Microsatellite Markers Developed Based on Transcriptomic Data Reveal the Genetic Diversity and Population Genetic Structure of Angulyagra polyzonata in Guangxi, China

<i>Angulyagra polyzonata</i> is a significant freshwater snail species in southern China. However, its wild resources have sharply declined due to overfishing. To assess the current status of germplasm resources in the Guangxi region, during this study, we first successfully developed nine pairs of primers that enable the amplification of highly polymorphic microsatellite markers (SSRs) with trinucleotide and tetranucleotide repeat sequences (PIC values ranging from 0.662 to 0.861) using transcriptomic data. Then, these designed primers were tested and applied for the genetic investigation of selected wild populations of the species. Finally, a genetic diversity analysis was conducted based on 12 wild populations (360 individuals) in Guangxi. After 798,244 SSR loci were screened out via high-throughput sequencing, the results showed that dinucleotide repeats accounted for the highest proportion (47.64%), mainly consisting of (AC/GT)n repeat units. Among the SSR loci in <i>A. polyzonata</i>, microsatellite loci with 5 to 20+ repeats are the most abundant. All nine selected and tested SSR loci significantly deviated from Hardy-Weinberg equilibrium (<i>p</i> < 0.001) and had heterozygote deficiency (average inbreeding coefficient of <i>F</i> = 0.390), indicating widespread inbreeding. The fixation index among populations was high (average <i>Fst</i> = 0.175), with 73% of the genetic variation occurring within populations and 27% between populations. Gene flow (<i>Nm</i>) was generally restricted (most population pairs had <i>Nm</i> < 1), with the (Tiandeng) TD and (Long'an) LA populations showing the smallest differentiation (<i>Fst</i> = 0.017), and the (Qinnan) QN and (Yinhai) YH populations showing the greatest differentiation (<i>Fst</i> = 0.409). UPGMA clustering and structure analysis (K = 2) divided the 12 populations into two subgroups. Overall, our research suggests that the genetic diversity of the wild population of <i>A. polyzonata</i> in the Guangxi region has declined. Thus, prioritizing the protection of highly genetically diverse populations, such as the LA population, is urgently needed. This study provides a scientific basis for the protection and sustainable utilization of <i>A. polyzonata</i> resources in Guangxi.