The chicken and the ink

[MichelleL11]

I was wondering what exactly of the egg is actually used to make glair. It is not the beaten egg white but the liquid egg white that forms on the bottom of the container after a few hours. As I understand it, beating the egg white breaks down the proteins ( denaturation ). That probably has a negative impact on any analysis although the primary biochemical structure remains unchanged.

Focusing on egg white proteins, here are some possibilities:

You are not allowed to view links. Register or Login to view., Mann and Mann

You are not allowed to view links. Register or Login to view., Arena et al.

and -- a possible candidate gene:

You are not allowed to view links. Register or Login to view., Kinoshita et al.

So -- what you want is a gene with high genetic variability but can also be distinguished from other similar gene sequences.  Please note that "high genetic variability" will very likely result in high protein sequence variability -- but not necessarily.  Thank you for understanding that I'm not trying to be discouraging, just want to bring a realistic approach:

The reason why high genetic variability doesn't necessarily translate to high protein variability is because the way that DNA (or RNA) is translated into amino acids is through nucleotide triplets.  The third position of the triplet is particularly "flexible" (often termed "wobble" or degenerate codons) -- thus, triplets of different nucleotide sequence results in the same amino acid being added to the protein.  Note there are 64 different triplet codons, but only 20 amino acids -- so you can change the triplet codon and end up with the same amino acid.  Also, some of the codons are "metadata" -- like the "stop" codons.

Here is a chart that illustrates this principle.  In this chart, U, C, A, and G are the four nucleotides found in the mRNA (uracil, cytosine, adenine, and guanine -- (uracil takes the place of the thymine (T) in DNA structures).

   

But, that being said, the authors do identify 11 "nonsynonymous" variations (a substitution that doesn't change the amino acid would be synonymous) in the 29 chicken breeds that they tested.  So I do think that the TENP gene (ovoglobulin G2 protein) could be a good candidate for differentiation.  I'll take a closer look at this paper sometime this weekend and will come back with further thoughts -- but for now, you do have a candidate that could be used focusing only on an egg white product.

Finally, please note that the variations in proteins aren't necessarily all due to changes in the primary sequence.  Proteins undergo a high amount of post-translational (mRNA --> amino acid step) modification.  Thus, you can see proteins that are distinguished from each other when isolated and run on a gel (movement through the gel is dependent on a combination of size and total charge) -- but the differences aren't at the amino acid levels but instead are differences in sugar molecules that "decorate" a finished protein sequence.  Different sugar molecules means changes in both size and charge -- so you see the difference on the gel migration.  But, a quick look shows they did find primary sequence differences (it's not just post-translational modifications) so that is positive for your purposes.  Again, I'll look more closely when I have more time.  But, in my opinion, this is a good development for your proposed approach.