Miao Jian, Wang Qingyu, Zhang Zhe, Wang Qishan, Pan Yuchun, Wang Zhen
College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Building 11, Yongyou Industrial Park, Yazhou District, Sanya, Hainan, 572025, China.
BMC Biol. 2025 Mar 26;23(1):89. doi: 10.1186/s12915-025-02194-y.
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.
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.
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.
与参考基因组遗传距离较远的品种在DNA片段上往往存在显著差异，这使得难以实现准确的映射。猪参考基因组（Sscrofa11.1）与中国本土猪之间的遗传差异可能导致映射偏差，并影响后续分析。
我们的分析表明，泛基因组在映射准确性上优于Sscrofa11.1，将假阳性映射减少了1.4%，错误映射减少了0.8%。此外，与Sscrofa11.1相比，泛基因组产生了更准确的单核苷酸多态性（SNP）（F1：0.9660对0.9607）和插入缺失（INDEL）（F1：0.9226对0.9222）基因型。在实际测序数据中，与通过Sscrofa11.1鉴定的单核苷酸多态性相比，从泛基因组中调用的不一致单核苷酸多态性表现出更低的基因组杂合性，包括观察到的杂合性和核苷酸多样性。在鸡的泛基因组中也发现了同样程度的杂合性高估降低。
本研究量化了Sscrofa11.1在中国本土猪中的映射偏差，表明映射偏差会导致中国本土猪品种杂合性的高估。采用猪泛基因组可减轻这种偏差，并更准确地反映这些群体的遗传多样性。
