BackgroundIn shrimp farming, major production losses are caused by viruses. Hepatopancreatic parvovirus (HPV) is one of the viral pathogens that infect banana shrimp (Fenneropenaeus merguiensis). HPV is thought to slow down growth and cause mortality in the juvenile stages of banana shrimp. Genetic improvement through selection of shrimp resistant to viral diseases is one approach to address this issue. This is the first detailed report on an aquaculture species that investigates whether viral titre varies among families and is heritable, and thus whether viral titre per se is a possible candidate trait for selection to produce resistant stock.ResultsHPV titre was measured by quantitative polymerase chain reaction of DNA extracted from 1137 offspring (from 48 full-sib families). Estimated heritability of HPV titre, based on the linear animal mixed model, was moderate (h2 = 0.41). Genetic correlations of HPV with body traits (weight, length and width of body, head and tail) ranged from −0.13 to −0.38. HPV titre was negatively correlated with raw and cooked body colour (−0.33 and −0.43, respectively).ConclusionsThis is the first study based on a large dataset that provides evidence that viral titre may have a genetic component in penaeid shrimp or even in any aquaculture species. The moderate heritability estimated for this trait suggests that resistance to HPV may be achieved by selecting for low HPV titre. With moderate and negative correlations, selection for resistance to HPV should gradually improve body traits and colour of banana shrimp.

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Background Viral diseases are a major problem in shrimp aquaculture facilities as these diseases reduce growth rates, which inevitably lead to production and profit losses. Hepatopancreatic parvoviruses (HPV) are common diseases in shrimp that appear to be associated with high or low levels of replication in specific genetic lineages. Selective breeding may result in resistance to HPV and improved body traits such as body weight, meat yield and shrimp colour, facilitating shrimp farming. HPV virus titre is commonly determined by quantitative PCR (qPCR), which is a time-consuming method requiring laboratory equipment unsuitable for field implementation. The aim of this study was to develop a simple, robust, rapid and reliable method to detect HPV in low-resource environments. Methods We developed a rapid shrimp HPV test that uses (1) a simple three-step sample preparation protocol, followed by (2) isothermal recombinase polymerase amplification (RPA) and lateral flow strip detection (LFD). Analytical sensitivity testing was performed in a background banana shrimp sample matrix, and retrospective testing of Fenneropenaeus merguiensis hepatopancreas tissues (n = 33) with known qPCR viral titres was used to determine diagnostic sensitivity and specificity. Results The rapid shrimp HPV test could detect as little as 35 genome-equivalent copies per reaction in homogenized F. merguiensis banana shrimp. Retrospective testing of stored tissues (n = 33) indicated 100% diagnostic sensitivity (95% confidence interval, CI: 86–100%) and 100% specificity (95% CI: 66–100%) for detection of HPV. Conclusion The rapid shrimp HPV test could be completed in only 40 minutes, and required only homogenization pestles, some pipettors, and a small heating block for single temperature incubation at 39°C. Critically, our procedure eliminated the time-consuming purification of nucleic acids from samples and when combined with RPA-LFD offers a user-friendly HPV detection format that can potentially be performed on-site. Our approach represents a major step forward in the development of a simple and sensitive end-point method for quick determination of unfavourable HPV virus numbers in shrimp, and has great potential to advance on-site management of shrimps in aquaculture.

Pedigrees are essential components in selective breeding programs to manage genetic diversity and obtain accurate genetic parameter estimates to ensure long-term response to selection in captive populations. High throughput and cost-effective sequencing technologies has offered opportunities of using single nucleotide polymorphisms (SNPs) to resolve penaeid shrimp pedigrees from mass spawning cohorts and communal rearing. Effects of SNPs for sibship assignment were investigated on 546 shrimp using two software programs, Colony and Sequoia. Assignment rates and accuracies using SNP subsets with six different minor allele frequencies (MAFs), four sets of SNPs, and five genotyping error rates were compared to the microsatellite-based pedigree established in a previous study. High MAFs and numbers of SNPs contributed to significant increases in assignment rates and accuracies, whereas genotyping error rates showed negligible impacts on assignment results. Sibship assignments achieved rates and accuracies of 98% and 83%, respectively, with a minimum number of 91 SNPs (average MAF ≥ 0.14), and the two different programs exhibited similar resulting patterns for different SNP subsets. High consistencies between SNP-based and microsatellite-based pedigrees showed that accurate pedigrees could be achieved by using SNPs and thus contribute to the long-term response to selection in farmed banana shrimp.