Beyond genotyping: Using ddRADseq GBS for pathogen surveillance in aquaculture – A case study in Barramundi (Lates calcarifer)
1
Issued Date
2026-03-15
Resource Type
eISSN
23525134
Scopus ID
2-s2.0-105024098294
Journal Title
Aquaculture Reports
Volume
46
Rights Holder(s)
SCOPUS
Bibliographic Citation
Aquaculture Reports Vol.46 (2026)
Suggested Citation
Terence C., Poon Z.W.J., Senapin S., Dong H.T., Clarke S.M., Brauning R., Dodds K.G., Thanh Vu N., Shen X., Gibson-Kueh S., Jerry D.R., Domingos J.A. Beyond genotyping: Using ddRADseq GBS for pathogen surveillance in aquaculture – A case study in Barramundi (Lates calcarifer). Aquaculture Reports Vol.46 (2026). doi:10.1016/j.aqrep.2025.103273 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/114442
Title
Beyond genotyping: Using ddRADseq GBS for pathogen surveillance in aquaculture – A case study in Barramundi (Lates calcarifer)
Author's Affiliation
James Cook University
Faculty of Science, Mahidol University
Asian Institute of Technology Thailand
Thailand National Center for Genetic Engineering and Biotechnology
AgResearch Invermay
James Cook University, Singapore
ARC Research Hub for Supercharging Tropical Aquaculture through Genetic Solutions
Faculty of Science, Mahidol University
Asian Institute of Technology Thailand
Thailand National Center for Genetic Engineering and Biotechnology
AgResearch Invermay
James Cook University, Singapore
ARC Research Hub for Supercharging Tropical Aquaculture through Genetic Solutions
Corresponding Author(s)
Other Contributor(s)
Abstract
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.