Genetic variability in wild and selected populations of Ctenopharyngodon idella using microsatellite markers

To evaluate the genetic diversity and population structure in two generations of selected populations after using selective breeding, we carried out the genetic analysis in four wild populations (Hanjiang, Jiujiang, Shishou, Wujiang) and two selected populations (F₁ and F₂) of Ctenopharyngodon idella using a multiplex microsatellite PCR method. The results showed that the genetic variations of six C. idella populations were relative high and the genetic diversity parameters of two selected populations lower than wild populations except for average number of alleles (N_a). The Hardy-Weinberg equilibrium results showed that 62 loci of the 120 population-locus combinations deviated significantly from the Hardy-Weinberg equilibrium. The F_is of 51 loci were positive value while the others were negative in the 62 population-loci combinations. The AMOVA analysis showed that 3.75% of the variation were among populations, and 96.25% of that were within populations. The overall genetic differentiation index (F_st) was 0.038. The F_st analysis showed that the F_st values between the Shishou population, F₁ population and F₂ population were higher than 0.05, which were moderately differentiated. There was lower differentiation among the remaining populations. The F_st between F₂ population and four wild populations were higher than those between F₁ population and four wild populations. The Nei’s genetic distance (D_n) results showed that the D_n values between two selected populations and four wild populations were higher than those among four wild populations. The UPGMA phylogenetic tree based on Nei’s genetic distance showed genetic relationships between selected populations and wild populations were farther than those among four wild populations. The above results showed that the genetic diversity of two selected populations decreased compared to four wild populations, but they still have higher level of genetic diversity. The selective breeding had already changed population structure of two selected populations, but the change was not obvious. The results in this study provided an important reference for the establishment of a more complete and effective breeding program.