Abstract:
In this study, we evaluated an admixed South African Simbra crossbred population,
as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to
understand their genetic architecture and detect genomic regions showing signatures
of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K).
Genomic structure analysis confirmed that the South African Simbra cattle have an
admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra
genome maintains favorable traits from both breeds. Genomic regions that have been
targeted by selection were detected using the linkage disequilibrium-based methods
iHS and Rsb. These analyses identified 10 candidate regions that are potentially under
strong positive selection, containing genes implicated in cattle health and production
(e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles
likely contribute to the biological and cellular functions determining phenotype in the
Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from
the breed’s original indicine and taurine ancestors. The Simbra breed thus possesses
derived parental alleles that combine the superior traits of the founder Brahman and
Simmental breeds. These regions and genes might represent good targets for ad-hoc
physiological studies, selection of breeding material and eventually even gene editing, for
improved traits in modern cattle breeds. This study represents an important step toward
developing and improving strategies for selection and population breeding to ultimately
contribute meaningfully to the beef production industry.
