Genetic diversity and performance trait analysis of the SA Boerperd

[摘要] This study aimed to determine the occurrence and frequency of mutations that influencecertain performance-associated traits within the indigenous SA Boerperd, to determine thelevel 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 theSA Boerperd. Two of these SNPs attribute to height (BIEC2_808543 & BIEC2_1105377) andtwo influence alternative gaits (DMRT3_Ser301STOP & BIEC2_620109). A total of 100 horsesoriginating from different geographical areas within South Africa were included in the studyfor DNA sequencing. The obtained SNP data revealed that the mutated C-allele ofBIEC2_808543 was present within 5% of horses, whilst 57% of the population possessed theA-allele of BIEC2_1105377. It was not possible to assess whether either of these heightassociatedSNPs cause the formation of tall individuals. The majority of the studied populationwere three-gaited, whilst 14% of horses were five-gaited. Both gait-associated SNPs occurredat low frequencies within the breed. The gait keeper mutation (DMRT3_Ser301STOP) had anallelic frequency of 0.105 and the SNP BIEC2_620109 a frequency of 0.091. It was establishedthat neither height-associated SNP are informative within the SA Boerperd breed. Either oneof the two gait-associated SNPs can however be screened for, but it is not guaranteed that anindividual possessing these mutations will be able to showcase five gaits.Genotypic data for 363 horses, consisting of 17 microsatellite markers, were obtained fromUnistel Medical Laboratories to determine the breed's genetic diversity. The currentheterozygote estimate (Ho = 0.679) of the breed was similar to that determined by a studyconducted 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 thepopulation structure revealed that two distinct subpopulations (K=2) are present within thebreed (based on STRUCTURE results). One of the 12 studs had 83.6% of its horses placed in aseparate cluster. It was established that a high degree of variation is still present within theSA Boerperd, despite the influence of selective breeding. Levels of inbreeding are at presentstill 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 aboveaverage levels of heterozygosity and a high number of private alleles (17.6%). Both FST-valuesand structure analysis suggested that the SA Boerperd is closely related to the Andalusian andStandardbred. Other breeds, specifically of American origin, are thought to have influencedthe SA Boerperd and should in future also be investigated.Results obtained within this study can be used by SA Boerperd breeders to further thedevelopment of the breed, whilst simultaneously conserving its genetic potential. Similarstudies can also be conducted in other equine breeds to further their conservation andunderstand their relationship to the SA Boerperd.

[发布机构] University of the Free State