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

Abstract

Structural variants (SVs) are a major yet underused source of adaptive variation in aquaculture. We built a genome‐wide SV atlas for 180 Penaeus vannamei from six commercial breeding populations and discovered 1,159,046 SVs, with uneven chromosomal distributions and multi‐type hotspots. Over 63.53% of SVs overlapped repeats—especially simple sequence repeats, DNA transposons, and LINEs. SV and SNP densities were highly correlated. Across populations, 482 k 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 78–193 sweep windows per population encompassing 38–161 candidate genes. These genes were predominantly enriched in population‐specific processes such as chromatin regulation, meiotic recombination, membrane‐associated functions, suggesting that structural variants may contribute to divergence in reproductive, metabolic, and structural pathways across breeding programs. Nevertheless, 10 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 candidate loci for marker‐assisted or genomic selection in P. vannamei breeding.