Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

About 4000 years ago, humans interbred indicine and taurinesubspecies of cattle, most likely to cope with a multi-century drought. Here we report haplotype-resolved chromosome-level genome assemblies of these two cattle types, which comprise the majority of the global cattle population. The high-quality genomes of economically important Angus and Brahmanbreeds were produced from an F1 cross using the trio binning approach and enabled us to identify structural and copy number variants that differentiate indicine from taurineanimals, phase transcripts to detect allele-specific expression, and to study genome-wide selective sweeps. Six gene families with immune related functions are expanded in the indicine lineage. An indicus-specific extra copy of fatty acid desaturaseis under positive selection and may contribute to indicine adaptation to heat and drought. Our assemblies pave the way for the precise introduction of beneficial genetics to develop cattle that are adapted to climate change.