Fine mapping of growth-related quantitative trait loci in Yellow River carp (Cyprinus carpio haematoperus)

Genetic linkage map and quantitative trait loci (QTL) mapping are powerful tools for genetic analysis of a series of economic traits in aquatic animals. Yellow River carp (Cyprinus carpio haematoperus), one of the famous common carp strains, is widely cultured in northern China, however, genetic and genomic bases of growth-related traits have been rarely studied in this carp strain. In present study, an F2 family of Yellow River carp (8 months old) was used for constructing genetic linkage map and detecting potential QTL for growth traits, including total length (TL), body length (BL), body height (BH), head length (HL) and body weight (BW). A high-density genetic linkage map was constructed mainly based on 2b-RAD technology, with 6230 SNPs and 65 SSRs assigned onto 50 linkage groups, covering 98.2% of the Yellow River carp genome (average 0.59 cM/marker). Comparative mapping showed high levels of syntenic relationship between our map and the genomes of two cyprinid fish (Denio rerio and Ctenopharyngodon idellus), while a lower synteny was detected between our map and C. c. carpio genome. Twelve chromosome-wide and two genome-wide growth-associated QTL were detected in our study, with the phenotypic variance explained ranging from 11.9% to 16.2%. These QTL were scatteredly distributed on 8 LGs of our sex-averaged linkage map. Fifteen candidate genes (e.g. INSIG1, 3 beta-HSD, HGF) were identified by BLAST searching the sequences of QTL-linked markers in Yellow River carp against Denio rerio genome, and their functions involve in the regulation of development, cell-proliferation, energy metabolism, and so on. The identification of significant QTL and potential growth-related genes in this study provides valuable genomic resources for the study of genetic mechanism underlying growth and development, and would contribute to accelerate the progress of marker-assisted selection in Yellow River carp.