Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.

ABSTRACT:

Background

The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represents a limitation when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of sequencing read mapping to the current bovine genome assembly.

Results

In this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome, using as a backbone the Hereford ARS-UCD1.2 reference genome assembly, and incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Us

SUBMITTER: Sorin V 

PROVIDER: S-EPMC12551211 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature