Generation of a linkage map for the hybridising toads Bombina bombina and B. variegata

This study provides a dense linkage map for the hybridising toads Bombina bombina and B. variegata. These anciently diverged toads with large genomes (7.8 Gbp) hybridise freely wherever their distribution ranges adjoin in Central Europe. The linkage map facilitates the genomic analysis of natural hybrids and of patterns of introgression. A draft genome of a B. v. variegata male was assembled from Illumina short reads and molecular baits were designed for 5000 target loci. Enriched genomic libraries for 162 F2 offspring of a B. bombina x B. variegata cross were sequenced and and the taxon of origin was inferred for the 324 F2 haplotypes at each target locus. The linkage map contains 12 linkage groups corresponding to the 12 Bombina chromosomes. It also identifies males as the heterogametic sex in these taxa with homomorphic sex chromosomes and locates the sex-determining region within 7 cM of LG5 (homologous to Xenopus tropicalis chromosome 5)