Genetic linkage mapping and genetic analysis of QTL related to eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs

A group of 68 F1 hybrid common carp was used to construct a linkage map using JoinMap4.0 software. A total of 507 microsatellite and SNP markers isolated from genomic library (186 SSR and 321 SNP markers) were assigned to construct the genetic map, comprising 62 linkage groups. The total length of the linkage map for the common carp is 2805.85cM with an average linkage group length of 6.31cM. Both eye diameter and eye cross were located on the genetic map. Eight QTL were found to be associated with eye diameter, explaining 16.60–36.70% of the total phenotypic variation. Eleven QTL were found to be related to eye cross, explaining 13.6–31.6% of the total phenotypic variation. Five major QTL for eye diameter and nine major QTL for eye cross explained the highest fraction of the phenotypic variation. The relationship of eye cross and eye diameter with other commercial traits and QTL linkage group analysis suggests that eye diameter and eye cross might be used to assist in indirect selection for body weight and aggregate breeding could achieve multiple effects. These findings have implications for future genetic studies and breeding of the common carp. ► Many SNP markers were used to construct the genetic linkage maps. ► SNP markers were able to provide more genetic information. ► Genomic regions for eye cross and eye diameter were accurately located. ► This essay provides information for further research on eye cross and eye diameter. ► The correlation analysis would assist and improve the future of breeding work.