Haplotype-resolved genome assemblies for Norwegian Red cattle

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Abstract
Norwegian Red (NR) cattle are the main dairy breed in Norway, bred according to a broad breeding goal including health and fertility since the 1970s. Genomic studies on NR cattle have relied on the public Hereford reference, thus increasing the risk of missing or misrepresenting NR breed-specific variation. Moreover, the Hereford reference is a pseudohaploid assembly, representing homologous chromosomes in a collapsed manner, which results in loss of haplotype-specific alleles and misrepresentation of complex variants. To develop more refined NR specific resources, we utilised long-read sequencing (PacBio HiFi + ONT) and trio-binning to construct six new haplotype-resolved assemblies representing NR genomes. These six NR2025 assemblies show high completeness (BUSCO: 95.82-98.11%) and contiguity (N50: 73.8-88.5 Mb) and are accurately phased (hamming error rate: 0.46-2.52%). Most autosomes have been assembled into the acrocentric centromere, and mapping of bovine satellite sequences reveal distinct organisational patterns of different satellite units across this highly repetitive region. The NR2025 assemblies provide a valuable resource for identification of novel variants and haplotypes in the NR population, which will enable more accurate association studies of genotype-to-phenotype relations and genomic predictions in NR cattle, ultimately enhancing the efficacy of selection for desirable traits.
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