**4.2. BeadChip-based Infinium assay (Illumina)**

It includes whole genome amplification followed by hybridization to oligonucleotide probe attachedtoabead,extension,anddetectionoffluorescencebyiScanReader.Theassayconsiders upto fourmillionSNPs ina single sample run, or evenupto severalhundredthousandmultiple samples in the same array. The chemistry involves incubation of samples on bead chip where they anneal to locus-specific 50-mers covalently linked to beads followed by allele-specific single-base extension, fluorescent staining, signal amplification, scanning in a dual-color channel reader, and analysis. This technology is advantageous as one can use a premade array that is easily available commercially for selected species. Hamilton et al. [26] identified 69,011 high confidence SNPs from six potato cultivars and used for genotyping with the Infinium platform. A total of 96 ofthese SNPs were used to assess allelic diversity in 248 germplasms and found 82 informative SNPs for subsequent analyses. In 2012, Felcher et al. [166] reported "Infinium 8303 Potato Array" comprising of 8303 functional markers which includes 3018 from candidate genes of interest by utilizing the transcriptome data from Hamilton et al. [26]. These were used for the genotyping and development of linkage maps. In tomato, a large-scale SNP genotyping array using 8784 SNPs were obtained from transcriptome sequencing [30] and later used for construction of a high-density linkage map of tomato [70].
