Abstract
Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p < 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.
Highlights
South Africa has a great diversity of agro-ecological zones and abundant Farm Animal Genetic Resources (FAnGR)
The results show that twenty-five outliers were significant to each Principal Components (PC), only 5 could be retained, which were found on chromosomes 10, 15, 20, and 21, and were associated with the PC2, while the gene search did not reveal any genes
The communal indigenous goat populations showed a weak sub-structuring with admixed individuals with evidence of gene flow and shared genome ancestry with commercial goat populations, while the Limpopo population separated to form its own cluster
Summary
South Africa has a great diversity of agro-ecological zones and abundant Farm Animal Genetic Resources (FAnGR). It has more than 6 million indigenous goats, which are distributed across geographic regions of South Africa [1]. Diversity in indigenous goats is important for maintaining biodiversity and is the basis of conservation and genetic improvement. Indigenous goats in Southern Africa have low growth rates, small body size, low milk yield, and low carcass weights, their characteristics such as adaptation to local feed resources and response to environmental factors; heat tolerance, and disease and parasite tolerance have a potential for improvement and conservation of these resources [6,7]
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