Construction of the first high-density genetic linkage map of pikeperch (Sander lucioperca) using specific length amplified fragment (SLAF) sequencing and QTL analysis of growth-related traits

Abstract

High-density genetic linkage maps play an important role in genome assembly, quantitative trait locus (QTL) mapping, and marker-assisted selection. Pikeperch (Sander lucioperca) is a popular inland aquaculture species in Europe and Asia, but the genetic improvement of this species is still in its infancy. In this study, genomic DNA extracted from two pikeperch parents and 150 F1 offspring was subjected to high-throughput sequencing and specific length amplified fragment (SLAF) library construction. In total, 436.58 M reads (87.28 G data) were acquired, with average sequencing depths of 100.16-fold for the parents and 19.51-fold for each F1 offspring. A total of 237,687 high-quality SLAFs were detected, 34,774 of which were polymorphic and used for linkage map construction. The final merged linkage map consisted of 8159 SLAFs in 24 linkage groups (LGs) and spanned 3421.81 cM, with an average inter-marker distance of 0.46 cM. Based on this high-density genetic linkage map, 21 QTLs were identified for eight growth-related traits: total length, body weight, body length, head length, body height, body thickness, body girth, and slaughter weight. Three QTLs for each trait, including slaughter weight, body girth, body weight, and body thickness, were detected on LG6 or LG16. Moreover, five QTLs for body length were detected on LG6, LG9, and LG18. QTLs for total length, body height, and head length were detected on LG6. The linkage map and QTLs for growth-related traits identified in this study should be useful for improving pikeperch marker-assisted selection in the future.