High-quality phased genome assemblies of line-bred Korean Hanwoo cattle.

The Korean cattle breed, Hanwoo, has been selected as a meat cattle breed since the late 1980s in Korea, but has suffered from reduced genetic diversity due to repeated selection within a single population. In this study, we generated high-fidelity long-read sequencing data (~Q30, 98-146 Gb) for three Hanwoo Research Center (HRC) Hanwoo individuals from early, intermediate, and current breeding generations of the genetically distinct HRC population. These datasets yielded four partially phased genome assemblies of early and intermediate generations and two fully phased genome assemblies of the current generation. Furthermore, we construct a graphical pangenome reference by combining 19 publicly available cattle assemblies with our six new assemblies, identifying 39.3 M single-nucleotide variants (SNVs) and 60.7 K structural variants (SVs). Among these, 27.8 K SNVs and 26 SVs were uniquely found in the HRC Hanwoo population. These high-quality genomic resources provide valuable insights into the genetic characteristics of HRC Hanwoo and will facilitate future breeding strategies and genetic improvement efforts.