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November 20, 2025Communications BiologyOpen Access

An updated Pig Haplotype Reference Panel (PHARP 4.0) comprising 13,298 haplotypes

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Authors

QWQingyu WangZZZhenyang ZhangXYXiaowei Ye

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Overview

Haplotype reference panel improves imputation accuracy in pigs, suggesting advancements for breeding programs.

Key Points

  • To present an updated pig haplotype reference panel (PHARP 4.0) for genetic research.
  • Introduced PHARP 4.0 with 6449 pig genomes from 154 breeds.
  • Compared imputation accuracy of PHARP 4.0 with existing panels.
  • Optimized RNA-seq-based imputation pipeline for multiple breeds.
  • PHARP 4.0 encompasses 50.3 million SNPs and 5.8 million indels.
  • Achieved CR > 0.99 and R² > 0.98 for European breeds.
  • Identified significant SNPs likely representing causal variants in two GWAS.

Cite This Study

Wang et al. (2025) studied this question.

synapsesocial.com/papers/6924f07ac0ce034ddc34ff3chttps://doi.org/10.1038/s42003-025-09052-1
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