Abstract:
Local cattle and sheep populations are important for animal production and food security in
South Africa. These genetic resources are well adapted to the diverse climatic conditions
and hold potential to be utilized in production systems subjected to climate change. The
local beef breeds are well integrated into commercial livestock production systems with
access to performance recording and genetic evaluations, while local sheep breeds are
mainly utilised in smallholder and communal systems. The GeneSeek® Genomic Profiler™
Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding
status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara
and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina®
Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian,
Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino
and SA Merino) populations. Although ascertainment bias was indicated by the low MAF
(the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for
cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean Ho
ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels
of ROH-based inbreeding were calculated for cattle (FROH range: 0.018–0.104), than for
sheep populations (FROH range: 0.002–0.031). The abundance of short ROH fragments
(mean proportion of <4Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated
ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based
clustering and phylogenetic analyses, with high levels of admixture observed within the
Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction
could be seen between the dual-purpose breeds, the meat breed and the indigenous
breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was
moderate with low inbreeding. The non-commercialized, indigenous sheep populations
are more vulnerable with small effective populations. These results emphasise the value of
genomic information for effective management to exploit the potential contribution of local
genetic cattle and sheep resources in a changing environment.
Description:
SUPPLEMENTARY MATERIAL: Image 1 : Whole-genome SNP characterisation provides insight for sustainable use of local South African livestock populations.
Image 2 : Whole-genome SNP characterisation provides insight for sustainable use of local South African livestock populations.
Image 3 : Whole-genome SNP characterisation provides insight for sustainable use of local South African livestock populations.