Genomic dosage values of dihaploid progeny of potato accession PI 310467 reveal translocation 8-7

Large scale structural variations (SV), such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple method aimed at identifying translocations using only dosage variation information. Using sequence-based analysis of copy-number haplotypes in segregating populations we identify regions of the genome that exhibit unexpected linkage. For each dosage-polymorphic 1Mb bin, we tested linkage disequilibrium in nine potato (Solanum tuberosum) dihaploid families. In two populations we found evidence for translocation: in cv. PI 310467, a non-reciprocal translocation between chr. 7 and chr. 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma”, the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted ar...