Genotyping-by-Sequencing in Potato

Genotyping-by-sequencing (GBS) is one of the most cost-effective approaches to sequencing in potato (SNP) discovery and genotyping. The reduction of genome complexity that is central to the GBS approach is useful in the analysis of many plant genomes in which large size and polyploidy can prove challenging. In previous work in our lab, GBS has been explored and optimized on a tetraploid potato using two different enzymatic approaches (ApeKI and PstI/MspI) and two modes of genotyping (diploid and tetraploid) (Bastien et al., Submitted). This chapter describes the GBS process, starting with library preparation to sequencing data analysis and single nucleotide polymorphism (SNP) calling and filtering of GBS-derived markers. It also presents examples of the obtained results, an assessment of marker quality and their potential uses.