Companion animals

Low pass whole genome sequencing plus targeted capture: a platform for high accuracy genotyping, trait discovery, and genomic evaluation in working dogs

---

Abstract

Working dogs provide critical value across agriculture, security and defense, assistance work, detection, and companionship, yet the supply of healthy, high-performing, purpose-bred dogs remains limited. Many traits essential to working dog success-including health, behavior, and longevity-are complex, polygenic, and often late-onset, constraining the effectiveness of phenotypic selection alone. Broader adoption of genomic approaches has been hindered by the lack of scalable, affordable genotyping platforms that support both routine health screening and the large genomic reference populations required for discovery and genomic evaluation.Here, we present and evaluate a dual-purpose genotyping strategy that integrates low-pass whole-genome sequencing (LP-WGS) with targeted capture. This hybrid approach enables simultaneous genome-wide variant discovery and high-confidence genotyping at prioritized disease-, health-, and aesthetic trait-associated loci relevant to applied breeding programs. We designed a custom capture panel targeting 341 variants across 398 genomic regions (~71.5 kb) and evaluated performance in a pilot cohort of 96 dogs sequenced on Illumina and Element platforms.Observed coverage was consistent with design targets, with mean genome-wide depths of 1.68à— (Illumina) and 1.08à— (Element) and robust enrichment of targeted regions, where most targets achieved moderate (≥30à—-50à—) to high (≥100à—) coverage across samples. Genotype concordance with prior array- and PCR-based testing at prioritized loci was high, and concordance between Illumina and Element sequencing platforms reached 99.90% (3,066/3,069 genotype comparisons). Genotypes at morphology-associated loci were also consistent with owner-supplied photographs from a community science cohort, providing qualitative validation.Together, these results demonstrate that hybrid LP-WGS with targeted capture supports accurate, scalable genotyping for genomics-driven health screening while establishing a foundation for genomic discovery and future genomic evaluation in dogs.

Keywords: 2026

How to Cite:

Chen, F., Kenney, B., Indap, A., Sohrab, V., Bryc, K., Megquier, K., Russenberger, J., Zimmermann, M., Leighton, E., Fragomeni, B. & Karlsson, E., (2026) “Low pass whole genome sequencing plus targeted capture: a platform for high accuracy genotyping, trait discovery, and genomic evaluation in working dogs”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287144. doi: https://doi.org/10.31274/wcgalp.24221

Rights: 1