Genetic diversity and performance trait analysis of the SA Boerperd
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Date
2018
Authors
Breytenbach, N.
Journal Title
Journal ISSN
Volume Title
Publisher
University of the Free State
Abstract
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.
Description
Keywords
SA Boerperd, Performance-associated traits, Genetic diversity, Microsatellite markers, Selective breeding, Single nucleotide polymorphisms, Subpopulations, Inbreeding, Height, Alternative gaits, Dissertation (M.Sc. (Genetics))--University of the Free State, 2018