of genome structure and organization and enable the identification of molecular markers linked to traits in an experimental segregating progeny, leading ultimately to the elucidation of the genetic basis of the trait of interest. As a result, maps have been developed for many diverse plant species [1–9]. Traditionally, transferable linkage map development has been achieved through the scoring of restriction fragment length polymorphisms (RFLPs) , microsatellites (SSRs) and gene specific markers  in a segregating progeny. Using such markers, saturated reference linkage maps for many plant species have been developed. Reference maps inform the selection of markers for mapping in other progenies [10–12] and have been used to anchor, order and orientate physical map BAC contigs, and genome sequencing scaffolds for the assignment of pseudo-chromosomes for whole genome sequence initiatives [13–17].
Single nucleotide polymorphisms (SNPs) are the most abundant mutations between related DNA molecules. The advent of affordable second generation sequencing technologies in recent years has led to the release of whole genome reference sequences for many plant species [6, 14, 18–20], and the identification of abundant SNPs throughout the genomes of these organisms [21–23]. Thus, SNPs are becoming increasingly important as markers for both fundamental and applied genetics research in plants. Relatively low throughput methods have been developed for the analysis and mapping of SNPs. These include high resolution melting (HRM) , and the cleaved amplified polymorphic DNA (CAPs) assay . Additionally, medium and high throughput genotyping assays have been developed that permit hundreds of thousands of SNPs to be interrogated simultaneously on a single multiplexed array. Platforms for genotyping in this way include SNPlex, Golden Gate, Infinium and Axiom, which have been employed successfully for genotyping in many plant species including apple, peach, grape and purple false brome [22, 23, 26–29]. Genotyping arrays have many advantages over other techniques for genetic analysis, however an essential prerequisite for array development is a predetermined set of SNPs, preferably located at known positions on a reference genome sequence. Additionally, the transferability of heterozygous SNPs between species has been shown to be low  and as such, in many genera, arrays must be developed specifically for the species under investigation. Thus for minor crops and for genotyping interspecific progenies or species complexes, the development of arrays is currently not a viable experimental solution.
Despite the second generation sequencing ‘revolution’ in the biological sciences, many crops of significant economic importance remain without a reference genome sequence, or an abundance of SNP data in public repositories. High throughput SNP genotyping for these organisms using array-based technologies is not economically viable, yet rapid, high-throughput SNP genotyping would be immensely advantageous for the progression of classical mapping and QTL analyses, for genome-wide association studies and pedigree-based analyses, genomic selection and for the development and implementation of marker-assisted breeding and selection.
Second generation sequencing has offered the possibility to genotype sequence variation in the genome of an organism for use in mapping experiments through whole genome re-sequencing. Whole genome re-sequencing has been employed for mapping in eukaryotic species with a relatively small genome size and on a selective mapping populations such as for the fungus Venturia inequalis. However, for the majority of organisms, even those with relatively small genomes such as the diploid strawberry Fragaria vesca[14, 21] a complexity reduction step must be performed prior to sequencing to enable sufficient depth of coverage of the same regions in all genomes of a segregating progeny to permit segregation to be scored. Genotyping through the sequencing of reduced representation genomic libraries developed through restriction digestion of genomic DNA (restriction-site associated DNA; RAD) was initially proposed by Miller (2007)  and adapted to incorporate barcoding for multiplexing with Illumina sequencing technology by Baird et al. (2008) . The RAD procedure has been used successfully to identify SNPs in a number of plant species including eggplant, barley, and globe artichoke [33–35] and its utility to linkage map development and QTL analysis in a large mapping population was demonstrated recently by Pfender et al. (2011) . Subsequently, Elshire et al. (2011) proposed a method for the construction of highly multiplexed reduced complexity genotyping by sequencing (GBS) libraries. The procedure is based on a similar restriction digestion technique to RAD, however it is substantially less complicated, resulting in time and cost savings in library preparation, but the resultant data contains a larger number of missing genotype calls.
Rubus is a genus in the Rosaceae family containing more than 600 species, some of which, such as R. idaeus subsp. idaeus L. (red raspberry) and Rubus L. subgenus Rubus Watson (blackberry) are of economic importance as cultivated fruit crops. Breeding methods for these species have remained largely unchanged since the first empirical breeding programs were initiated. However, changes in cultural practices, the withdrawl of soil fumigants, and demands for increased fruit quality, shelf-life and for the extension of the traditional cultivation season, have necessitated novel breeding techniques to satisfy the demand for new cultivars. The development and application of molecular tools for Rubus would increase the speed and precision of the breeding process, particularly for traits that are difficult to characterize phenotypically, such as pyramided resistances to pests or pathogens. Looking further forward, Rubus breeding would greatly benefit from genomic selection approaches that have recently become popular in crops such as maize, barley, and wheat  because even modest gains from genomic selection could save years of in-field evaluation. An essential precursor to the development of such tools is the characterization of an abundance of informative molecular markers with which to perform marker-trait association analyses. In Rubus, the majority of molecular markers that have been developed and mapped in the genus to date are SSRs [4, 39–43]. More recently, low throughput methods were employed for mapping SNP markers in an interspecific Rubus mapping progeny [44, 45], but high throughput methods for the identification and mapping of molecular markers have yet to be reported for the genus.
In this investigation, we have exploited the recent advances in low-cost sequencing and multiplexed library preparation  to generate segregation data for SNP markers distributed throughout the R. idaeus genome. We used these markers for linkage map construction in a red raspberry progeny from the cross ‘Heritage’×‘Tulameen’ (H×T). The segregation data was generated using multiplexed sequencing on the Illumina HiSeq sequencing-by-synthesis platform. Shallow genome sampling resulted in a data set containing a large proportion of missing values, and thus we developed a pipeline which includes a novel imputation algorithm (Maskov) to deal with the missing and putatively erroneous data through comparison of genotypes in internal genotype bins following initial co-segregation analysis. The challenges and solutions to generating and handling segregation data from thousands of loci for linkage mapping are discussed.