We have begun the project!!  Two types of data are being collected.   Data for genotyping and data for phenotyping.
 

Genotyping

Genes are arranged on DNA like beads on a string.

Markers are qualitative differences like the one shown here.  Because there are not enough of these visual phenotypes we use molecular phenotypes, changes in the DNA itself,  for qualitative markers.

For genotyping we use DNA from each dog.  From each owner we receive a sample of blood from which we extract DNA.
 

Each molecular phenotype is a region of the DNA which we can copy and examine.  To copy the region of the DNA we use a special enzyme shown here by the blob with the arrow, which is busy putting T's opposite A's and G's opposite C's following the rule for building a DNA molecule from the A, G, T and C building blocks.

Each region has a characteristic length, which can vary from one dog to another depending on its ancestors.  To measure the length of the region which we have copied, we put it in an electric field and measure how rapidly it moves through a gel like substance.  Big molecules move slowly, small ones move fast.

In this illustration taken from two different parents and their heterozygote offspring you can see where different length pieces are found on the gel.  Each animal has two copies of every gene.  In this example the two copies are the same in each parent (they are homozygous for this gene), but because the parents differ, their DNA moves differently in the electric field.  The puppy has inherited one copy from each parent and is heterozygous. You can see how readily this can be detected.

Actual data from a group of dogs is shown below.

Because there are so many dogs to be analyzed for each of at least 400 DNA markers, genotyping will take a long time to complete.  The time required can be estimated from the number of dogs and markers i.e. 400 x 400 = 160,000 analyses.  Currently we are analyzing 300 of these each day or around 1500/week.  At that rate the genotyping will require about 100 weeks.  It seems likely that we will need to double our rate of analysis.

We have already been able to use the genotyping to determine that our pedigrees are accurate.  Because there are so many samples there is always the possibility that mistakes can occur in which blood samples become confused.  We have used the pedigrees and the genotyping to check on this and have been pleased to find that there are very few errors.