How can genomic technology strengthen the future of South African horse breeding? Johan Griesel explains the transition from traditional microsatellite DNA testing to SNP-based genomic testing, which offers more reliable parentage verification, including cases involving closely related potential sires. Genomic information can also support the screening of beneficial and disease-causing genetic variants and provide a foundation for scientifically informed breeding programmes. The article highlights the need to build a better understanding of South Africa?s equine genetic resources, protect pedigree integrity and use genetic information to reduce harmful conditions while promoting superior breeding stock.
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The future of South African horse breeding By Johan Griesel, geneticist, SA Stud Book
A Stud Book is joining hands with local horse breeders to unlock an exciting opportunity to deepen the genetic understanding of South Africa’s equine population and to build scientifically sound breeding regimens. Such an approach can help breeders combat genetic diseases and rear animals of superior genetic merit, supported by a clearer understanding of the underlying genetics. At present, genomic technology and genetically informed breeding programmes remain underutilised in South African horse breeding. Those who adopt these strategies are likely to gain a competitive advantage.
From microsatellites to genomics Microsatellite technology gained global traction in the early 1990s and was marketed as ‘DNA testing’, even though it does not examine the DNA sequence itself. Instead, it measures the length of specific DNA regions, known as microsatellite regions. By comparing the lengths of these regions, geneticists can deduce parentage (and identity) through deductive reasoning. While this approach has served the industry well, it has become outdated worldwide. Manufacturers are phasing out the hardware and software required for testing. Over the past two decades, SNP-based genomic methods have become the global standard. SNPs (single nucleotide polymorphisms) are markers that occur at specific positions in the DNA sequence and differ frequently enough among individuals to be reliably used to track DNA regions, genes, and ultimately heritage (and parentage). Unlike microsatellite markers, which measure DNA length, SNP data reflects the actual genetic code at a specific location. Knowing the genetic code at a specific point on an
animal’s DNA can reveal much about the surrounding DNA.
Enter equine testing SA Stud Book introduced genomic testing in 2013. In equine testing, the Illumina Equine 80K Select BeadChip is used, reading approximately 80 000 SNP markers – far more than the 42 microsatellite markers traditionally used in equine testing. This substantial increase makes the test significantly more reliable and far less likely to fail. Because SNPs represent direct sequence data, it is also more useful and concrete than length-based data derived from microsatellite testing. Traditional DNA testing can struggle to resolve parentage among closely related animals, such as when potential sires are father and son, or full- and halfbrothers. It also requires samples from both parents and the progeny and can only exclude parentage with certainty. Furthermore, it provides limited insight into the gene content of an animal and has little use …
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