Beyond genotyping: Using ddRADseq GBS for pathogen surveillance in aquaculture – A case study in Barramundi (Lates calcarifer)

Genotyping by sequencing (GBS) is widely employed in aquaculture selective breeding programs to acquire SNP genotypes for various applications, including pedigree reconstruction, GWAS, and in the estimation of genetic parameters, genomic relationships and breeding values. Because sequencing libraries encompass all DNA present in fin-clip tissue, they also recover the non-host metagenomic fraction, including pathogens. We leveraged this property to survey for the presence of scale-drop disease virus (SDDV), responsible for 40–90 % mortality in farmed barramundi, while simultaneously genotyping the host. Raw reads from 4484 fish of four commercial cohorts (2239 moribund, 2245 asymptomatic) were aligned to the SDDV reference genome, and viral reads were normalised as reads per million (RPM) per individual. SDDV prevalence and load were tightly associated with clinical status: 88.9 % of moribund fish carried SDDV at 21.8 ± 0.6 RPM, whereas only 0.2 % of healthy fish were positive with 0.002 ± 0.001 RPM. Independent validation by quantitative PCR on fin and spleen from a nested subset of 172 fish (81 moribund, 91 healthy) yielded viral copy numbers strongly correlated with ddRADseq RPM (Spearman’s ρ = 0.84 for fin; ρ = 0.76 for spleen; both P < 0.0001). Viral load was consistently higher in fin (mean 281 ± 45 copies ng⁻¹ DNA) than spleen (147 ± 32 copies ng⁻¹), corroborating the suitability of non-lethal fin tissue for surveillance. Prevalence and load distributions were homogeneous across cohorts, and no qPCR-positive individuals escaped detection by ddRADseq. These findings show that routine ddRADseq datasets in barramundi can also be repurposed into a sensitive epidemiological assay that unites SDDV monitoring with genomic improvement. Further, these findings suggest that breeding programs generating large ddRADseq GBS datasets may also serve pathogen surveillance purposes where the target pathogen infects the host genotyped tissue.