Guddanti, Gopala K., Massault, Cecile, Jones, David B., Jerry, Dean R., and Zenger, Kyall R. (2026) Calculating genomic breeding values for growth using DNA pools within commercially reared black tiger shrimp (Penaeus monodon). Aquaculture, 621. 743971.

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Abstract

Genomic estimated breeding values (gEBVs) are routinely used in genomic selection; however, their practical application in commercial shrimp aquaculture is impeded by high genotyping costs and unequal family contributions. DNA pooling offers a cost-efficient alternative to generate reliable gEBVs through hybrid genomic relationship matrixes (h-GRMs) and ranked phenotype groups. Despite its conceptual advantages, this approach has not been tested on commercial shrimp data. We evaluated pooled genotype data to predict genomic estimated breeding values (gEBVs) for body weight in Penaeus monodon. Reconstructed pools (RPs) of 2, 5, 10, 15, 20, and 25 individuals ranked by body weight across the population were generated in-silico using individual genotypes across 5097 DArTCap SNPs. In addition, the in-silico predictions from pool size (PS) 10 was tested using physical DNA pools (PDP) genotyped using a custom Axiom 70 k SNP array. Across the RP and PDP pools, gEBVs were estimated using a GBLUP animal model examined for three scenarios. First, parental gEBVs predicted from RPs showed high accuracy with small pool size (0.92 ± 0.005, PS2) and continuously declined as pool size increased (0.82 ± 0.07, PS25). Second, sibling gEBV prediction across ponds displayed high accuracy with small pool sizes (0.94 ± 0.15 for PS2) and reduced sharply in larger pool sizes (0.58 ± 0.62 for PS25). Within the top 20% of siblings, the gEBV accuracy ranged from 0.67 ± 0.57 (PS2) to 0.48 ± 1.59 (PS25). Together, these outcomes indicated PS10 represents an optimum balance between cost and accuracy. In the third scenario, gEBV accuracy was tested using PDP-PS10, and a higher prediction accuracy was obtained in a pond with moderate genetic diversity (0.53 ± 0.01) than in one with low diversity (0.43 ± 0.01). Pooling DNA from 10 ranked individuals would reduce genotyping costs up to eightfold; however, prediction accuracy decreased by 27%–30% when compared to individual genotyping. Although pooling reduces accuracy, the implementation of a structured pool design and moderate genetic diversity in reference populations can enable reliable gEBV estimation. These findings validate DNA pooling as a practical and cost-effective tool for genomic selection in commercial breeding programs for P. monodon.

Item ID:	92140
Item Type:	Article (Research - C1)
ISSN:	1873-5622
Keywords:	Aquaculture, Black tiger shrimp, DNA pool genotyping, Genomic prediction
Copyright Information:	© 2026 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Funders:	Australian Research Council (ARC)
Projects and Grants:	ARC ITRH Research Hub Program (IH130200013), ARC ITRH Research Hub Program (IH210100014)
Date Deposited:	08 Jun 2026 23:40
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