Genome wide identification of hard and soft selective sweeps reveals distinct selection signatures in Karan Fries cattle

Natural selection shapes the genome by favoring beneficial mutations, leading to selective sweeps through the hitchhiking effect. Identification of such sweeps provides valuable insights into genomic regions influencing adaptation and economically important traits. The present study was aimed to characterize hard and soft selective sweeps in Karan Fries (KF) cattle developed from crossing Holstein Friesian (HF) and Tharparkar (TH). A haplotype frequency spectrum-based approach using the T-statistics was employed to detect selective sweep signatures across the genome. KF exhibited a markedly higher number of hard sweeps (491) compared to HF (183) and TH (136), whereas the number of soft sweeps was comparable among the three breeds. The elevated hard sweep count in KF reflects rapid fixation of novel allelic combinations generated by Bos taurus and Bos indicus admixture under nine generations of intense artificial selection, producing a functionally heterogeneous hub-gene network spanning reproductive (GAS8), genome-maintenance (EXO1, ERCC1), and immune-regulatory (DBNDD1, DEF8) axes rather than converging on a single pathway as in the parental breeds. HF hard sweep hub genes (POLR2E, RPL19, EIF4A3) converged on ribosome biogenesis supporting lactational protein synthesis, while TH hub genes (GABRA4, GABRA5, GABRB1, GABRB3, GABRG3, IFNAR1) reflected tropical neurological and reproductive adaptation. Soft sweep hub genes across breeds converged on ribosomal and mitochondrial ribosomal proteins (KF: MED1, MRPL16, MRPL22; HF: RACK1, RPL27A, MRPS11; TH: MRPL1, MRPS12, MRPL24), indicating shared polygenic selection on translational efficiency. QTL analysis identified milk production as the dominant trait category. These findings offer candidate loci for customized genomic selection panels supporting sustainable tropical dairy production. This article aligns with SDG 2 (Zero Hunger) of the UN Agenda for Sustainable Development.