Linkage Map and Single Nucleotide Polymorphism Association with Growth Traits and Flesh Color in the Oyster Pompano (trachinotus Anak)

The oyster pompano (Trachinotus anak) is an emerging aquaculture species in Asia with limited genomic resources. This study constructed a SNP-based genetic linkage map and performed a genome-wide association study (GWAS) to identify loci associated with growth and flesh color traits. A total of 42,667 SNP markers were generated from sequencing, of which 5360 high-quality SNPs were retained after stringent quality filtering for GWAS, while 21,356 SNPs were retained for linkage map construction. The linkage map comprised 24 linkage groups, providing a robust genomic framework for marker ordering and trait mapping. GWAS identified 105 SNPs significantly associated with body weight, along with additional SNPs linked to other growth traits, indicating a polygenic genetic architecture. In contrast, only limited associations were detected for flesh color traits. Annotation of genomic regions surrounding significant and suggestive SNPs identified ten candidate genes shared among growth traits, including Neuroligin-4, MTFMT, Urah, AGRN, IL1RAP, col27a1b, CASKIN2, CYBA, VPS35, and LEPR. These genes are involved in key biological processes such as cytoskeletal organization, energy metabolism, mitochondrial function, and skeletal development. Gene Ontology enrichment analysis further revealed significant pathways related to growth and metabolism, including muscle hypertrophy and protein hormone receptor activity. Overall, these findings provide valuable genomic resources and insights into the genetic architecture of economically important traits in T. anak, supporting future genomic selection and breeding programs.