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

Tlou Caswell Chokoe, Khanyisile Mdladla-Hadebe, Farai Muchadeyi, Edgar Dzomba, Tlou Matelele, Tumudi Mphahlele, Takalani J. Mpofu, Khathutshelo Nephawe and Bohani Mtileni
Additional contact information
Tlou Caswell Chokoe: Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Private Bag X973, Pretoria 0001, South Africa
Khanyisile Mdladla-Hadebe: Agricultural Research Council-Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa
Farai Muchadeyi: Agricultural Research Council-Biotechnology Platform, Private Bag X5, Onderstepoort, Pretoria 0110, South Africa
Edgar Dzomba: Discipline of Genetics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, South Africa
Tlou Matelele: Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Private Bag X973, Pretoria 0001, South Africa
Tumudi Mphahlele: Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Private Bag X973, Pretoria 0001, South Africa
Takalani J. Mpofu: Department of Animal Sciences, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
Khathutshelo Nephawe: Department of Animal Sciences, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa
Bohani Mtileni: Department of Animal Sciences, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa

Sustainability, 2020, vol. 12, issue 24, 1-16

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 H o revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 H o in LP to 0.42 ± 0.09 H o 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 F ST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest F ST value ( F ST = 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 F ST 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.

Keywords: genetic diversity; communal indigenous goat population; heterozygosity; commercial breeds; SNP genotype (search for similar items in EconPapers)
JEL-codes: O13 Q Q0 Q2 Q3 Q5 Q56 (search for similar items in EconPapers)
Date: 2020
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