Article
Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle.
Nature communications - 30 Jan 2026
Yang Liu, Gao Yahui, Kuhn Kristen L, Bhowmik Nayan, Li Wenli, Zanton Geoffrey, Fang Lingzhao, Cole John B, Li Congjun, Baldwin Vi Ransom L, Van Tassell Curtis P, Rosen Benjamin D, Ma Li, Smith Timothy P L, Liu George E
Abstract excerpt
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...
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