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<p>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.</p>

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Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月30日

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  • Liu Yang,
  • Yahui Gao,
  • Kristen L. Kuhn,
  • Nayan Bhowmik,
  • Wenli Li,
  • Geoffrey Zanton,
  • Lingzhao Fang,
  • John B. Cole,
  • Congjun Li,
  • Ransom L. Baldwin, VI,
  • Curtis P. Van Tassell,
  • Benjamin D. Rosen,
  • Li Ma,
  • Timothy P. L. Smith,
  • George E. Liu

摘要

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.