Article
Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.
Nature communications - 3 Jul 2026
Yang Liu, Wang Junjian, Kuhn Kristen, Li Wenli, Zanton Geoffrey, Neupane Mahesh, Boschiero Clarissa, Cole John B, Li Bingjie, Li Congjun, Baldwin Vi Ransom L, Van Tassell Curtis P, Rosen Benjamin D, Smith Timothy P L, Jiang Jicai, Fang Lingzhao, Ma Li, Liu George E
Abstract excerpt
Pangenomes of several species have been assembled recently, facilitating the detection and genotyping of structural variants. As part of the FarmGTEx Project, we previously constructed a Holstein pangenome (H20D) based on 40 phased haploid assemblies. Here, we use this breed specific pangenome to genotype 93,059 structural variants from whole-genome sequences of 1,571 cattle. We then develop a Holstein pangenome...
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