Companion animals

Preliminary Genomic Profiling and Population Structure Analysis of the Boerboel dog breed (BBD): Determining the Lineage Status of coat colour

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Abstract

The Boerboel dog (BBD) breed is a large breed developed in Southern Africa for guarding and companionship. Recently, the appearance of black-coated dogs has sparked significant controversy regarding breed purity and registry recognition. The objective of this study was to presents a preliminary genomic profiling and population structure analysis of the South African BBD population, with a specific focus on determining the lineage status associated with coat colour variation using both pedigree and genomic data. The analyses performed were principal component analysis (PCA, PLINK v1.9), phylogenetic tree (iTOL v6), pedigree-based (PopReport) and genomic inbreeding (R version 4.5.1), effective population size (Ne) (PopReport), heterozygosity, and runs of homozygosity (ROH) (Plink v1.9). Fifty-one individuals were genotyped with Illumina® CanineHD 170k Bead Chip, and pedigree data were analysed for 115,671 animals (1940-2025). Despite the 170k Bead Chip associated to ascertainment bias for non-European breeds, the average minor allele frequency (MAF) was 0.18, which indicate moderate polymorphism. Pedigree-based inbreeding coefficient was low (Fped = 0.03), while genomic inbreeding coefficient suggested slightly higher heterozygosity (Fgen = -0.03). The positive correlation (r = 0.31) indicates that pedigree alone only partially reflects realized genomic inbreeding. The average rate of change in additive genetic relationships (Δf) and inbreeding coefficients (ΔF) between 1973 and 2025 was 0.001 and 0.0012 per year, respectively, corresponding to 0.004 and 0.005 per generation, with estimated Nₑ of approximately 130 (based on Δf) and 96 (based on ΔF). Overall, the population shows moderate diversity and low inbreeding (0.00-0.09). To compare expected and realized genetic structure, PCA was performed using both pedigree and genomic data. Pedigree-based PCA showed no evidence of stratification by coat colour (PC1:1.78%; PC2:1.30%), confirming minimal differentiation at the pedigree level. In contrast, the genomic PCA revealed distinct clustering of brindle-coloured dogs, explaining 12.93% (PC1) and 8.94% (PC2) of the variation. PC1 represented the shared structure of brown and pale dogs, while PC2 distinguished brindle dogs, showing a negative relationship with the brown and pale individuals. In order to provide a baseline for lineage differentiation, this research focused on the underlying structure of established phenotypes, although black-coated individuals remain to be a focal point of breed controversy. Furthermore, the prevalence of small ROH segments (3,989 total, majority < 2 Mb) suggests a historic bottleneck with maintained variation. In conclusion, the BBD population retains a moderate level of genetic diversity, but the discrepancy between genomic clustering and pedigree, particularly with regard to the brindle phenotype, raises the possibility that underlying genetic sub-structures may be concealed by visual traits. To properly determine the ancestry status of disputed traits like the black coat, more whole-genome sequencing study is needed.

Keywords: 2026

How to Cite:

Madula, R., Visser, C., Mafolo, K. & Makgahlela, M., (2026) “Preliminary Genomic Profiling and Population Structure Analysis of the Boerboel dog breed (BBD): Determining the Lineage Status of coat colour”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2323423. doi: https://doi.org/10.31274/wcgalp.24394

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