Genetic variation among different springbok (Antidorcas marsupialis) colour variants

The linebreeding of southern African antelope species, involving selection for specific coat colour phenotypes, is a wide-spread practice in the South African game farming industry. Concerns have been voiced with regards to the genetic status of these line-bred colour variants, due to the high risk of inbreeding. The springbok (Antidorcas marsupialis) is one of the most well-known examples of such linebreeding. Numerous colour variants have been observed, with the most notable the black, copper and white colour phenotypes. To our knowledge, no research has been performed on the genetic basis of these springbok colour variants. In this study, we aimed to 1) assess the level of genetic variation within and among the common, black, copper and white colour variants of springbok, and 2) investigate the possible genetic mechanisms involved in the coat colour of these variants. Portions of the mtDNA control region (CR) and two immune-linked Toll-like receptor (TLR4 and TLR7) genes were sequenced for the genetic diversity estimates. A 50 K Bovine SNP chip was also screened to assess the level of genetic diversity of a subset of samples. The complete melanocortin 1 receptor (MC1R) gene was targeted for the second aim. Comparable levels of diversity were identified across specimens. Pairwise genetic diversity analysis of the SNP data identified the white springbok as a unique group within springbok, with Bayesian clustering analysis supporting this observation. A possible reason for this clustering pattern was linked to the historical occurrence of white springbok in nature. The level of genetic diversity observed for each colour variant was associated with 1) the large historical and extant population sizes of springbok providing a deep genetic pool and/or 2) the management practices of the managers/farmers that are aimed at preventing or minimizing inbreeding and loss of genetic diversity. The MC1R assessment identified a nonsynonymous SNP (c. G902A) unique to white springbok (homozygous AA). A 24 bp deletion was observed in black, copper and king springbok colour variants. This deletion was complete for similar to 21 % of black springbok. The heterozygous variant was observed in similar to 88 % of copper springbok and similar to 5 % of black springbok. This would suggest that additional genetic factors are involved in coat colour determination (due to the incomplete association of the 24 bp deletion). Further research is therefore needed to identify the other possible genetic factors involved. (C) 2019 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.