Abstract

Litopenaeus vannamei , a key species in global aquaculture, shows excellent growth and adaptability, making it central to shrimp farming. As genetic improvement progresses, the genomic characteristics of L. vannamei populations continue to evolve. To clarify their genetic status, we analyzed selection signals using resequencing data and environmental factors, identifying adaptive genomic regions. In this study, offspring were produced by hybridizing six L. vannamei populations (two breeding and four introduced). The offspring were subjected to ammonia nitrogen and low pH stress experiments, and extreme difference groups were established based on survival time under stress. Whole-genome resequencing was performed on the six original populations and stress groups (320 individuals). After quality control, 17,104,219 high-quality SNPs were obtained. Using the multi-reference population rotation method, we identified population-specific selection regions in six L. vannamei populations through F st and θπ ratio analyses. Functional enrichment revealed multiple cross-functional modules and conserved genes across populations. This distribution indicates that L. vannamei adaptive evolution features both population differentiation and conservation of core pathways. Further multi-method joint analysis using F st , θπ ratio, and XP-CLR identified 356 (ammonia nitrogen) and 370 (low pH) candidate genes in the stressed populations. After GO/KEGG annotation, selection signal screening, and ROH detection, five core stress response genes, including Vang and Coq8 . Genome-wide selection signal analysis in L. vannamei populations revealed key functional genes, thereby enriching genetic resources and facilitating the breeding of new varieties.