Whole-genome sequencing reveals genomic diversity and selection signatures for adaptation in South African Afrikaner and Bonsmara cattle

The indigenous Afrikaner and composite Bonsmara cattle breeds are hardy and adapted to the diverse South African climate and biomes. Both breeds have been successfully used in the South African stud and commercial industries. This study explored the genomic diversity and population structure, as well as identified selection signatures within and between the Afrikaner and Bonsmara breeds with a focus on signatures related to adaptation traits. Short-read whole genome sequencing data of 42 Afrikaner and 43 Bonsmara cattle were analysed. Diversity analysis revealed comparable nucleotide diversity levels in the Afrikaner and Bonsmara populations, with the Bonsmara having weaker average linkage disequilibrium between adjacent single nucleotide polymorphisms as well as having fewer runs of homozygosity. Furthermore, genetic structure analysis revealed distinct clustering of both populations, with the exception of a subset of Afrikaner individuals having been infused with Bonsmara genetics. Between and within breed selection signatures were detected using the fixation index and integrated haplotype score approaches, respectively. Several gene ontology terms were described based on the detected selection signatures, with the most significant being nervous system development and multicellular organismal processes. Finally, functional annotation of the candidate genes from the within-breed selection signature analysis revealed several genes (<i>B3GLCT</i>, <i>HSPA2</i>, <i>HSPH1</i>, <i>STING1</i>) relating to adaptive traits in both populations. The location of the within and between breed selection signatures in this study population is consistent with the performance and adaptive characteristics of both breeds and may enhance future breeding strategies with the inclusion of these breeds in crossbreeding programs. Furthermore, a comprehensive genomic characterization of these breeds through whole genome sequencing data is important as these adapted breeds are valuable reservoirs of genetic variation.