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

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    descriptionPublicationkeyboard_double_arrow_right Article , Journal , Other literature type 2020Publisher:MDPI AG
    Authors: Tlou Caswell Chokoe; Khanyisile Mdladla-Hadebe; Farai Muchadeyi; Edgar Dzomba; +5 Authors

    doi: 10.3390/su122410361

    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.

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  • The African Goat Improvement Network: a scientific group empowering smallholder farmers

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    descriptionPublicationkeyboard_double_arrow_right Article , Other literature type 2023 United States, Italy, France, France, Italy, France Publisher:Frontiers Media SA
    Authors: Curtis P. Van Tassell; Benjamin D. Rosen; M. Jennifer Woodward-Greene; M. Jennifer Woodward-Greene; +28 Authors

    doi: 10.3389/fgene.2023.1183240 , 10.60692/d2vvm-krr93 , 10.60692/qz590-k1j54

    pmid: 37712066

    pmc: PMC10497955

    handle: 20.500.14243/453301 , 10568/132569 , 20.500.12876/dvmqQRnv , 10568/136011

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

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    descriptionPublicationkeyboard_double_arrow_right Article , Journal , Other literature type 2020Publisher:MDPI AG
    Authors: Tlou Caswell Chokoe; Khanyisile Mdladla-Hadebe; Farai Muchadeyi; Edgar Dzomba; +5 Authors

    doi: 10.3390/su122410361

    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.

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  • The African Goat Improvement Network: a scientific group empowering smallholder farmers

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    descriptionPublicationkeyboard_double_arrow_right Article , Other literature type 2023 United States, Italy, France, France, Italy, France Publisher:Frontiers Media SA
    Authors: Curtis P. Van Tassell; Benjamin D. Rosen; M. Jennifer Woodward-Greene; M. Jennifer Woodward-Greene; +28 Authors

    doi: 10.3389/fgene.2023.1183240 , 10.60692/d2vvm-krr93 , 10.60692/qz590-k1j54

    pmid: 37712066

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