Genetics of Base Coat Colour Variations and Coat Colour-Patterns of the South African Nguni Cattle Investigated Using High-Density SNP Genotypes

Nguni cattle are a Sanga type breed with mixed B. taurus and B. indicus ancestry and proven resistance to ticks, diseases and other harsh conditions of the African geographical landscape. The multi-coloured Nguni coats have found a niche market in the leather industry leading to breeding objectives towards the promotion of such diversity. However, there is limited studies on the genomic architecture underlying the coat colour and patterns hampering any potential breeding and improvement of such trait. This study investigated the genetics of base coat colour, colour-sidedness and the white forehead stripe in Nguni cattle using coat colour phenotyped Nguni cattle and Illumina Bovine HD (770K) genotypes. Base coat colour phenotypes were categorised into eumelanin (n = 45) and pheomelanin (n = 19). Animals were categorised into either colour-sided (n = 46) or non-colour-sided (n = 94) and similarly into presence (n = 15) or absence (n = 67) of white forehead stripe. Genome-wide association tests were conducted using 622,103 quality controlled SNPs and the Efficient Mixed Model Association eXpedited method (EMMAX) implemented in Golden Helix SNP Variation Suite. The genome-wide association studies for base coat colour (eumelanin vs. pheomelanin) resulted into four indicative SNPs on BTA18 and a well-known gene, MC1R, was observed within 1 MB from the indicative SNPs (p < 0.00001) and found to play a role in the melanogenesis (core pathway for melanin production) and the MAPK signalling pathway. GWAS for colour-sidedness resulted in four indicative SNPs, none of which were in close proximity to the KIT candidate gene known for colour-sidedness. GWAS for the white forehead stripe resulted in 17 indicative SNPs on BTA6. Four genes MAPK10, EFNA5, PPP2R3C and PAK1 were found to be associated with the white forehead stripe and were part of the MAPK, adrenergic and Wnt signalling pathways that are synergistically associated with the synthesis of melanin. Overall, our results prove prior knowledge of the role of MC1R in base coat colours in cattle and suggested a different genetic mechanism for forehead stripe phenotypes in Nguni cattle.