Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.

ABSTRACT: Based on a pangenome graph platform, we simultaneously analyzed the impacts of SNPs and SVs in the population structure and phenotypic formation of global cattle using 2,409 individuals from 82 breeds. We demonstrated that SVs, like SNPs, effectively explain the population structure of global cattle. Genomic regions under strong selection, identified using both SNPs and SVs, consistently revealed footprints associated with human-mediated selection of economic traits in European improved cattle or natural selection of geographical adaptations. Notably, we detected that ∼40.14% of SVs were not tagged (LD, r2 < 0.6) by nearby SNPs. These "orphan" SVs may uncover new genetic signals and represent recent mutations associated with specific selection pressures or local environmental adaptation. S

SUBMITTER: Dai S 

PROVIDER: S-EPMC12401084 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature