European taurine vs Indian indicine cattle: a comparative genomic study reveals regions of differentiation during evolution and selection during crossbreeding

Cattle are broadly classified into two subspecies: Bos taurus, adapted to temperate climates, and Bos indicus, adapted to tropical environments. Indicine cattle show better heat tolerance and stronger disease resistance, whereas taurine cattle are known for higher milk yield and better meat quality. Improving milk yield while maintaining resistance to heat stress and infectious diseases is an important objective in cattle breeding. Marker-assisted selection is an effective approach for improving economically important traits, highlighting the need to understand genetic differences between taurine and indicine cattle. However, genome-wide comparisons between European taurine and Indian indicine cattle remain limited. To address this gap, whole-genome sequencing of 48 Indian indicine cattle was performed and combined with publicly available data. This enabled a comparative genomic analysis of 74 Indian indicine and 83 European taurine individuals to identify genes involved in heat tolerance and immune response. Genome-wide analyses using Fst and XP-CLR identified 4,343 and 1,457 differentiated genes, respectively, with 826 genes common to both methods. These genes were mainly associated with immune response, protein stability, and cytoskeletal structure. Strong selection signals were observed in three heat shock protein genes (DNAJC11, DNAJC5, and DNAJB11) and 229 immune-related genes. To examine the inheritance of these genes through crossbreeding, a haplotype-resolved genome assembly was generated for the Indian crossbreed Sunandini, which showed predominantly taurine ancestry (69.13-96.04%), with a smaller indicine contribution (1.22-1.87%). Several genes related to heat tolerance and immune response were inherited exclusively from indicine cattle, highlighting their importance for environmental adaptation and future breeding programs.