Mulloway (Argyrosomus japonicus) are a threatened species in NSW. Declining fisheries have led to restocking programs in NSW. These restocking programs currently rely on wild caught broodstock, that are then spawned in captivity, and the release of offspring into the wild. As the current broodstock reaches the end of its productive period, there is a need to establish a new breeding stock. Procuring new broodstock is costly and time consuming as wild individuals often do not breed readily in captivity making it important to optimise existing genetic resources. This study focused on generating tools to identify genetically robust offspring that can be used as future broodstock and for restocking without compromising the genetic diversity or similarity to wild populations.
To achieve this, we employed DArT-seq technology, a next-generation sequencing method that identifies single nucleotide polymorphisms (SNPs) across the genome. DArT-seq was applied to all broodstock and a subset of offspring over three spawning events spanning three years. This approach allowed us to track the genetic contribution of individual parents and assess the relatedness among broodstock and their offspring. SNP data enabled accurate determination of genetic relationships between individuals, allowing us to classify which F1 offspring were most valuable for future breeding efforts, and which were most suitable for release into the wild. This approach allowed us to understand breeding of mulloway in captivity and assess relative broodstock performance.
We calculated key population genetics metrics, including effective population size (Ne), inbreeding coefficient (FIS), observed heterozygosity (Ho), and expected heterozygosity (He) for aquaculture bred fish and compared these with wild Mulloway populations. These comparisons provided a benchmark for assessing the genetic health of the aquaculture stock relative to the wild populations. Additionally, we identified a DArT-based sex marker, which enhances our ability to manage and optimise breeding lines. By determining sex and genetic identity, it is possible to maintain distinct genetic lines, avoiding inbreeding, and ensur the long-term sustainability of breeding programs. The findings from this study will inform immediate breeding decisions and provide a foundation for ongoing efforts to improve the genetic management of Mulloway aquaculture, ensuring that future broodstock are both genetically diverse and closely aligned with wild populations.