Evidence map›Paper›PMID 41266802›Full record

ArticleCommunications biology2025

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

Qingyu Wang, Zhenyang Zhang, Xiaowei Ye, Jiamin Gu, Jiabao Sun, Caiyun Cao, Qian Xiao, Qiang Chen, Zhong Xu, Kejun Wang and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Qingyu Wang *Key Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0009-0003-7496-147X
Zhenyang Zhang *Key Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Xiaowei YeKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0009-0005-0079-3930
Jiamin GuKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Jiabao SunKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Caiyun CaoKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Qian XiaoHainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou, China.
Qiang ChenFaculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
Zhong XuHubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, China.
Kejun WangCollege of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.
Wei ZhaoKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Hao SunCollege of Animal Science, Jilin University, Changchun, China.
Qingbo ZhaoCollege of Animal Science & Technology, Nanjing Agricultural University, Nanjing, China.
Qishan WangKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0000-0002-6475-0009
Yuchun PanKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
Zhe ZhangKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China. zhe_zhang@zju.edu.cn.ORCID http://orcid.org/0000-0001-5320-3125
Zhen WangKey Laboratory of nutrition and breeding for high-quality animal products, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China. wangzhen20@zju.edu.cn.ORCID http://orcid.org/0000-0002-1896-3716

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

High-throughput genome sequencing and genotyping have significantly accelerated genetic research. However, the high cost of whole-genome sequencing (WGS) remains a barrier to large-scale studies like genome-wide association studies (GWAS) and genomic prediction. Genotype imputation offers a cost-effective alternative by inferring unobserved variants from lower-density data using haplotype reference panels. In this study, we present the updated Pig Haplotype Reference Panel (PHARP) 4.0, comprising 6449 pig genomes from 154 breeds. PHARP 4.0 encompasses 50.3 million SNPs and 5.8 million indels, making it the largest and most diverse pig reference panel to date. PHARP 4.0 demonstrated superior imputation accuracy compared to existing panels (SWIM, AHC, AGIDB, and PGRP), achieving concordance rates (CR > 0.99) and correlation coefficients (R² > 0.98) in European breeds and improved accuracy in Chinese Jinhua pigs (CR = 0.936, R² = 0.924) when imputing from 80 K SNP chip data to whole-genome sequencing (WGS). We further optimized an RNA-seq-based imputation pipeline by incorporating multiple breeds and applying a 6× sequencing depth filter, achieving CR > 0.95 and R² > 0.90 in European breeds, and a CR of 0.93 with an R² = 0.92 in Chinese Jinhua pigs. Additionally, increasing the specific reference panel size to approximately 400 samples improved the imputation of rare variants. Utilizing PHARP 4.0, we successfully imputed low-density SNP chip data for two GWAS, identifying significant SNPs likely representing causal variants. Overall, PHARP 4.0 serves as a valuable resource for advancing pig genetic research and supporting breeding programs.

Indexed as

HaplotypesSus scrofaAnimalsGenome-Wide Association StudyPolymorphism, Single NucleotideSwineWhole Genome Sequencing

Identifiers

PMID41266802
PMCPMC12635135

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.