Abstract:
The smallholder dairy sector in South Africa is characterized by a low input production
system and poor animal productivity. Research has been carried out to benchmark
cow productivity on smallholder dairy herds; however, there is a paucity of information
on the current status of breeding practices and the genetic consititution of cattle used
in this production system. This information is vital for the development of sound and
sustainable breeding programs for SHD production, which can have an enormous
positive impact on food security and rural livelihoods. Thus, the aim of this study was
to evaluate the levels of genetic diversity and population structure in South African
smallholder dairy (SHD) herds using single nucleotide polymorphism (SNP) markers.
A total of 192 animals from SHD dairy herds were genotyped using the GeneSeek®
Genomic Profiler (GGP) 150K-BeadChip. Four specialized dairy breeds included the
Ayrshire(n = 200), Holstein(n = 231), Jersey (n = 224) and Nguni (n = 209) were used
as the reference populations. The mean MAF values ranged from 0.30 Ayshire (AYR),
Jersey (JER), and Nguni (NGI) to 0.31 Holstein (HOL) and SHD between the
populations. There were slight differences in the levels of genetic diversity ranged
between 0.39 (JER and NGI) to 0.40 (AYR, HOL, and SHD). A moderate level of
inbreeding (0.02) was observed in the SHD population, which results in high genetic
diversity among this herds. Principal Component Analysis (PCA) revealed four
homogeneous clusters comprising of AYR, HOL, JER, NGI, and a heterogeneous
cluster of the SHD. The heterogeneity observed in the SHD population indicates
widespread crossbreeding. The model-based cluster analysis corresponded with the
PCA and pointed out the predominance of HOL, JER, with marginal gene flow from
the AYR and NGI. These results have provided a useful insight into the genetic
structure and prevailing breeding practices on South African SHD herds.
