Development and Evaluation of the 40K Liquid SNP Array for Population Genetic Analysis in Golden Pompano (Trachinotus 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.