Conservation & local programs

Genomic signatures of selection within ecotypes of the Indigenous Veld Goat Breeds of South Africa

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Abstract

The Indigenous Veld Goat Breeders Society of South Africa was established to conserve and promote four indigenous ecotypes. The Nguni, Xhosa Lob Ear, Cape Speckled and Kunene ecotypes possess unique adaptive traits that enable them to thrive under harsh semi-arid conditions, making them ideal for climate-resilient production. The genetic characterization of ecotype adaptive traits promotes their sustainable use and enables policy makers to design informed sustainable strategies for improvement and conservation. This study aimed to investigate selection signatures in three ecotypes using the Illumina Goat 65K SNP array. A preliminary evaluation of 248 ecotypes and 38 929 SNP markers representing the Nguni = 32, Xhosa Lobear = 24, Cape Speckled = 43 were used along with reference populations of meat-types including the Boer = 81, Savanna = 19, Kalahari red = 29, and the feral Tankwa = 20. Genomic regions under selection were identified using Integrated Haplotype Score (iHS) using the rehh package in R. Population structure analysis revealed distinct genetic clusters reflective of the breeds' unique production traits and localised adaptation. A total of 73 SNPs were under selection (iHS > 4) across all three ecotypes. Candidate genes under selection within the ecotypes varied with 48 genes in Nguni, 27 genes in the Cape Speckled, and 26 genes in the Xhosa Lob Ear. The genes under selection were associated with production traits such as meat, milk as well as local adaptation (i.e., health, and coat characteristics). Common signals detected included the prion locus (PRNP/PRND) associated with disease resistance as well as coat colour and quality genes, milk composition gene DGAT1, TLCD2, FAT1, CORIN, DGAT1, ABCC2, COX15 genes for local environmental adaptation. The detection of selected genes related to meat, milk and adaptive traits supports the breed standards the Indigenous Veld Goat Breeders Society. The study findings highlight the multi-purpose potential of these animals and has implications for breed and ecotype definitions that can influence policy makers in the management of this breed. Candidate SNPs under selection within each ecotype can be used as the basis for a breed assignment panel for indigenous veld goats.

Keywords: 2026

How to Cite:

Gcabashe, S., Segakoeng, M. & Hadebe, K., (2026) “Genomic signatures of selection within ecotypes of the Indigenous Veld Goat Breeds of South Africa”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286469. doi: https://doi.org/10.31274/wcgalp.24020

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