ArticleNature communications2026
Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.
Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- Multi-omics integration and artificial intelligence for the conservation and utilization of local chicken genetic resources.Poultry science · 2026Review
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Resolving Cattle GWAS Loci: Current Progress, Persistent Challenges and Future Directions.Current issues in molecular biology · 2026Review
- Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.Nature communications · 2026Article
- Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.Nature communications · 2026Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Structural variants are an underexplored source of genetic diversity. As part of the FarmGTEx Project, here we report a Holstein breed-specific pangenome graph (H20D) using Minigraph-Cactus and 40 phased haploid assemblies from 20 cows. H20D outperforms both assembly- and read-based long-read callers, and far exceeds short-read approaches, identifying over 10,000 additional structural variants per sample. It also significantly improves structural variant detection and genotyping relative to graphs built across breeds or from fewer/unphased assemblies, with particular advantages in complex regions. Using H20D, we genotype variants in 173 cattle and performed a GWAS, where a larger fraction of structural variants than SNPs reach genome-wide significance, implicating them as potential causal variants. Together, these results demonstrate the power of phased, within-breed pangenome graphs for accurate SV genotyping and trait mapping in dairy cattle.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.