Genome-Wide Scan for Selection Signatures in Zebu and Taurine Cattle Reveals Regions Associated with Adaptive and Production Traits

Over the course of their evolutionary history, modern cattle breeds have been exposed to a wider range of ecological stressors and human guided selective breeding. Natural environmental selective pressures have likely shaped the genome of African cattle populations adapted to marginal and heterogeneous landscapes. On the other hand, temperate Bos taurus cattle breeds have been continuously selected for economically importance traits. To identify genomic regions under divergent selection for ecological and production traits, we performed a genome-level scan using 68,007 autosomal SNPs derived from indicine breeds in Ethiopian cattle populations (n = 272), Nellore (n = 99), Bangladeshi zebu (n = 52), taurine reference populations, Holstein, (n = 21) and Hanwoo, (n = 22) based on a population differentiation (F_ST) test. We identified potential candidate genes involved in thermo-tolerance (DNAJB5/Hsp40, DNAJB6, and HSPA13), parasite loads and resistance (BBS9, FAM177A1, SRP54, PSMA6, PLD4, and CDCA4), fertility (INHBC, STAT6, ID3, and MSRB3), disease/immune response (ARG2, AKIRIN2 and TRIM24), body stature (LYN, CHCHD7, and SDR16C5, and POLR2), and growth and meat traits (TG, ASAP1, MEF2A, and HERC3). The identified genes are involved in different pathways (vasopressive-regulated water reabsorption, metabolism, melanogenesis, and thyroid and hormone synthesis). The results from the present study can be used as a basis for further understanding and exploitation of the molecular basis of adaptive and production traits.