Genetic diversity analysis of four consecutive selective breeding generations in even years of white-carapaced strain of Eriocheir sinensis based on SSR markers

To explore the dynamic variation patterns of genetic diversity in the white-carapaced strain of Chinese mitten crab (Eriocheir sinensis) during the even-year breeding process, we utilized 25 microsatellite loci to analyze four consecutive selective breeding generations of white-carapaced strain, with unselected green-carapaced crabs serving as the control group. A total of 669 alleles were detected across eight populations. The results indicate a declining trend in genetic diversity among generations of white-carapaced strain, with effective population sizes of 189.0, 226.9, and 213.2 from the first generation (G1) to the third generation (G3). The effective population sizes values for the control group were 184.2, 250.5, and 252.3, respectively. Both populations maintained relatively high levels of genetic diversity. Hardy-Weinberg equilibrium tests show that 66% of the data significantly deviated from equilibrium, indicating an unstable genetic structure within the breeding population. The genetic distance between the offspring and the founding population (G0) progressively increased across generations, rising from 0.273 to 0.360, with low genetic differentiation (F_st<0.05) observed between G0 and G3. AMOVA analysis reveals that 99% of genetic variation was attributable to differences within individuals, while only 1% was due to variation between populations. In summary, after four generations of selective breeding, the genetic diversity of white-carapaced strain had slightly decreased but remained at a relatively high level. Future breeding programs should ensure sufficient breeding stock and effective population size to maintain genetic diversity and prevent inbreeding depression.