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).解析群体内的遗传信息，对于维持遗传多样性以及规划后续选育工作的战略方案均具有重要意义。本研究依托12个微卫星标记（microsatellite markers）的基因分型数据与全基因组重测序数据，对凡纳滨对虾（Litopenaeus vannamei）的6个群体（含2个选育群体、4个引入群体，总计180个个体）的遗传多样性展开评估。经重测序与数据过滤后，共获得14136203个有效位点用于遗传多样性分析，并基于该遗传数据计算了6个凡纳滨对虾群体的各项遗传多样性参数。 在简单序列重复（Simple Sequence Repeat，SSR）标记分析中，6个群体里SIS群体的遗传多样性最高，XH-F群体的多样性最低；在单核苷酸多态性（Single Nucleotide Polymorphism，SNP）标记分析中，结果显示XH-F群体处于选择压力之下，且为6个群体中遗传多样性最低的群体，SIS群体的杂合度水平最低，但多态性较高，拥有更多低频位点。 群体分化分析结果显示，两种分子标记的分析趋势一致：XH-F与SyAqua群体与其余群体的遗传分化程度较高。 主成分分析（Principal Component Analysis，PCA）结果表明，不同群体间存在显著的遗传差异。 在系统发育树与祖源推断分析中，SSR标记仅能将6个群体划分为3个类群；在个体水平上，SSR标记更适用于区分个体间的遗传差异，且当K值升高时，SSR标记难以将群体进一步细分为6个，存在一定应用局限性。与之相比，SNP标记的判别能力更强，可将6个群体清晰划分为6个类群。 本研究产生的数据与结果，将有助于丰富凡纳滨对虾的遗传资源，为其人工繁育与遗传改良工作提供重要的参考依据。 本数据集包含微卫星测序数据（格式为.fsa）与重测序过滤后数据（格式为VCF）。