Genetic diversity and association analysis of two duplicated ODC genes polymorphisms with weight gain in Cyprinus carpio L.

Abstract

Ornithine decarboxylase (ODC) is a rate-limiting enzyme in polyamine synthesis, and its activity can be used as an indicator of protein synthesis. In this study, we cloned two ODC1 genes from Cyprinus carpio var. Jian, namely CcODC1a and CcODC1b, identified five and three single nucleotide polymorphism (SNP) loci in the CcODC1a and CcODC1b sequences, respectively. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to discriminate the genotypes of these SNP loci in a Jian carp breeding base population. Except for a-E6-A212G and b-I3-A126G, all other SNP loci strayed from Hardy–Weinberg equilibrium. The polymorphism information content ranged from 0.28 to 0.38. The expected heterozygosity and observed heterozygosity were 0.34–0.50 and 0.347–0.626, respectively. So the population had medium heterozygosity and abundant variation, suggesting that sufficient breeding potential existed in the population. Stepwise regression method results indicated the additive effects of three SNPs (a-E6-A98C, a-E9-A19G and b-I3-A126G) on body weight gain were extremely significant at 0.01 level, and the dominant effects of b-I3-A126G was also significant at 0.05 level. All the three additive effects SNPs had body weight gain advantageous genotype AA. The individuals inherited advantageous genotype AA of b-I3-A126G with the highest body weight gain, showed the greatest potential of being important candidate molecular marker, which could be used in fast growing common carp breeding in the future.