Disease & heat resistance

Genomic Selection for Acute Hepatopancreatic Necrosis Disease in Pacific White Shrimp (Litopenaeus vannamei) under Challenge Conditions

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Abstract

Infectious diseases pose a main threat to shrimp aquaculture globally. Acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio parahaemolyticus producing PirAB binary toxin, is a highly infectious disease that causes immeasurable economic losses in Pacific white shrimp (Litopenaeus vannamei). Crustaceans do not have adaptive immunity, and it is known that they rely primarily on the innate immune system which restricts the development of vaccines. Additionally, the use of antibiotics causes concerns regarding environmental contamination and development of antimicrobial resistance (AMR). Therefore, the objective of this study was to implement a genomic selection program of AHPND resistance in two lines of Pacific white shrimp. A total of 4,352 shrimp were genotyped with 37,285 SNPs and evaluated for binary survival. Data were collected in a fast and a slow growth line (FG and SG, respectively). Phenotypes were collected on 4,800 Specific Pathogen Free individuals after two independent 3-days immersion challenges using V. parahaemolyticus at 4.95x107 CFU/ml. In each challenge, 40 family lines were divided into 20 fast-growth and 20 slow-growth lines. Each family line had three replicate tanks and ten animals/tank (20 L size tank). Disease challenges were performed in 2022 and 2023. For the 2023 challenge, the families with higher and lower mortality in the 2022 challenge were selected. Variance components were estimated under an animal threshold model using a GBLUP approach. Later, GEBVs were back-solved to SNP effects for a GWAS. The two lines were analysed together and separately. GEBVs were validated using the LR method with different validation populations. Mortality at the end of the challenge was higher for the slow-growth line, especially in the 2022 challenge. Heritability estimates were moderate to high (h² (SE) = 0.39(0.17)-0.54(0.2))), confirming substantial additive genetic variance for AHPND resistance in both lines. The accuracies calculated within lines varied across the validation approach: forward-in-time yielded lower accuracies (rₐ = 0.26 FG, 0.12 SG) than backward-in-time produced higher values (rₐ = 0.33 FG, 0.21 SG). The across line K-means clustering accuracies varied from 0.3 to 0.15. gave intermediate accuracies (0.15). GEBVs were severely deflated with the forward in time validation and inflated with the K-means clustering, while the backward in time resulted in slightly inflated values. The Manhattan plots showed a highly polygenic genetic architecture with 29 windows explaining more than 0.1% of the genetic variance. Two windows were identified in the individual lines in GWAS containing candidate genes linked to immune response and metabolism. The results demonstrate that genomic selection is a feasible tool to improve AHPND resistance in L. vannamei and data collection must continue over more generations to further validate the results.

Keywords: 2026

How to Cite:

Fragomeni, B., Ampofo, I., Mai, H., Grevers, D., Luna, M., Wright, H. & Dhar, A., (2026) “Genomic Selection for Acute Hepatopancreatic Necrosis Disease in Pacific White Shrimp (Litopenaeus vannamei) under Challenge Conditions”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286521. doi: https://doi.org/10.31274/wcgalp.24038

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