Genetic diversity and performance trait analysis of the SA Boerperd
This study aimed to determine the occurrence and frequency of mutations that influence certain performance-associated traits within the indigenous SA Boerperd, to determine the level of diversity in the breed, and to investigate its relationship with other equine breeds. The occurrence of four single nucleotide polymorphisms (SNPs) were investigated within the SA Boerperd. Two of these SNPs attribute to height (BIEC2_808543 & BIEC2_1105377) and two influence alternative gaits (DMRT3_Ser301STOP & BIEC2_620109). A total of 100 horses originating from different geographical areas within South Africa were included in the study for DNA sequencing. The obtained SNP data revealed that the mutated C-allele of BIEC2_808543 was present within 5% of horses, whilst 57% of the population possessed the A-allele of BIEC2_1105377. It was not possible to assess whether either of these heightassociated SNPs cause the formation of tall individuals. The majority of the studied population were three-gaited, whilst 14% of horses were five-gaited. Both gait-associated SNPs occurred at low frequencies within the breed. The gait keeper mutation (DMRT3_Ser301STOP) had an allelic frequency of 0.105 and the SNP BIEC2_620109 a frequency of 0.091. It was established that neither height-associated SNP are informative within the SA Boerperd breed. Either one of the two gait-associated SNPs can however be screened for, but it is not guaranteed that an individual possessing these mutations will be able to showcase five gaits. Genotypic data for 363 horses, consisting of 17 microsatellite markers, were obtained from Unistel Medical Laboratories to determine the breed’s genetic diversity. The current heterozygote estimate (Ho = 0.679) of the breed was similar to that determined by a study conducted 15 years ago, and the level of inbreeding had decreased to an acceptable 3.2%. The breed’s allelic richness had however declined from 4.212 to 3.804. Analysis of the population structure revealed that two distinct subpopulations (K=2) are present within the breed (based on STRUCTURE results). One of the 12 studs had 83.6% of its horses placed in a separate cluster. It was established that a high degree of variation is still present within the SA Boerperd, despite the influence of selective breeding. Levels of inbreeding are at present still manageable. The genotypic data of the SA Boerperd was compared to that of nine other equine breeds. These consisted of the Tennessee Walker, Andalusian, Standardbred, Appaloosa, Friesian, Hackney, Thoroughbred and Icelandic. Compared to these breeds, the SA Boerperd had above average levels of heterozygosity and a high number of private alleles (17.6%). Both FST-values and structure analysis suggested that the SA Boerperd is closely related to the Andalusian and Standardbred. Other breeds, specifically of American origin, are thought to have influenced the SA Boerperd and should in future also be investigated. Results obtained within this study can be used by SA Boerperd breeders to further the development of the breed, whilst simultaneously conserving its genetic potential. Similar studies can also be conducted in other equine breeds to further their conservation and understand their relationship to the SA Boerperd.