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 arrangement in PI 310467. Using LD analysis in 192 natural accessions of Arabidopsis thaliana, we identified no translocations, but also noted that dosage haplotypes tended to vary continuously and resulted in higher noise. This method should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.

Experimental population

The input table is from a segregating population, i.e. dihaploids produced by a potato haploid induction cross. 

Solanum tuberosum var. PI 310467 (listed as Desiree in the GRIN germplasm collection) (4x) x S. tuberosum phureja var. IvP48 (2x)

the progeny individuals were sequenced and subjected to bin-by-sam analysis. These individuals had a diploid genome content and represent maternal gametes since the paternal genome was eliminated. Reads mapping in a given bin were standardized by the mean counts obtained in the same bin.

https://github.com/lcomai/cnv_mapping