Acute Hepatopancreatic Necrosis Disease (AHPND), caused by Vibrio parahaemolyticus, poses a significant threat to the global shrimp industry, primarily affecting white leg shrimp, L. vannamei. Despite stringent biosecurity measures and water quality management, outbreaks remain common. Well-structured selective breeding programs have the capability to select for improved survival to diseases provided that the trait is heritable and shows significant genetic variation. In this study we investigated the efficacy of genomic selection in improving survival under AHPND challenges.
Test groups of approximately 1000 juvenile shrimp from multiple families across several generations in the Kona Bay breeding program underwent AHPND challenges. Each challenge was preceded by LD50 trials to determine the optimal pathogen concentration, aiming for around 50% mortality. Time to death (expressed in hours) was recorded for each juvenile in the main challenge. Both challenged individuals and their siblings, selection candidates in the breeding program, were genotyped using a custom SNP chip. Genomic data were analysed using Genome Studio and SNP and Variation Suite. Selection candidates for the next generation were selected using GBLUP multi-trait genomic selection. Each subsequent generation was subjected to a new disease challenge, replicating the conditions of previous challenges, varying only the concentration of the pathogen.
The average heritability of time to death was 0.089(0.013). Despite increasing concentrations of V. parahaemolyticus over generations, time to death improved (Fig. 1), indicating improved survival against the specific pathogen. To demonstrate the effectiveness of genomic selection we also performed cross validation where 50% of the challenge data was used to predict the time to survival in the other 50% (masked) data. This was done in five random iterations to obtain an accurate predictive power of the data. Correlations between predicted genomic and estimated pedigree breeding values (corrected phenotypes) were on average 0.86 (sd = 0.023) which demonstrates that genomic selection can be used effectively to select for improved survival.