Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.

ABSTRACT:

Background

Traditional genomic analysis relies on a single reference genome, which struggles to effectively characterize the genetic diversity among populations. This is due to the substantial genetic differences between the genome of the studied species and the reference genome, potentially introducing reference bias.

Results

In this study, we focused on Guanzhong Black pigs (GZB), Danish Large White pigs (DLW), and their hybrid offspring, Qinchuan Black pigs (QCB). We provided two high-quality parental genomes at the chromosomal level and constructed a parental genomic reference panel to detect SNPs (single nucleotide polymorphisms), INDELs (insertions and deletions), and SVs (structural variations). Compared with the single-reference method, the integrated parental genomi

SUBMITTER: Lv G 

PROVIDER: S-EPMC12276683 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature