Parentage verification or paternity testing is the process by which scientists use DNA to establish which individual is the parent (mother or father) of another individual. This can be done because DNA markers are passed on from parent to offspring.
There are different types of DNA markers that can be used to verify parentage. In the last two decades the marker of choice was microsatellite markers, but recently SNP markers had gained a lot of popularity.
During this study we will identify SNP marker that are useful in parentage analysis. There isn't a set number of SNPs to be used in parentage studies but between 120 and 200 markers should be sufficient. SNP markers are single bases or nucleotides that differ between individuals. For example, one bird might have an A at a specific position and another bird might have a G at that position. SNPs are passed on from parent to offspring. So if the offspring has an A at that position it is more likely to be the first bird's offspring that to be an offspring of the second bird.
Parentage is verified based on the statistical probability that one bird is more likely to be the parent than another bird. If the young has mismatched bases at many of the tested SNPs with a male that might be its father, it is impossible that this male can be the biological father. It is important to note that one or two mismatches alone cannot be used to conclude if the bird is the father or not. A panel consisting out of around 150 SNPs are needed before a final decision is made.
The mother doesn't have to be tested but in cases where the birds are inbred or where two brothers are possible fathers, testing the mother increases the statistical power of the test. This is because each allele (thus one copy of the SNP on each of the chromosomes) are inherited from each parent. Therefore if the offspring is for example AG at a specific position (meaning there is an A on one of its chromosomes and a G on the other) and the mother is AA at that specific position, we know that the father had to pass a G to the offspring. Therefore all the males that don't have a G at that position cannot be the father of the young.