Haplotype-Resolved Genome Assemblies for Norwegian Red Cattle.

Area of Science:

• Genomics
• Animal Breeding
• Bioinformatics

Background:

• Norwegian Red (NR) cattle breeding prioritizes health and fertility.
• Current genomic studies use a Hereford reference, risking NR-specific genetic variation misrepresentation.
• The Hereford reference assembly is pseudohaploid, leading to data loss and inaccurate variant representation.

Purpose of the Study:

• To develop refined, NR-specific genomic resources.
• To construct high-quality, haplotype-resolved genome assemblies for NR cattle.
• To overcome limitations of existing reference genomes for NR cattle.

Main Methods:

• Utilized long-read sequencing technologies (PacBio HiFi and Oxford Nanopore).
• Employed trio-binning to phase and construct haplotype-resolved assemblies.
• Performed quality assessment using BUSCO for completeness and contiguity metrics (N50).

Main Results:

• Generated six highly complete (95.82%-98.11%) and contiguous (N50: 73.8-88.5 Mb) NR2025 genome assemblies.
• Achieved accurate phasing with low Hamming error rates (0.46%-2.52%).
• Identified distinct organizational patterns of satellite DNA in repetitive centromeric regions.

Conclusions:

• The NR2025 assemblies are a valuable resource for NR cattle genomics.
• Enables accurate identification of novel variants and haplotypes in the NR population.
• Facilitates improved genotype-to-phenotype association studies and genomic predictions for enhanced trait selection.