# Development and validation of a 70K SNP genotyping array for Atlantic halibut (Hippoglossus hippoglossus)

## TL;DR

This paper introduces a new 70K SNP genotyping array for Atlantic halibut to improve breeding and genetic research.

## Contribution

The first mid-density SNP array for Atlantic halibut, enabling genomic selection and high-resolution genetic studies.

## Key findings

- A 70K SNP array was developed with 59,491 robust assays showing 99.64% call rate and 99.0% concordance with WGS data.
- 133 gender-specific SNPs were identified for genetic sex determination in Atlantic halibut.
- The array supports high-resolution genetics research and genomic selection in the species.

## Abstract

The analysis of single nucleotide polymorphism (SNP) genotypes which capture genome-wide polymorphic variation can be used to improve the accuracy of selection in breeding programs and reveal the genetic architecture of quantitative traits. Mid-density SNP genotyping arrays containing > 60 K SNP markers have been developed for numerous production species and have been used to enable enhanced breeding progress. Despite recent genomic advances, Atlantic halibut lacks mid-density genotyping tools, limiting the application of genomic selection and high-resolution association studies in this species. The evolving Atlantic halibut (Hippoglossus hippoglossus) industry is also interested in genetically informed selection of breeding candidates to facilitate genetic improvement. The present study reports the development of the first mid-density SNP-array for use in Atlantic halibut and describes its performance in samples from different breeding populations.

Variant discovery was performed using whole genome sequencing (WGS) data from 40 individuals and resulted in the detection of more than 8 million small genetic variants including 6,224,375 SNPs and 2,131,436 insertion-deletion variants (INDELS). An Affymetrix Axiom custom array containing 70,824 assays (including 697 for determining genetic gender) was created and used to genotype 1152 Atlantic halibut samples. Assays for 59,491 SNP loci (84% of the array total) performed well and generated reliable genotypes, with an average SNP call rate of 99.64% and genotype concordance of 99.0% with whole-genome sequencing data. Of the gender-specific loci, 133 SNP assays could be used to assign genetic gender.

This article describes the first mid-density SNP genotyping array for Atlantic halibut. It contains nearly 60 K robust assays for genome-wide dispersed SNP loci, along with those suitable for determining genetic gender. The array is amenable for use as a platform for high-resolution genetics research into traits of evolutionary and economic importance and the results have practical relevance for genomic selection in Atlantic halibut.

The online version contains supplementary material available at 10.1186/s12864-025-12128-1.