Data from: A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination

Genetic linkage maps are essential for comparative genomics, high quality
genome sequence assembly and fine scale quantitative trait locus (QTL)
mapping. In the present study we identified and genotyped markers via
restriction-site associated DNA (RAD) sequencing and constructed a genetic
linkage map based on 1,597 SNP markers of an interspecific F2 cross of two
closely related Lake Victoria cichlids (Pundamilia pundamilia and P. sp.
'red head'). The SNP markers were distributed on 22 linkage
groups and the total map size was 1,594 cM with an average marker distance
of 1.01 cM. This high-resolution genetic linkage map was used to anchor
the scaffolds of the Pundamilia genome and estimate recombination rates
along the genome. Via QTL mapping we identified a major QTL for sex in a
∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus
LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination
gene (amh).