Abstract:
BACKGROUND : The detection of selection signatures in breeds of livestock species can contribute to the identification
of regions of the genome that are, or have been, functionally important and, as a consequence, have been targeted
by selection.
METHODS : This study used two approaches to detect signatures of selection within and between six cattle breeds in
South Africa, including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31)
and Holstein (n = 29). The first approach was based on the detection of genomic regions in which haplotypes have
been driven towards complete fixation within breeds. The second approach identified regions of the genome that
had very different allele frequencies between populations (FST).
RESULTS AND DISCUSSION : Forty-seven candidate genomic regions were identified as harbouring putative signatures
of selection using both methods. Twelve of these candidate selected regions were shared among the breeds and
ten were validated by previous studies. Thirty-three of these regions were successfully annotated and candidate
genes were identified. Among these genes the keratin genes (KRT222, KRT24, KRT25, KRT26, and KRT27) and one heat
shock protein gene (HSPB9) on chromosome 19 between 42,896,570 and 42,897,840 bp were detected for the Nguni
breed. These genes were previously associated with adaptation to tropical environments in Zebu cattle. In addition, a
number of candidate genes associated with the nervous system (WNT5B, FMOD, PRELP, and ATP2B), immune response
(CYM, CDC6, and CDK10), production (MTPN, IGFBP4, TGFB1, and AJAP1) and reproductive performance (ADIPOR2,
OVOS2, and RBBP8) were also detected as being under selection.
CONCLUSIONS : The results presented here provide a foundation for detecting mutations that underlie genetic variation
of traits that have economic importance for cattle breeds in South Africa.
