Microsatellite and SNP sequencing data of different populations of Litopenaeus vannamei

Knowledge of the genetic information within the population is crucial for the stabilization of genetic diversity and for the strategic planning of subsequent selection processes. This study assesses the genetic diversity of six populations (two breeding populations and four introduced populations, totaling 180 individuals) of Litopenaeus vannamei based on genotyping data from 12 microsatellite markers and whole-genome resequencing. After resequencing and filtering, 14136203 loci were used for genetic diversity analysis. Genetic diversity parameters were calculated for six populations of L. vannamei based on these genetic data. In SSR analysis, population SIS diversity was the highest and XH-F diversity was the lowest among the six populations. In SNP analysis, the results indicate that the XH-F was under selection and has the lowest genetic diversity among these six populations, SIS heterozygosity level was the lowest, but the polymorphism was high, with more low-frequency loci. In population differentiation analysis, the results of the two markers were similar. The results of population differentiation analysis of the two markers showed that populations XH-F and SyAqua were highly differentiated from other populations. In the present study, both molecular markers were able to clearly classify different populations of L. vannamei. PCA analysis showed that there were obvious differences among different groups. In phylogenetic tree and ancestral estimation analysis, SSR can only classify six populations into three groups. At the individual level, SSR was more suitable for distinguishing genetic differences among individuals. When the K value increases, SSR may face limitations that prevent further subdivision of the population into six groups. In contrast, SNPs exhibit stronger discriminative ability and can clearly divide these six populations into six groups. The data and results generated from this study will contribute to enriching the genetic resources of L. vannamei and provide important reference information for its artificial breeding and genetic improvement. About this data, it is composed of microsatellite sequencing data (.fsa) and resequencing filtered data (VCF format).