Development of a haplotype reference panel and analysis of genetic structure in Golden Pompano (Trachinotus ovatus)

Trachinotus ovatus, a valuable marine fish, is primarily farmed in the South China Sea. Intensive aquaculture can lead to genetic uniformity and disease risks. Additionally, the high cost of genome sequencing restricts knowledge of genetic variation, hindering genetic analysis and breeding advancements. This study investigated the genetic diversity and structure of Trachinotus ovatus populations within the South China Sea aquaculture context, with the goal of strengthening sustainability. Additionally, the study also enhanced breeding strategies by developing a high-quality haplotype reference panel and an efficient imputation process. Through high-throughput sequencing (depth＞20X), 173 samples from three key breeding sites (SanYa, Hainan; Zhanjiang, Guangdong; and Beihai, Guangxi) were analyzed, revealing substantial genetic diversity and distinct population structures. Notably, the Beihai (BH) population exhibited significant stratification, suggesting regional genetic uniqueness. Low levels of genomic inbreeding coefficient and the identification of unique SNP loci across populations underscored the genetic richness within these Trachinotus ovatus communities. A major constructed of this work is the creation of the first high-quality haplotype reference panel for the species, demonstrating genotype imputation's viability as a cost-effective alternative for large-scale genetic studies in aquaculture. In particular, a Shapeit reference panel with 5476,550 SNPs was created, excelling in accuracy across various depths, notably achieving up to 95.8 % imputation accuracy at 1X sequencing depth. This high accuracy across populations shows the importance of genetic diversity in the panel. This research not only advances the understanding of Trachinotus ovatus genetic foundations but also provides crucial insights for conservation efforts and genetic analysis. By establishing a robust haplotype reference panel for Trachinotus ovatus helps lower the costs of future genetic research and variation studies, this study lays the foundation for sustainable aquaculture practices and breeding programs.