Sequencing & Pangenomes

Extending ICAR parentage verification certification to whole-genome SNP comparisons

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Abstract

Parentage verification certification in dairy cattle currently relies on the standardized 195 ISAG parentage verification single nucleotide polymorphism (ICAR-SNP) panel. While this approach remains robust for low-density genotyping systems, it poses limitations in modern genomic contexts where animals are genotyped with a wide variety of SNP panels, densities and technologies - particularly in cases where not all 195 SNP calls are available for the parent or the animal. To address this, a framework extending the SNP parentage verification certification guidelines to full SNP array comparisons was evaluated. The goal was to establish empirically supported thresholds for classifying parentage relationships based on genome-wide data while ensuring scientific rigor and international applicability. Genotypic data representing five dairy breeds available at the Council on Dairy Cattle Breeding (CDCB, USA) were analyzed using large subsets of known parent-offspring pairs and unrelated animal pairs. Comparisons were conducted using autosomal SNPs only, applying only basic quality control filters to exclude SNP and arrays with known poor genotyping performance (for example, SNP arrays with overall poor clustering and probe performance). Both duo (parent-offspring) and trio (offspring-sire-dam) configurations were examined to determine the added value of each approach under whole-genome conditions. Results demonstrated that whole-genome SNP comparisons provide sufficient discriminatory power to accurately identify true parentage relationships, even across datasets combining multiple chip types and densities. The study found that, when genome-wide information is available, duo-based comparisons yield high accuracy and reproducibility, while trio testing contributes minimal additional resolution. Consequently, full SNP comparison-based verification was shown to offer an effective, flexible alternative for organizations using diverse genotyping technologies, particularly in cases where standardized panels are incomplete or re-genotyping is not feasible. Beyond analytical performance, this approach enables broader applicability across breeds, including crossbreds and less common populations, provided that appropriate pre-screening is conducted to minimize ascertainment bias. Although computational requirements are higher than for limited-marker panels, the process remains feasible using standard and basic computing resources for routine verification tasks. This study supports the inclusion of full-genome SNP comparison guidelines within ICAR's DNA technology framework as a complementary standard to existing ISAG-based protocols. The proposed methodology enhances consistency in parentage verification certification across varying genotyping platforms and provides a scientifically sound path toward harmonizing international practices. By emphasizing data completeness and empirical thresholds over fixed marker sets, this framework promotes more reliable, scalable, and future-proof parentage testing strategies in the genomic era.

Keywords: 2026

How to Cite:

Nicolazzi, E., McClure, M., Jansen, G. & Wiggans, G., (2026) “Extending ICAR parentage verification certification to whole-genome SNP comparisons”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2273838. doi: https://doi.org/10.31274/wcgalp.23419

Rights: 1