Related Experiment Video
Updated: May 20, 2025

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
Published on: August 12, 2019
Pangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs
Jian Miao1, Qingyu Wang1, Zhe Zhang1
1College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
Background:
Breeds genetically distant from the reference genome often show considerable differences in DNA fragments, making it difficult to achieve accurate mappings. The genetic differences between pig reference genome (Sscrofa11.1) and Chinese indigenous pigs may lead to mapping bias and affect subsequent analyses.
Results:
Our analysis revealed that pangenome exhibited superior mapping accuracy to the Sscrofa11.1, reducing false-positive mappings by 1.4% and erroneous mappings by 0.8%. Furthermore, the pangenome yielded more accurate genotypes of SNP (F1: 0.9660 vs. 0.9607) and INDEL (F1: 0.9226 vs. 0.9222) compared to Sscrofa11.1. In real sequencing data, the inconsistent SNPs called from the pangenome exhibited lower genome heterozygosity compared to those identified by the Sscrofa11.1, including observed heterozygosity and nucleotide diversity. The same reduction of heterozygosity overestimation was also found in the chicken pangenome.
Conclusions:
This study quantifies the mapping bias of Sscrofa11.1 in Chinese indigenous pigs, demonstrating that mapping bias can lead to an overestimation of heterozygosity in Chinese indigenous pig breeds. The adoption of a pig pangenome mitigates this bias and provides a more accurate representation of genetic diversity in these populations.
Related Concept Videos
Viral Recombination
Pleiotropy
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Epistasis
Single Nucleotide Polymorphisms-SNPs

