Genetic Diversity and Differences among Three F1 Families and Two Wild Populations of Genus Scylla Using Microsatellite Markers

Genetic diversity is the determinant of the allocation of germplasm resources in the genetic improvement of aquaculture species. In this study, three F1 families, including a hybrid Scylla family (S. paramamosain ♂ × S. serrata ♀), a paternal family of S. paramamosain, a maternal family of S. serrata, and two wild populations, including a paternal population of S. paramamosain and a maternal population of S. serrata, were used to investigate the genetic diversity and genetic difference. The results indicated that 98 alleles of nine microsatellites loci were observed in five Scylla populations. The highest average value of Ho (observed heterozygosity), He (expected heterozygosity), and PIC (polymorphic information content) of the wild S. paramamosain population were 0.790, 0.799, and 0.771, respectively, suggesting the wild paternal population has high genetic diversity. The comparative analysis of PIC, Fst (fixation index), and HWE (Hardy–Weinberg equilibrium) indicated that the paternal S. paramamosain may be more suitable for artificial breeding than the maternal S. serrata from the perspective of allele frequency. Analysis of molecular variance analysis (AMOVA) showed that the total genetic variation mainly occurred within populations (73.28%), demonstrating that artificial breeding may induce genetic differentiation of the family groups of Scylla. The results of the analysis of Fst value, UPGMA (unweighted pair-group mean analysis) dendrogram, and genetic diversity indicated that the F1 hybrid offspring had a close genetic distance and high genetic identity with the paternal S. paramamosain populations. It indicated that the F1 hybrid offspring showed potential paternal genetic affinities and a similar potential for artificial breeding with S. paramamosain. The study will provide valuable information to evaluate the difference in the genetic diversity and population structure between hybrid offspring and distinct parental populations of Scylla.