Barramundi (Lates calcarifer) rare coloration patterns: a multiomics approach to understand the “panda” phenotype

Abstract

The barramundi (Lates calcarifer), a significant aquaculture species, typically displays silver to bronze coloration. However, attention is now drawn to rare variants like the “panda” phenotype, characterized by blotch-like patterns of black (PB) and golden (PG) patches. This phenotype presents an opportunity to explore the molecular mechanisms underlying color variations in teleosts. Unlike stable color patterns in many fish, the “panda” variant demonstrates phenotypic plasticity, responding dynamically to unknown cues. We propose a complex interplay of genetic factors and epigenetic modifications, focusing on DNA methylation. Through a multiomics approach, we analyze transcriptomic and methylation patterns between PB and PG patches. Our study reveals differential gene expression related to melanosome trafficking and chromatophore differentiation. Although the specific gene responsible for the PB–PG difference remains elusive, candidate genes like asip1, asip2, mlph, and mreg have been identified. Methylation emerges as a potential contributor to the “panda” phenotype, with changes in gene promoters like hand2 and dynamin possibly influencing coloration. This research lays the groundwork for further exploration into rare barramundi color patterns, enhancing our understanding of color diversity in teleosts. Additionally, it underscores the “panda” phenotype's potential as a model for studying adult skin coloration.