Comparative RAD sequencing for detecting SNPs with differential allele frequency between potato genotypes with high and low tuber yield, starch content and starch yield

Potato tuber yield, starch content and starch yield are complex agricultural traits. Their optimization is important in potato breeding programs. The genes and their natural allelic variation, which control these traits, particularly yield and starch yield, are mostly unknown. To discover these genes we grouped 90 potato varieties and breeding clones according to field evaluation of tuber yield and starch content in three pairs of genotype groups (case-control populations) with high and low mean tuber yield (24 genotypes per group), high and low mean tuber starch content (24 genotypes per group) and high and low mean starch yield (21 and 24 genotypes, respectively). RAD libraries were constructed from the 90 genotypes (6 genotypes were replicated) and sequenced. The sequences were mapped against the potato genome sequence. The sequence reads of individual genotypes were assigned to the three case-control populations and pooled for cases (high phenotypic mean value) and controls (low phenotypic mean value). Bi-allelic SNPs were called within case-control populations and their allele frequencies were compared to detect differential SNPs.