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Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle
Liu Yang1,2, Junjian Wang3, Kristen Kuhn4
1Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA.
Nature Communications
|July 3, 2026
Summary
Researchers developed HolPIP, a Holstein pangenome variation imputation reference panel. This panel aids in identifying structural variants linked to complex traits in cattle, highlighting their importance in dairy genetics.
Area of Science:
- Genomics
- Animal Breeding
- Bioinformatics
Background:
- Recent advancements in pangenome assembly facilitate structural variant (SV) detection.
- The FarmGTEx Project previously established a Holstein pangenome (H20D) from 40 phased haploid assemblies.
Purpose of the Study:
- To genotype structural variants in a large Holstein cattle cohort using a breed-specific pangenome.
- To develop a robust imputation reference panel for Holstein pangenome variations.
- To investigate the association of SVs with complex traits in cattle through genome-wide association studies (GWAS).
Main Methods:
- Genotyping of 93,059 SVs in 1,571 cattle using the H20D pangenome.
- Development of the Holstein Pangenome Variation Imputation reference panel (HolPIP).
- Imputation of SVs for 50,299 bulls with high accuracy (Beagle R² ≥ 0.8).
- GWAS utilizing imputed SVs and phenotypes for 43 complex traits.
- Fine-mapping to prioritize candidate SVs.
Main Results:
- Successfully genotyped 93,059 SVs and imputed 86.65% of SVs for a large bull population.
- Identified 1,225 SV-trait associations across 43 complex traits.
- Prioritized 32 high-confidence candidate SVs, including a deletion in ANKRD11 (dairy form, rump width, stature) and an insertion in DHX32 (RNA metabolism).
- Observed stronger genome-wide enrichment of SVs compared to SNPs for most complex traits in cattle.
Conclusions:
- Structural variants play a significant role in the genetic architecture of complex traits in Holstein cattle.
- The HolPIP panel provides a valuable resource for SV imputation and association studies in this breed.
- SVs are crucial contributors to the genetic basis of dairy traits and other complex phenotypes.
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