Aquaculture

Deciphering the genetic architecture of key economic traits in Atlantic cod breeding using a custom designed SNP Array

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Abstract

Abstract: The objective of this study was to develop a high-resolution SNP panel for Atlantic cod and demonstrate its utility in the estimation of genetic parameters, genome-wide association analyses (GWAS), and comparative prediction of breeding objective traits. Improving cod aquaculture competitiveness requires complementing traditional family-based selection with advanced genomic approaches. Genomic selection (GS) enables within-family selection, increasing accuracy and selection intensity, thereby accelerating genetic progress. This approach is particularly valuable for traits that are costly or logistically challenging to measure, such as disease resistance or early maturation, which often require large-scale experimental testing. We utilized whole-genome sequence data from 111 individuals generated within a previously funded project by the Research Council of Norway (Project #207680) and supplemented these with sequence data from 30 wild Atlantic cod obtained from a public repository. Sequence reads were aligned to the Atlantic cod reference genome (gadMor3.0), and variants were called using the GATK pipeline. After stringent quality filtering, approximately 6.1 million SNPs were retained, which were further reduced to approximately 900,000 based on genotype quality, informativeness, and genotyping rate. Final panel markers were selected using multiple criteria, including regional density relative to chromosome size, functional relevance, chromosome-wide coverage, and linkage disequilibrium structure. Following technological guidelines from Illumina, approximately 21,000 SNPs were incorporated into a GGP Illumina Infinium array. The SNP panel was validated using 3,672 individuals from three year classes of the National Cod Breeding Program. Body weight was recorded for all year classes, while sexual maturation data were available for YC2019 and YC2023. Body weight for YC2016 was recorded in November 2018, whereas weight and maturation for YC2019 and YC2023 were recorded in March 2021 and March 2025, respectively. Genetic parameters were estimated using linear mixed models with pedigree and genomic relationship matrices, and GWAS was performed to identify trait-associated quantitative trait loci. A validation scheme assessed prediction accuracy for BW and SM using genomic versus pedigree information. Genomic heritability estimates were 0.37 for BW and 0.21 for SM, confirming substantial genetic variation. A combined-data GWAS for SM identified a consistent QTL on chromosome 20 exceeding the chromosome-wide significance threshold. The array also reproduced a previously reported sex QTL, confirming reliability. Genomic models improved prediction accuracy by approximately 30% for BW and 19% for SM. Overall, this study provides a genomic resource for Atlantic cod and demonstrates its utility for estimating genetic parameters, implementing genomic selection, and detecting QTLs. The SNP panel represents a valuable tool to enhance breeding efficiency and genetic gain in Atlantic cod aquaculture. These results highlight the robustness of the panel across cohorts and support its application in routine breeding programs, enabling more accurate selection decisions and contributing to sustainable and efficient Atlantic cod production systems in the future overall.

Keywords: 2026

How to Cite:

Aslam, M., Kettunen, A., Hansen, Ø. & Lillehammer, M., (2026) “Deciphering the genetic architecture of key economic traits in Atlantic cod breeding using a custom designed SNP Array”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286523. doi: https://doi.org/10.31274/wcgalp.24039

Rights: 1