The replacement of fishmeal with plant protein is widely regarded as a key strategy for sustainable aquaculture. However, carnivorous marine fish often show limited tolerance to fishmeal-free diets. Here, we investigated growth performance, hepatic physiological responses, and molecular mechanisms underlying adaptation to a soy protein concentrate-based diet (SPCD) in golden pompano (Trachinotus ovatus). An 8-week feeding trial was conducted under communal rearing conditions, followed by the phenotypic stratification of SPCD-fed fish into high- and low-growth subgroups. Growth performance, serum biochemical indices, and liver histology were assessed, and integrated transcriptomic and metabolomic analyses were performed on liver tissue. At the population level, the SPCD resulted in reduced growth, a lower feed intake, and decreased feed utilization efficiency compared with a fishmeal-based diet. Notably, marked inter-individual variation was observed: fish fed the SPCD exhibited significantly lower final body weights and a higher FCR compared with the FMD group (p < 0.001), and pronounced growth divergence was observed between the PB and PS subgroups, with a subset of SPCD-fed fish maintaining growth comparable to fishmeal-fed controls, whereas others exhibited severely constrained growth. Divergent phenotypes were associated with distinct hepatic alterations, including aggravated vacuolation, the enrichment of tight junction-related and immune regulatory pathways, and the broad reprogramming of lipid metabolism. Integrated multi-omics analysis identified arachidonic acid metabolism as the most significantly perturbed pathway, characterized by altered membrane phospholipid composition, the upregulation of RARRES3L, increased COX/LOX-derived eicosanoids, and the suppression of the CYP–EET branch. Collectively, these findings indicate that soy protein replacement induces coordinated hepatic structural and metabolic remodeling, with tight junction disruption and arachidonic acid metabolic reprogramming contributing to inflammatory imbalance and divergent growth phenotypes in T. ovatus.

Single nucleotide polymorphism (SNP) arrays provide efficient and scalable platforms for genetic diversity assessment, population genomic analysis, and molecular breeding in aquaculture species. However, a high-throughput SNP genotyping platform specifically developed for golden pompano (Trachinotus ovatus), an economically important marine aquaculture fish, remains limited. This study aimed to develop and evaluate a liquid SNP array for T. ovatus and assess its applicability in population genetic analyses. Genome-wide SNP resources were generated from 200 individuals representing 10 cultured populations of T. ovatus. Following SNP discovery, quality filtering, probe evaluation, and marker optimization, a 40K liquid SNP array, designated Changxin-I, was constructed. The performance of Changxin-I was evaluated using an independent validation cohort of 144 individuals from five cultured populations with both WGS-derived and array-derived genotype data available. The array exhibited high genotyping performance, with an average SNP detection rate of 99.94% and a genotype concordance rate of 96.23% with WGS data. Genetic diversity and population structure analyses were performed using Changxin-I genotype data, and the inferred population patterns were compared with those obtained from whole-genome resequencing (WGS) data from the same individuals. A total of 40,476 SNPs were selected for the final Changxin-I array, including 40,442 genome-wide background markers and 34 trait-associated SNPs. The validation results showed high genotyping quality, with an average mapping rate of 98.87% and a mean SNP detection rate of 99.94%. Most SNP markers (99.93%) exhibited minor allele frequencies (MAF) greater than 0.10. Changxin-I successfully revealed genetic diversity and population differentiation among cultured populations, and the population structure patterns were consistent with those obtained from WGS-based analyses. Changxin-I represents a reliable and efficient genomic tool for large-scale SNP genotyping in golden pompano. This array provides a practical platform for population genetic studies, germplasm characterization, and future genomic-assisted breeding applications in T. ovatus.

Background: Longfin batfish (Platax teira) is an important economic species in southern China. In recent years, its wild population has significantly declined due to overfishing. Around 2015, breakthroughs in the artificial large-scale seedling technology for P. teira have promoted the growth of its aquaculture scale in regions such as Hainan and Guangdong. Methods: To study the genetic diversity, inbreeding status, and population structure of the current P. teira farming populations in China, we performed whole-genome resequencing technology and high-density SNP markers to analyze the genetics of four main farming populations. A total of 109 individuals from four populations (NA, ZP, XL, and XC) were sequenced, identifying 5,384,029 high-quality SNPs. Results: The results showed that the nucleotide diversity (π) of each population ranged from 0.00155 to 0.00165 and observed heterozygosity (Ho) ranged from 0.253 to 0.282, which indicated low levels of genetic diversity. The results of the ROH analysis show significant inbreeding in the NA population. Genetic differentiation analysis revealed that the genetic differentiation among NA, XC, and ZP populations was relatively low (F_ST = 0.021–0.029). Conclusions: NA, XC, and ZP populations likely share a common origin of their fry stocks. Based on a phylogenetic tree, principal component analysis (PCA), and population structure analysis, the four populations were divided into four genetic groups. This study is the first analysis of the genetic diversity and population structure of P. teira farming populations in China, laying the foundation for the establishment of a base breeding population and the implementation of genetic improvement programs.