PotatoMASH

We have developed PotatoMASH (Potato Multi Allele Scanning Haplotags), a novel low cost, genome scanning marker platform. We designed a panel of 339 multiallelic regions placed at 1 Mb intervals throughout the euchromatic portion of the genome. These regions were assayed using a multiplex amplicon sequencing approach, which allows to genotype hundreds of plants at a cost of 5 euro per sample. We applied PotatoMASH to a population of over 700 potato lines. We obtained tetraploid dosage calls for 2,012 short multiallelic haplotypes in 334 loci, which ranged from 2 to 14 different haplotypes per loci. The system was able to diagnose the presence of targeted pest resistance markers, to detect quantitative loci traits (QTLs) by Genome wide association study (GWAS) in a tetraploid population, and to track variation in a diploid segregating population. PotatoMASH efficiently surveys genetic variation throughout the potato genome, and can be implemented as a single low cost, genotyping platform that will allow routine and simultaneous application of MAS and other genotyping applications in commercial potato breeding programmes.