Divergent adaptation to highland and tropical environments in Bolivian Creole cattle

Bolivian Creole cattle populations evolved under low levels of breeding management and, during more than 500 years of natural selection, became adapted to various environments such as the contrasting highland and subtropical environments. Recently, highland Creole cattle were crossbred with Holstein to improve dairy production. The aim of this research was to evaluate the divergent adaptation through selection footprints of Bolivian Creole cattle from Andean highland and tropical lowlands, and to evaluate the effect of Holstein introgression in highland Creole. For this purpose, 130 Creole cattle (75 highland, 55 lowland) and 88 Holstein were genotyped using a microarray. The database was used to determine population structure and admixture and detect selection sweeps using F_ST, Rsb, XP-EHH, and ROH. Ancestry inference suggested that selection peaks were not due to Holstein introgression. The NCBI database was used to retrieve genes from the common regions and then perform gene ontology analysis. The most prominent selection peaks were on BTA20 and BTA23 and included the PRLR (slick phenotype) and Class I and IIa BoLA genes. Other windows contained candidate genes for hypoxia (ANXA2, NDUFA4L2), angiogenesis and haematological parameters (ANXA2, CPLANE1, NRP1, NRP2), immune response (IL7R, IL6ST, IL31RA, C6, C7, STAT6, NKG2A, IRAK4, KLR, CLEC), oxidative stress (GSTA, HSD17B6) and morphological traits (PLAG1, CHCHD7, CAP2, ARL15). GO analysis revealed enrichment terms and pathways related to immune response, glutathione and retinol metabolism and reported QTLs for coat characteristics, immune response and tick resistance. The results suggest the complex mechanism in the adaptation of Bolivian Creole cattle to the contrasting highland and subtropical environments.