Genetic linkage map of the Australian barramundi (Lates calcarifer) reveals potential to leverage extreme sex-specific recombination and sequential hermaphrodism for ultimate breeding program control

Background Lates calcarifer (barramundi or Asian seabass) is a key aquaculture species with a protandrous life cycle, maturing first as male and later as female. As global breeding programs advance to improve traits such as growth and disease resistance, the absence of a high-density genetic linkage map limits progress and constrains understanding of genome architecture and recombination. Such maps are essential for marker-assisted selection, genomic breeding strategies, and comparative genomics, providing a foundation for accelerating genetic improvement. Results Our analysis reveals striking sex-specific recombination differences within the Australian lineage: females recombine only in centromeric regions, while males recombine exclusively in distal regions, with no overlap. This pronounced heterochiasmy has not been observed in Southeast Asian populations. Additionally, we detected 10 chromosomal inversions, expanding known structural variation across the species’ range. Conclusions Given their sequential hermaphroditism, this recombination landscape could allow breeders to strategically utilise sex-specific recombination through the creation of optimal allele combinations, increasing genetic gain and enhancing genetic diversity in L. calcarifer aquaculture populations. Beyond its practical applications, our findings establish L. calcarifer as a model for studying heterochiasmy, as well as providing insights into how this can be leveraged for advanced genomic breeding programs.