Genome Wide Structural Variants Provide Insights into Population Structure and Genetic Divergence in Pacific White Shrimp (Litopenaeus vannamei) Breeding Populations

Structural variants (SVs) are a major yet underused source of adaptive variation in aquaculture. We built a genome‑wide SV atlas for 180 Litopenaeus vannamei from six commercial breeding populations and discovered 1,159,046 SVs spanning 15 bp to 999 kb, with uneven chromosomal distributions and multi‑type hotspots. Over 45.52% of SVs overlapped repeats—especially simple sequence repeats, DNA transposons, and LINEs. SV and SNP densities were highly correlated. Across populations, 482k SVs were shared and 145,623 were singletons; the fraction of deletions increased from shared to singleton classes. BMK and KH harbored more singletons than SIS, RH and CP, indicating greater divergence. PCA and ADMIXTURE recovered three major clusters and revealed the substructure in RH, mirroring SNP analyses. Selection scans identified 171-274 sweep windows per population encompassing 123-238 candidate genes. Functional enrichment yielded 976 significant GO terms, 90.79% population‑specific, underscoring divergent breeding objectives. Nevertheless, 17 genes showed parallel signals in over 3 populations; many carry short deletions likely affecting regulatory or coding elements. Together, these results show that genome architecture and domestication jointly shape the shrimp SV landscape; that SVs alone robustly resolve population history; and that a small set of recurrent, deletion‑bearing regulatory genes may underpin convergent improvement. The SV map and candidate loci provide diagnostic markers for germplasm tracing and actionable targets for marker‑assisted or genomic selection in L. vannamei breeding.