Genetic gain & Inbreeding

Assessing inbreeding levels in two pilot community-based breeding program sites with common breeding objectives in South Africa

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Abstract

Indigenous goats are an important Animal Genetic Resource (AnGR), central to the African socio-cultural heritage, rural household economy and food security. Inbreeding in communally kept herds, can compromise genetic variation, fitness and adaptability of these populations. Community-based breeding programs (CBBPs) were implemented in two sites to address the production and breeding challenges for an improved system. The aim of the study was to assess inbreeding levels as a constraint on genetic progress and herd productivity in smallholder systems in the two pilot sites of uMkhanyakude District in KwaZulu-Natal and Buffalo City District in Eastern Cape, South Africa. A total of 212 randomly selected communally farmed goats from 195 herds were genotyped using the Illumina 65K Goat SNP BeadChip (IGGC) to investigate the population structure, inbreeding, and runs of homozygosity (ROH). Genomic clustering confirmed that the uMkhanyakude goats are Nguni ecotype and the Buffalo City goats Xhosa Lobear ecotype, demonstrating high level of purity; challenging common perceptions that communal goats are non-descript. Inbreeding coefficients (FIS) in Buffalo City and uMkhanyakude were 0.21 ±0.03 and 0.29 ±0.02 respectively, and the genomic inbreeding coefficients based on ROH (FROH) were 0.08 ±0.04 and 0.14 ±0.02. These differences are due to the pooling of random mating multiple herds with different allele frequencies at district level and suggests low individual inbreeding levels. The number of shared IBD segments was higher in Buffalo City (31.1 ±31.5) than in uMkhanyakude (22.8 ±12.7). The average length of shared IBD segments was 11.33 ±11.16cM in Buffalo City and 8.05 ±6.46cM in uMkhanyakude, with evidence of both distant and recent shared ancestry among goats within each region. A total number of ROH segments was 14627 in Buffalo City and 14162 in uMkhanyakude with the short ROH category (1-2Mb) with higher genomic coverage. Runs of homozygosity hotspots (top 1%) overlapped with 998 genes across the genome. Some of the overlapping genes found in the uMkhanyakude population included melanocortin 2 receptor (MC2R) and melanocortin 5 receptor (MC5R) located on chromosome 24, which are involved in melanogenesis. The study results suggest mating of closely related individuals likely due to preferential selection of white coat-coloured bucks and castration without records or performance strategy in the regions. These practices threaten the diversity and increase the risk of deleterious recessive traits such as hypopigmentation which can cause skin damage in the nose, ears and udder, especially in hot climates. Designing community level structured strategy that responds to inbreeding coupled with training farmers on record-keeping, trait selection and culling is important for sustainability of the CBBPs.

Keywords: 2026

How to Cite:

Segakoeng, M., Mpofu, T., Nephawe, K., Mtileni, B. & Hadebe, K., (2026) “Assessing inbreeding levels in two pilot community-based breeding program sites with common breeding objectives in South Africa”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285806. doi: https://doi.org/10.31274/wcgalp.23799

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