Transcriptomic profiling reveals the adaptive mechanisms of Penaeus vannamei alkali-tolerant families under combined pH and alkalinity stress.

Soil salinization is an increasingly critical global issue for which fishery-based utilization has emerged as a promising mitigation strategy. Penaeus vannamei is an ideal species for aquaculture in saline-alkali waters; however, the differences in alkali tolerance among various families and their underlying mechanisms remain largely unexplored. In this study, alkali-tolerant families were identified through median lethal time (LT50) assays under high alkalinity and elevated pH. Comparative analyses with wild-type family revealed that alkali-tolerant families showed significant differences in energy metabolism and ion transport (Na+/K+-ATPase (NKA), carbonic anhydrase (CA), and cystic fibrosis transmembrane conductance regulator (CFTR)) Transcriptomic analysis showed that alkali-tolerant families had pathways related to cytoskeletal remodeling, including actin cytoskeleton organization (GO:0030029) and myosin complex (GO:0016459). KEGG analysis further revealed enrichment in cardiac muscle contraction (ko04260) and adrenergic signaling in cardiomyocytes (ko04261). We propose that CaCO3 precipitation reduces extracellular Ca2+ levels and disrupts the carbonate buffering system under high pH and alkalinity. In response, alkali-tolerant families mitigate pH and alkalinity stress by enhancing ion regulation and energy efficiency while simultaneously downregulating high-energy Ca2+ regulatory pathways and remodeling gill microstructures. Collectively, these findings provide novel insights into the alkali adaptation mechanisms of P. vannamei and support selective breeding strategies to improve stress resilience in saline-alkali aquaculture.