Genetic diversity analysis and fingerprint construction for different geographical populations of the sea cucumber (Apostichopus japonicus) based on SSR markers

Abstract:

To evaluate the genetic diversity of the sea cucumber (Apostichopus japonicus) populations, thirteen simple sequence repeat (SSR) loci were used to amplify eight different geographical populations of sea cucumbers collected from China, Korea and Russia. The results showed that the average observed heterozygosity (Ho) and average expected heterozygosity (He) of 13 microsatellite loci were 0.47 and 0.80, respectively. The polymorphism index content (PIC) of the 13 loci ranged from 0.465 (AJ06) to 0.909 (AJ09). Except for AJ06, the loci were moderately polymorphic (0.250.5). The number of alleles (A) ranged from 10 (AJ06) to 34 (AJ07), with an average of 19.4. The total number of effective alleles was 83.8. The number of effective alleles (Ne) ranged from 1.7 (AJ06) to 11.8 (AJ09), and the average number was 6.5. The results of genetic diversity analysis showed that the PIC ranged from 0.6392 (SK-MP-B) to 0.7122 (QD), indicating that all populations had high genetic diversity. The construction of DNA fingerprints could distinguish all eight populations. The eight populations of sea cucumbers were allocated to three free-mating groups using Structure software, which were consistent with those generated using UPGMA cluster analysis. UPGMA cluster analysis showed that the Qingdao, Yantai, and Mokpo black populations were clustered into one group, whereas the Russian, Posco yellow, Kunsan black, and Posco black populations were clustered into another group. The Posco red population was located in the exception group and was located on a separate branch. Cluster analysis showed that the genetic structure and differentiation of the populations of sea cucumbers were not only related to the geographic location but was also related to body color. The results provided the foundation for the genetic identification and genetic resource conservation of the sea cucumber.