Elite allele mining for growth rate traits in common carp (Cyprinus carpio) by association analysis

Growth is one of the important economic traits to be improved in the breeding of common carp, yet the genetic basis in it remains unclear. In this study, a GoldenGate assay containing 1,536 SNP was used to genotype a full-sib panel of 68 individuals of mirror carp Cyprinus carpio. Association studies were carried out between SNP and growth rate for three consecutive months of the panel. 15 loci significantly associated with growth rate were identified using the general linear model and the mixed linear model, which located in eight chromosomes (chr6, 8, 9, 11, 20, 28, 32 and 35) and four scaffolds (scaffold902, 28835, 29008 and 29015). The phenotypic variance of these associated loci ranged from 6.4% to 19.2%. The elite alleles were mined based on the average phenotypic allele effect (AAE) of each allele. 15 elite alleles were screened out with 6.60% higher than the average phenotypic allele and 16.88% higher than the non-elite ones among the four traits. Meanwhile, 15 candidate genes were scanned and annotated. The loci and elite alleles of growth rate identified may facilitate marker-based breeding for rapid growth in common carp.

Automated summary

This study identified 15 loci and elite alleles significantly associated with growth rate in common carp, which could be used for marker-based breeding to achieve rapid growth in fish species.