An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

In this study, we report the construction of an ultra-high density linkage map for pikeperch based on single nucleotide polymorphisms (SNPs). Genomic DNA from 18 broodstock (11 males and 7 females) and 375 individuals from the progeny was isolated. One male fish from the broodstock was sampled twice, giving a total of 394 samples from 393 different individuals. Whole genome pair-end sequencing was performed on each of the samples. The sequence data was used for SNP discovery and with the resulting SNP database we constructed an ultra-high density linkage map. This map represents an important tool for improving the contiguity and accuracy of the current genome assembly for pikeperch.