Genetic gain & Inbreeding

Runs of homozygosity detects inbreeding coefficients in South African beef cattle

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Abstract

Runs of homozygosity (ROH) are contiguous stretches of DNA where both chromosomes in a pair are identical because they were inherited from a common ancestor. They are a result of recent or ancient inbreeding and their length can indicate recent relatedness, as longer runs are more indicative of recent inbreeding. This study aimed to assess the level of inbreeding in South African beef cattle using Runs of Homozygosity (ROH) to estimate the inbreeding coefficient (FROH). The Illumina BovineSNP 150K BeadChip were used to genotype 96 individuals representing four South African beef cattle breeds i.e. Nguni (n = 28), Bonsmara (n = 21), Angus (n = 22), and Simmental (n = 25) and genomic data was processed using Genome Studio 2.0 software. StructuRly database was used for population structure and identify individuals' clusters using triangle plots. ROH segments were identified using the detectRUNS package in R and allowing for the estimation of inbreeding coefficient (FROH) in total genome length. Results confirmed four different population structure of the South African beef cattle breeds. Distribution of ROH length within the genome revealed Nguni had the highest ROH segments in the genome between class (0-6Mb) followed by Simmental, Angus and Bonsmara. However, between class of (6-12Mb) and (12-24Mb) Angus showed the most significant ROH within the genome. Furthermore, the observed number of SNPs in a ROH peaks ( >75%) observed for Angus breed on chr 1, 4, 6, 9, 11,13,14,16, 19 and 21, for Simmental on chr 2, 6, 7, 11, 14, 21, and 22 and for Nguni on chr 1 and 6, while Bonsmara revealed lower SNPs in ROH (< 75%). Inbreeding coefficient (FROH) revealed the highest inbreeding for Angus with the highest median ROH (~0.30) and a narrow distribution, suggesting a relatively higher level of inbreeding. Bonsmara shows a wider distribution with a median of ~0.22, while Nguni has a lower median ROH (~0.15) and more variation. Simmental has a relatively high median (~0.25), with a wider range for some individuals with lower values. Proportion of PI-HAT was high to moderately with values ranging from (~0.50) to (~0.25). In conclusion, this study reports on ancient inbreeding in Nguni breed highlights a history of inbreeding or selection, while recent inbreeding observed in Angus reveals more homozygosity in a population.

Keywords: 2026

How to Cite:

Mtileni, B., Nephawe, K. & Modiba, M., (2026) “Runs of homozygosity detects inbreeding coefficients in South African beef cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286363. doi: https://doi.org/10.31274/wcgalp.23958

Rights: 1