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<p>Genotype imputation is a cost-effective strategy for achieving dense genome-wide genotyping, but its accuracy in rainbow trout (<i>Oncorhynchus mykiss</i>) has been hampered by the lack of a comprehensive, multi-population genome-wide variant and imputation resource. Here, we present TroutHap, a multi-population genome-wide variant and imputation resource constructed from 540 high-coverage whole-genome sequences (~12.58×) representing multiple geographic sources and breeding backgrounds, mainly from North America, Europe, and China. We identified 16,408,551 high-confidence SNPs and integrated them into a unified genome-wide variant map across all 30 chromosome pairs. Using this resource, we benchmarked genotype imputation across simulated low-coverage sequencing depths. At 1× sequencing depth, genotype accuracy achieves &gt;90%, while additional sequencing beyond 2× yielded smaller improvements. Supplementary cross-platform validation using a public 57 K SNP array dataset further evaluated compatibility with array-based genotyping data, with genotype concordance and genotype accuracy reaching 80.5% and 71.9%, respectively, after site-level filtering. TroutHap is released as an open community resource, including high-confidence SNP site lists, representative chromosome-level variant files, representative imputed genotype files, metadata tables, validation summaries, and reproducible workflow outputs. This dataset provides a reusable resource for low-coverage sequencing imputation, SNP-array-based genotype harmonization, and downstream genomic analyses in rainbow trout.</p>

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A multi-population genome-wide variant and imputation resource for rainbow trout derived from 540 high-coverage whole-genome sequences

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月23日

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  • Jinxin Zhang,
  • Xiaofei Yang,
  • Wei Wang,
  • Hongxia Hu,
  • Shaogang Xu,
  • Hailiang Song

摘要

Genotype imputation is a cost-effective strategy for achieving dense genome-wide genotyping, but its accuracy in rainbow trout (Oncorhynchus mykiss) has been hampered by the lack of a comprehensive, multi-population genome-wide variant and imputation resource. Here, we present TroutHap, a multi-population genome-wide variant and imputation resource constructed from 540 high-coverage whole-genome sequences (~12.58×) representing multiple geographic sources and breeding backgrounds, mainly from North America, Europe, and China. We identified 16,408,551 high-confidence SNPs and integrated them into a unified genome-wide variant map across all 30 chromosome pairs. Using this resource, we benchmarked genotype imputation across simulated low-coverage sequencing depths. At 1× sequencing depth, genotype accuracy achieves >90%, while additional sequencing beyond 2× yielded smaller improvements. Supplementary cross-platform validation using a public 57 K SNP array dataset further evaluated compatibility with array-based genotyping data, with genotype concordance and genotype accuracy reaching 80.5% and 71.9%, respectively, after site-level filtering. TroutHap is released as an open community resource, including high-confidence SNP site lists, representative chromosome-level variant files, representative imputed genotype files, metadata tables, validation summaries, and reproducible workflow outputs. This dataset provides a reusable resource for low-coverage sequencing imputation, SNP-array-based genotype harmonization, and downstream genomic analyses in rainbow trout.