Genetic Diversity of South African Indigenous Goat Population from Four Provinces Using Genome-Wide SNP Data

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.

Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep (Ovis aries) Breeds

“…Population geneticists have utilized DNA polymorphisms to study the “true” genetic structure, relationships of livestock species, within and between populations, for example, by using microsatellite markers [ 24 , 25 ], SNPs [ 26 , 27 ]. mtDNA CR, also referred to as the displacement loop (D-loop) is the most popular DNA polymorphism used to study matrilineal lineages and population history.…”

Breeding practices and trait preferences of goat keepers at Lepelle-Nkumpi Local Municipality, South Africa: implication for the design of breeding programmes

“…Commercial farmers keep Red Kalahari, Savannah, and Boer goats for meat production, Saanen and Toggenburg goats for milk production, and Angora goats for mohair production (Gwaze et al 2009 ). Mostly, communal farmers keep goats to fulfill multiple roles that include manure, traditional ceremonies, skin, milk, meat, and bush encroachment control (Saico and Abul 2007 ; Gwaze et al 2010 ; Chokoe et al 2020a , b ). Over six million goats are raised by communal farmers in South Africa (Chokoe et al 2020a , b ).…”

“…Mostly, communal farmers keep goats to fulfill multiple roles that include manure, traditional ceremonies, skin, milk, meat, and bush encroachment control (Saico and Abul 2007 ; Gwaze et al 2010 ; Chokoe et al 2020a , b ). Over six million goats are raised by communal farmers in South Africa (Chokoe et al 2020a , b ). However, communal goat keepers have low production resulting from limited knowledge in livestock genetic improvements (Yakubu et al 2019 ).…”

Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review

“…South Africa alone has approximately 5.2 million goats, with a provincial distribution ranging from 0.5% in Gauteng to 38% in the largest producing province, which is the Eastern Cape [ 2 ]. The majority of indigenous goats are owned and kept by smallholder farmers in rural areas [ 3 ] and are mostly kept for the value they bring to the livelihood of rural communities, through products such as meat, milk, skin, and mohair [ 4 ], and through their role in religious and cultural ceremonies.…”

“…Indigenous goats have diversified into unique ecotype populations over time due to geographical isolation, environmental dynamics, and selection pressures [ 4 ]. As a result, they are named after their place of origin, physical characteristics, and/or the ethnic tribes that own them [ 5 ].…”