Metabolomics‐Driven Pre‐Growout Phenotyping Identifies Candidate Metabolic Signatures Associated With White Shrimp Performance

Selective breeding has improved the performance of Pacific white shrimp ( Penaeus vannamei ), yet routine selection still relies mainly on late‐stage phenotypes that are costly to measure and sensitive to fluctuating pond environments. Here, we tested whether early‐life hepatopancreas metabolomes can capture line‐associated physiological differences relevant to production. Postlarvae at day 40 (PL40) from four breeding lines (designated as TK1–TK4) were profiled using an UHPLC–HRMS‐based untargeted metabolomics workflow in positive‐ion mode. Metabolomic signatures were related to a matched 60‐day grow‐out evaluation, in which TK3 achieved the highest final weight (15.80 ± 1.20 g) and the lowest observed feed conversion ratio (FCR) (1.50 ± 0.07), whereas survival varied substantially across lines (54.1%–89.5%), with TK3 and TK4 showing higher survival than TK1 and TK2. Principal component analysis (PCA) revealed line‐dependent clustering, and pairwise orthogonal partial least squares–discriminant analysis (OPLS‐DA) models supported exploratory discrimination of TK3 from each comparator line. Differential metabolite and pathway analyses implicated coordinated variation in amino acid and nitrogen handling, nucleotide turnover, and lipid utilization, with recurring enrichment of histidine metabolism, lysine degradation, purine metabolism, and glutathione‐related processes. Receiver operating characteristic (ROC)‐based prioritization further highlighted a subset of candidate metabolites for follow‐up targeted validation. Given the limited metabolomics cohort size, these findings should be interpreted as exploratory discovery‐stage signatures rather than validated biomarkers. By leveraging known grow‐out divergence among breeding lines, this study adopted a performance‐anchored retrospective design to nominate PL40 metabolic pathways and candidate metabolites that may support future pre‐growout screening in shrimp improvement programs after independent validation.