Two new publications from the group appeared online at the start of the new year! The first paper concerns ClusterCall, a new R package for making tetraploid genotype calls from the potato SNP array. Because commercial potato germplasm is autotetraploid, there are three possible heterozygous genotypes for bi-allelic SNPs, which complicates conversion of the raw signal intensity into reliable marker data. ClusterCall automates this process and provides a concordance metric that can be used to filter out unreliable markers. The R package and a tutorial can be downloaded from the software section of the website.
The second paper describes how data from the potato SNP array was used to curate pedigree records for more than 700 elite varieties and breeding lines. Pedigree errors can arise in several ways, and correcting them is important for legal, cultural, and technical reasons. Our research is notable because not only did we identify numerous genotypes with mistaken parentage, in many cases the true parents were discovered unambiguously. For example, Hodag is a new chip processing variety released in 2015, with recorded parentage Pike x C31-5-120 (a genetic stock from UW). From the marker data we discovered that C31-5-120 is not the male parent; the true father is Dakota Pearl.