Barramundi is an important tropical aquaculture marine food fish with well-established culture techniques. Despite genetic improvement efforts for growth traits and now looking towards resistance to various pathogens, barramundi farmed in Singapore face mass mortalities of 40-90% due to Scale Drop Disease Virus (SDDV). Although vaccines against SDDV are currently being developed, it is important to adopt a multi-pronged approach to the management of this disease. Given the moderate heritability (0.33 ± 0.01) for SDDV resistance, selective breeding presents as a long-term solution. To achieve this solution, we are applying genomic selection and integrating data from over 17,000 animals across multiple batches from both laboratory and natural challenges across multiple farm environments to begin to select for increased resistance to this devastating pathogen.
An Axiom 70k Barramundi SNP array was developed for this project based on millions of SNPs available in public repositories and on our group’s unpublished sequence databases. The array was designed to cover high-quality and evenly distributed SNPs across the barramundi genome, taking into account the genetic diversity of different farmed and wild populations across Southeast Asia and Australia. Additionally, the array includes SNPs from previously published QTLs for commercially important traits, as well as probes for 10 pathogens and parasites known to infect barramundi.
We developed a laboratory SDDV infection model for barramundi juveniles (~60-80g) which identified the SDDV LD50 dose from intraperitoneal injections. This dose represents the level at which approximately 50% of the more susceptible individuals within the population succumb to the infection within 2 weeks, and 50% of the more resistant individuals exhibit full recovery by the end of the 3rd week. Currently, we are conducting five separate laboratory challenges, each involving approximately 1,000 juveniles sourced from different batches. These fish are communally reared within a single tank to ensure that the data remains unbiased by environmental or husbandry variables, as well as potential co-infections. At the same time, barramundi juveniles from the same batches were distributed to commercial farms across Singapore and sampled during SDDV outbreaks and subsequently at the time of harvest. Long-term growth data is also being collected for incorporation in the genomic selection algorithms. The outcomes of this project are currently being translated into selection of broodstock improve growth rates and survival of farmed L. calcarifer against SDDV.