Sequencing & Pangenomes

Genome wide identification of runs of homozygosity in Nguni and F2 Nguni (Nguni x Angus) cattle of South Africa

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Abstract

The Nguni is a South African indigenous cattle breed adapted to low quality feed and resistant to internal and external parasites thus making it desirable to small-holder breeders with limited resources. Despite good characteristics, there is a need to improve traits of economic importance in Nguni through crossbreeding with taurine breeds. This study aimed to identify runs of homozygosity (ROH) in the Nguni and F2 Nguni that may be associated with production traits. An experimental population was generated by crossing Nguni cows with Angus bulls using artificial insemination to develop the F1 population. The F1 population was further inter-crossed to produce F2 generation. Prior to inter-crossing, parentage verification was conducted to prevent within family inter-cross. Genotype markers (SNPs) with MAF ≤ 0.02, call rates ≤ 0.95 or deviated from HWE frequency with a probability of ≤ 0.0001 and animals with a call rate ≤ 0.90, were excluded. For the Nguni a total of 412 animals and 40044 SNPs remained and 216 animals and 141746 SNPs for the F2 Nguni. Runs of homozygosity that were ≥1MB and ≥50 SNPs were detected using the slidingRuns method in detectRuns R package. The ROH were used to determine the length and distribution of the ROH in both datasets. The longest and shortest ROH were the same on both populations (long= 69,30Mb; short= 1,0Mb). For Nguni, chromosomes with high number of ROH was BTA1 and BTA7 (n=211), the least number was on BTA27 (n=63). For F2 Nguni, BTA1 had the highest number of ROH (n=603) while the least number was on BTA23 (109). For both Nguni and F2 Nguni, gene ontology revealed genes associated with biological regulation, metabolic processes and immune system processes, thus displaying evidence of adaptive characteristics in the breed. Most importantly genes associated with growth processes were also identified. This study reveals the genomic architecture and the important genomic regions that are not fully explored to improve the Nguni breed.

Keywords: 2026

How to Cite:

Mdyogolo, S., Nesengani, L., Mkize, N. & Mapholi, N., (2026) “Genome wide identification of runs of homozygosity in Nguni and F2 Nguni (Nguni x Angus) cattle of South Africa”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287042. doi: https://doi.org/10.31274/wcgalp.24200

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