Revealing the genetic and molecular drivers behind golden and platinum coloration in barramundi (Lates calcarifer)

Coloration is an important trait in many aquaculture species, particularly when rare color phenotypes hold high economic value. The barramundi (Lates calcarifer) is a valuable aquaculture species across its Indo-Pacific range. The wild-type (WT) skin color of barramundi is typically silver to bronze. However, occasional sightings of golden (xanthic), platinum (white), panda (golden with black patches), and black variants have been observed. Several of these rare color variants, such as the golden-colored fish, have significant commercial interest. Nonetheless, the genetic basis of skin coloration in barramundi remains poorly understood. In this study, transcriptomic differences between the rare color variants and the wild-type coloration were analyzed to understand the molecular drivers of barramundi skin colouration. Differential analysis of the RNA-seq count data for the rare color variants and the WT identified multiple Differentially Expressed Genes (DEG). Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) identified 14 modules of genes that exhibit common expression patterns and are associated with skin coloration. Notably, the circadian cycle, tyrosine metabolism, xanthophore-associated genes, and melanogenesis were among the top pathways that exhibited differences between the color morphs. Further analysis of gene expression within those pathways revealed statistical variations. To confirm the role of the gene oca2 in golden-skinned barramundi, a Protein-Protein Interaction (PPI) network was constructed using significant DEGs. The PPI network demonstrated its direct interaction with the circadian cycle, melanogenesis, and xanthophore-associated genes. For the platinum phenotype, potential gene candidates were discovered, namely myo5aa, mlpha, and kif5b, which are associated with the alteration of pigment transporters responsible for melanin, carotenoids, and pteridine. These genes may play an important role in the expression of the platinum color variant. [Display omitted] •RNA-seq analysis of rare color variants and WT identified multiple DEGs.•WGCNA identified 14 modules linked to coloration.•Top differing pathways: circadian cycle, xanthophore genes, melanogenesis.•PPI network reveals circadian-melanogenesis-xanthophore gene interactions.