QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp (Hypophthalmichehys nobilis)

Bighead carp (Hypophthalmichthys nobilis) is a popular Asian aquaculture species, but its genetic improvement is still in infancy. Marker-assisted selection (MAS) can improve the selection efficiency of breeding programs in fish. In this study, we constructed a genetic linkage map in a F1 family of bighead carp using microsatellite markers. A total of 905 microsatellites were assigned onto 24 linkage groups (LGs) of a consensus map, which spanned 1631.7 cM of bighead carp genome with an average interval of 1.8 cM. Comparative genomics revealed a high level of genomic synteny between bighead carp and zebrafish. QTL mapping for growth traits was performed based on this linkage map, and three significant and 8 suggestive QTL associated with four growth traits (body length, body height, head length, body weight) were detected on LG9 and LG17, with 18.6-25.5% of phenotypic variance explained. Three candidate genes for growth were identified in or near the QTL intervals, and a SNP in one of the three genes, TP53BP2, was significantly associated with growth traits in different populations of bighead carp. These results of the high-density SSR genetic map and genome scan for QTL provide a basis for MAS and breeding programs for growth in bighead carp.