Analysis of seven populations of cultured redclaw crayfish, Cherax quadricarinatus, using newly developed microsatellite markers

Cherax quadricarinatus, also known as the redclaw crayfish, is native to northern Australia and southern Papua New Guinea and is an important freshwater aquaculture species in many countries. Studying the genetic structure of the current cultured population can improve the breeding plan for redclaw crayfish to better manage the hybridization and germplasm bank and promote their rational utilization; however, microsatellite resources for redclaw crayfish remain insufficient. The purpose of this study was to analyze the genetic diversity of different redclaw crayfish populations in China. After screening 18 pairs of microsatellite markers from redclaw crayfish transcriptome data, 240 samples from seven main breeding areas (Changsha, Guangzhou, Haikou, Huzhou, Jiangmen, Wuxi, and Zhanjiang) were evaluated and detected using these microsatellite markers. In total, 97 alleles were detected, of which the minimum number was two and the maximum number was twelve. The observed heterozygosity ranged from 0.258 to 0.807, with an average of 0.559, and the expected heterozygosity ranged from 0.288 to 0.815, with an average value of 0.558. The polymorphic information content values of seven populations ranged from 0.268 to 0.791, with an average of 0.511. Moreover, pairwise genetic differentiation within the population was between 0.007 and 0.031. The UPGMA clustering results showed that the Zhanjiang population stands alone on a branch, but the genetic variation between branches is very small. Meanwhile, STRUCTURE analysis further revealed that the genetic backgrounds of each population are essentially identical, with no noticeable genetic differentiation arising from geographic differences. These results provide a basic assessment of the genetic diversity of the main cultured populations of redclaw crayfish and a molecular foundation for future genetic monitoring and selective breeding research.