Breed-Specific Genetic Recombination Analysis in South African Bonsmara and Nguni Cattle Using Genomic Data

Nozipho A. Magagula (), Bohani Mtileni, Keabetswe T. Ncube, Khulekani S. Khanyile and Avhashoni A. Zwane
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Nozipho A. Magagula: Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
Bohani Mtileni: Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
Keabetswe T. Ncube: Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
Khulekani S. Khanyile: Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, Pretoria 0062, South Africa
Avhashoni A. Zwane: Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0002, South Africa

Agriculture, 2025, vol. 15, issue 17, 1-14

Abstract: South African cattle comprise diverse breeds with distinct evolutionary histories, potentially reflecting differences in recombination landscapes. This study assessed genome-wide recombination rates and hotspots in Bonsmara (n = 190) and Nguni (n = 119) cattle using three-generation half-sib pedigrees genotyped with the Illumina Bovine SNP50 BeadChip. Phasing across 29 autosomes was conducted using SHAPEIT v2, and crossover events were inferred using the DuoHMM algorithm. The total number of crossover events detected was higher in Nguni (n = 8982) than in Bonsmara (n = 7462); however, the average recombination rate per 1 Mb window was significantly higher in Bonsmara (0.31) compared to Nguni (0.18) ( p < 0.01). This apparent discrepancy reflects differences in genomic distribution and crossover clustering across breeds, rather than overall recombination frequency. A critical limitation of the study is the reliance on half-sib families with small family sizes, which may underestimate recombination rates due to limited meiotic sampling and increased variance in crossover detection. We identified 407 recombination hotspots in Bonsmara and 179 in Nguni, defined as intervals exceeding 2.5 standard deviations above the mean recombination rate. Genes such as PDE1B and FP which are associated with productions traits were located within hotspot-enriched regions. However, functional causality between these genes and local recombination activity remains unverified. Our results provide statistically supported evidence for breed-specific recombination patterns and hotspot distributions, underscoring the importance of incorporating recombination architecture into genetic improvement strategies for South African cattle.

Keywords: diversity; hotspots; indigenous cattle; kinship; recombination (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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