SNP Testing vs. Microsatallite Testing
DNA is present in every living thing. It is the code that makes each of us unique albeit very similar. This code is made up of repeating units called “base pairs” and there are 4 possible “base pairs” which are known by the first letter of their name: A, T, G, and C. The sequence of A, T, G, and C gives every individual their unique genetic code, and except for identical twins, no two people have the exact same sequence of A, T, G, and C’s. This unique genetic code is passed on to offspring so that each offspring receives half its DNA from its father and the other half from its mother; creating a unique combination that is very similar to the parents. Knowing that every offspring is a combination of its parents’ DNA has allowed scientists to develop tests to determine which individuals are the parents of a given offspring.
There are several different technologies that can be used for DNA Testing. In livestock, two of the more common technologies used are Microsatellite Testing and SNP Testing (Single Nucleotide Polymorphism, pronounced “snip”). These two technologies are incredibly different. So different, in fact, that we cannot compare the results between them. Microsatellite Testing is based on counting the number of small repeating segments in an animal’s DNA. SNP Testing looks at the content of the DNA or what the actual A, T, G, or C is at a specific location in the genetic code.
Figure 1: Example of a Microsatellite. The microsatellite score is determined by counting the number of “base pairs” in each repeating section. This animal has a score of 16/20 because it received DNA from its father with 5 repeating blocks and 4 “base pairs” per block (5 x 4 = 20) and it received DNA from its mother with 4 repeating blocks and 4 “base pairs” per block (4 x 4 = 16). There is a 50% chance that this animal will pass the 20 to its offspring and a 50% chance that it will pass the 16 to its offspring. This animal cannot pass both the 16 and the 20 to its offspring.
Figure 2: Example of two SNPs. The SNP result is determined by determining which “base pair” is present at a specific location in the DNA. This animal would be reported as a G/T at the green SNP location and would be reported as a C/A at the blue SNP location. This animal received the G (green) and C (blue) from its father and received the T (green) and A (blue) from its mother. There is a 50% chance that this animal will pass the G (green) and C (blue) to its offspring and a 50% chance that it will pass the T (green) and A (blue) to its offspring. This animal cannot pass both the G and T (green) or both the C and A (blue) to its offspring.
One of the key differences between Microsatellites and SNPs is how many of them exist in an individual’s DNA. Microsatellites are relatively rare but in mammals, there is approximately 1 SNP for every 1000 “base pairs”. Just to note, mammals have approximately 3 billion “base pairs”. What this means, especially for parentage testing, is that there are many more locations in the DNA to use for comparing offspring with their potential parents. In practice, parentage testing with microsatellites utilizes between 12 and 40 locations in the genome, depending on the species. Using SNPs in parentage testing uses many more locations. For swine, Neogen starts with 96 SNPs spread across the pig’s DNA. If more than one boar or more than one sow matches to a piglet, then we will move to using 1000 SNPs. If 1000 SNPs cannot resolve ambiguous parentage matches, then we move to using 50,000 SNPs. Many other livestock species have switched to SNP parentage for the improved resolution it provides when related breeding animals are in the same mating group.
Further advantages of using SNP technology for DNA testing is that it has applications beyond parentage testing. Many other livestock species now use SNP testing for determining genetic condition status, physical trait status, and to improve the accuracy of traditional Expected Progeny Differences (EPDs) which provides more insight into how an animal’s offspring will perform for specific traits.
Looking to the future for the Kunekune breed, having a database of SNP genotypes that can laterbe paired with trait records by researchers could lead to the discovery of genetic markers for traits that are of interest to Kunekune breeders. By learning more about the genetics behind those interesting traits we can develop genetic tests to better predict how an animal will perform or what physical characteristics it will display.