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

IF 3.8 2区农林科学 Q1 FISHERIES

Aquaculture Reports Pub Date : 2026-03-15 Epub Date: 2025-12-09 DOI:10.1016/j.aqrep.2025.103273

Celestine Terence , Zhi Weng Josiah Poon , Saengchan Senapin , Ha Thanh Dong , Shannon M. Clarke , Rudiger Brauning , Ken G. Dodds , Nguyen Thanh Vu , Xueyan Shen , Susan Gibson-Kueh , Dean R. Jerry , Jose A. Domingos

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引用次数: 0

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.

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超越基因分型：利用ddRADseq GBS进行水产养殖病原体监测——以Barramundi（晚calcarifer）为例

通过测序进行基因分型（GBS）广泛应用于水产养殖选择性育种计划，以获取SNP基因型，用于各种应用，包括系谱重建，GWAS以及遗传参数，基因组关系和育种价值的估计。因为测序文库包含了鳍夹组织中存在的所有DNA，它们也恢复了非宿主宏基因组部分，包括病原体。我们利用这一特性调查了鳞片下降病病毒（SDDV）的存在，该病毒在养殖的undi中造成40 - 90% %的死亡率，同时对宿主进行了基因分型。来自四个商业队列的4484条鱼（2239条死鱼，2245条无症状鱼）的原始读数与SDDV参考基因组相匹配，病毒读数标准化为每百万分之一（RPM）每个个体。SDDV的流行和负荷与临床状态密切相关：88.9 %的死鱼在21.8 ± 0.6 RPM时携带SDDV，而健康鱼只有0.2 %的鱼在0.002 ± 0.001 RPM时呈阳性。通过对172条鱼（81条死亡鱼，91条健康鱼）的鳍和脾脏进行定量PCR的独立验证，发现病毒拷贝数与ddRADseq RPM密切相关（鳍的Spearman ρ = 0.84；脾脏的ρ = 0.76； P均为 <； 0.0001）。病毒载量在鳍（平均281 ± 45拷贝ng⁻¹）比脾脏（147 ± 32拷贝ng⁻¹）始终更高，证实了非致命性鳍组织用于监测的适宜性。各队列的患病率和负荷分布是均匀的，没有qpcr阳性个体逃过ddRADseq的检测。这些发现表明，澳大利亚undi的常规ddRADseq数据集也可以被重新利用为一种敏感的流行病学分析，将SDDV监测与基因组改善结合起来。此外，这些发现表明，当目标病原体感染宿主基因型组织时，产生大型ddRADseq GBS数据集的育种计划也可能用于病原体监测目的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Aquaculture Reports Agricultural and Biological Sciences-Animal Science and Zoology

CiteScore

5.90

自引率

8.10%

发文量

469

审稿时长

77 days

期刊介绍： Aquaculture Reports will publish original research papers and reviews documenting outstanding science with a regional context and focus, answering the need for high quality information on novel species, systems and regions in emerging areas of aquaculture research and development, such as integrated multi-trophic aquaculture, urban aquaculture, ornamental, unfed aquaculture, offshore aquaculture and others. Papers having industry research as priority and encompassing product development research or current industry practice are encouraged.