Barramundi (Lates calcarifer) as an important tropical aquaculture candidate is increasingly being subjected to genetic improvement programs. Whilst there are currently some genomic resources available for the species, to date there has been no high-resolution genetic linkage map produced that is useful to understand recombination rates within the genome and for QTL mapping. Here we genotyped 41,000 SNP in two b arramundi families (n= 266 progeny total) to develop the highest-resolution linkage map for the species thus far and the first constructed based on Australian L. calcarifer.
The linkage map shows substantial regions of male-only and female-only recombination zones across the chromosomes (Figure 1) , a striking finding given the protandrous nature of this species (fish are born as males and some transition to females later in life but have the same genome) . One of the motivations for constructing the linkage map was to accurately simulate inheritance of chromosomes across generations in “digital twin” simulations of b arramundi breeding programs, to evaluate the cost benefit of technologies such as genomic selection. The varying recombination rates between genders in our linkage map suggest the need to consider sex- specific inheritance patterns in such breeding program simulations.
Th e new linkage map offers valuable insights into recombination mechanisms and will be crucial for genomic selection efforts for L. calcarifer, improving breeding programs and enhancing our understanding of its biology.