A high-density genetic linkage map and QTL mapping for growth related traits in grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella), one of the most important freshwater food fish, has made a great contribution to freshwater aquaculture in China. Though a consensus linkage map of grass carp has been reported, the low marker resolution limited its application in fine mapping quantitative trait loci (QTL) of commercially important traits. In this study, a high-density linkage map was constructed based on a full-sib F-1 family of grass carp, which was further used for mapping QTL for five growth related traits: body weight (BWE), body length (BL), body width (BWI), body height (BH) and fatness (FN). This high-density genetic map was constructed with 3979 SNPs, consisting of 24 linkage groups (LGs). The total length of the linkage map was 1752.742 cM, with an average marker resolution of 0.44 cM. QTL mapping analysis detected two significant and 19 suggestive QTL for the five morphometric traits, distributed on 8 LGs. The phenotypic variations explained of these QTL ranged from 7.2% to 32.8%. Finally, comparative genomic analysis revealed that 23 out of the 24 LGs of grass carp showed high synteny with 23 chromosomes of zebrafish. Taken together, the high-density linkage map and the 21 growth-related QTL, provide valuable genomic resources for both marker-assisted selection (MAS) and comparative genomic studies in grass carp and its related species.