Sunday 15 March 2015

Some recent diversity studies in poodles and what they mean: Part 2

(see part 1)

Over the past few years, a study on a small part of the genome known as the DLA haplotype in poodles has been undertaken by Dr Kennedy at Manchester University. This portion of the genome is known to be involved with the immune system, and the equivalent area in other species has been found to be involved with autoimmune diseases. Thus far, 31 variations have been identified in poodles of all sizes. This test is of limited value to breeders as an estimate of diversity, partly since it concerns only one part of the whole genome, but also because the turnaround time is far too long, with some participants waiting more than a year for their result, and is therefore not suitable for aiding selection of pups to keep from a litter. More information is available here

A few years ago, Genoscoper of Finland made available a test called 'mydogdna' which analyses multiple points in the genome and generates a number for heterozygosity and a position on a graph showing how the dog fits into the population based on the results. This test usually has fast enough turnaround for litter assessment, and comes with a bonus of the neonatal encephalopathy genetic test plus some tests for colours (although the colour test for B is missing one of the alleles and is thus not reliable). For persons who have purchased a test, it's possible to see how the dog compares on an interactive graph to other poodles of different sizes and colours. In terms of answering the question 'how diverse is the breed?' Genoscoper's results would suggest perhaps more diverse than naysayers might like to think. The median heterozygosity for standard poodles is given as 31.4%. The average for all dogs (all breeds and some non-breed and mixed-breed dogs) given is 28.9%. In the technical details that are included with the 'mydogdna' test, the studies the researchers did to evaluate its effectiveness are shown. One of these studies is of a breed called the Kromfohrländer (a google image search shows it is a terrier-like dog with a rough or smooth coat). The average heterozygosity of the Kromfohrländer was 21% in the study, and to see if the test could distinguish the populations, they tested a litter of Kromfohrländer x standard poodle puppies. One can only assume the litter was an accident, or carried out for the purposes of scientific enquiry, as it is not at all apparent that the poodle would be a sensible choice to increase the genetic diversity of the terrier-like breed! The mix-breed puppies came out on the graph as having a heterozygosity of 32% -- that is, purebred standard poodles are on average only 0.6% less heterozygous in this study than a mutt of a poodle and a terrier-like dog!
More information here

The third study is being carried out as an extension of an earlier study into sebaceous adenitis by Dr Pedersen at the University of California/VGL coordinated by Natalie Green Tessier, and again involves the analysis of a number of different points across the genome. These include the DLA haplotype in the earlier study by Kennedy. Initially this study was open just to poodles suspected by pedigree analysis to have unusual genetics as it was not known how much interest it would generate or whether it would be viable as a paid test. Uptake has been very good, and it has now been developed into a usable test. Although the test is still in development, early indications are that it will be more detailed than the 'mydogdna' test and should be a more functional tool for selecting puppies and evaluating relatedness of potential breeding pairs, and promises to have a decent turnaround. Link to VGL

One of the most interesting things about the 'mydogdna' study is that it uses the genetic data to put points on a graph that shows how genetically related different dogs are to each other. Looking at the scatter plot for standard poodles and using the data from my own dogs and other dogs shared with me and made public, it's possible to see different bloodlines clustering together. The largest cluster in the diagram above made of magenta data points seems to correspond to the highly Wycliffe-influenced bloodlines. The teal outliers and cluster seem to be mostly apricot poodles, and may relate to OEA. The three unfilled data points at the bottom labelled Canen are two siblings and a cousin derived from a bloodline with relatively low influence from both OEA and Wycliffe, and the two unfilled circles above them are my dog from mixed lines including OEA, Wycliffe, and some obscure stuff, and his son.

In terms of making breeding decisions, however, the 'mydogdna' doesn't provide a great deal of detailed information. You can compare dogs to each other for potential matings and it gives you an estimate of the average heterozygosity of puppies, and this and the scatter graph are all you get, really.

The VGL test on the other hand provides a lot of hard data in the form of a PDF that provides a measure of heterozygosity (internal relatedness) compared to other dogs of the same breed plus numbered alleles for each of the 33 genetic markers sampled, and the two DLA haplotypes. To return to the card analogy, this would be each poodle having two of each card drawn from suites containing ace-33 plus a king and queen, although it's important to remember that they are markers throughout the DNA and not the entire genome. The example below is the dam/aunt of the two siblings and cousin shown in the above 'mydogdna' plot. Her COI over 15 generations is 15%, so her higher than average IR is not unexpected, although it does not always work this way, since as explained in the previous post, COI is a probability and these tests are actual DNA markers that provide some genetic information.

And just to demonstrate that COI isn't always an accurate predictor of heterozygosity, the dog below may well have the lowest IR in the study. His 15-generation COI is 12%.

The raw data from these certificates can then be used by third-party programs to generate analyses and run mating calculations. An extremely powerful one has already been developed as an extension to the existing Standard Poodle Database, which compares dogs' results and gives an average value for potential progeny, and in addition to this it can show you how common each of the (potentially up to) 66 markers and the four DLA haplotypes your dog has are in the breed overall. VGL provides information on the numbers of different alleles (suites) for each of the markers on its website. The early results seem to suggest there is quite a lot of diversity in poodles, but that the diversity is not very evenly distributed. Most of the markers have 10+ alleles, but some have fewer, such as 16 with currently only four identified (comparable to a choice of sixteen of hearts, diamonds, clubs, or spades for each dog).

So, how can these tests be used? First of all, I should like to say, there is no one breeding plan that every breeder must use. For the breed to survive, it must be diverse as a whole, and that means it has to be bred by many diverse people who have different ideas about how to do things. That said, these tests can actually be used to support many different approaches to breeding.

Anyone can test their poodles or ask for dogs they are considering using to be tested. The VGL test is the most useful, but if you want a colour test and the NE genetic test, the Genoscoper test is probably worth doing as well. You can then compare a bitch to potential mates and use the results as part of your decision. This does not just have to be on the IR value range they are likely to produce, but can be based on rare markers, or DLA haplotypes. If your poodle has anything other than 2001 in Class II, this is unusual and worth hanging on to if possible.

After you have chosen your mating and the puppies have arrived, you can then narrow down your choice to the pups in the litter whom you think are best suited for the purposes you are breeding for, and test them and use the test results as part of your decision process on which pups to keep or to sell to particular owners. You do not have to keep the pup that is tested as having the lowest IR, or the most unusual haplotypes/markers, or use the first dog SPD recommends in terms of compatibility, if you don't like this pup or this dog, but if more people use the test and make it part of their decision, gradually this will benefit the population as a whole. Individual dogs do benefit from a low IR, but the breed as a whole and the future of individuals benefits most when much diversity is evenly distributed. It does not help the breed a lot if it is swamped by heterozygous dogs who mostly have the same two suites at each locus, and this will make heterozygosity difficult to achieve in future generations. If you have something that is unusual, IR might be less of a priority than holding on to what makes it unusual, but if you have something that genetic analysis shows to be quite typical, low IR or adding something unusual might be more relevant.

Strategies like linebreeding may not appeal to everyone and may be currently out of political favour, but historically linebreeding kept many bloodlines genetically distinct from each other and benefited the diversity of the breed taken as a whole, and this is the case with many rare breed animals today. These tests can be used to support a programme that involves linebreeding, by selecting a pup whise IR indicates it may be more heterozygous than its COI might suggest, or choosing pups most genetically different from the mainstream where the objective is to preserve a 'different' line.

Remember that when you breed two dogs, they split their hands randomly to give new hands to the puppies. Each puppy can only have one of each card from each parent. This means that if you have a bitch and you only ever keep one puppy from her and sell the rest as pets, you, and the breed, will automatically lose half of her hand. In practice due to no dog being completely heterozygous, you will lose less than this because some of her cards will be the same, but it is still important to recognise that this happens and it is a significant loss when working with bloodlines off the beaten track where there are unlikely to be more distant relatives being bred and keeping the genetics going. It is a very good idea to aim to sell some male puppies to trustworthy people who will allow them to be used responsibly at stud, as in this case there is not the worry of selling a breeding prospect bitch to someone not in a good position to be responsible for having a litter, and it will help to combat the problem of popular sires and the increasing lack of choice for those looking for someone to breed their bitch to. It is also not useful to mate a bitch again to a dog she has already had a litter to (unless the litter died, was abnormally small, or there was no suitable puppy to be kept for breeding for whatever reason). Bitches in particular who are genetically unusual should be mated to different dogs and puppies from each mating retained as potential breeding dogs.

Popular sires (dogs who are used widely for whatever reason, and are influential on the breed in subsequent generations) are usually to be avoided, and it generally makes sense to try not to use over-popular dogs or allow one's own stud dog to be overused, but where a dog is shown by these tests to be unusual, allowing a dog to be used a bit more than you might otherwise might not be such a bad thing, as it helps to rebalance diversity in the breed.

A mating that produces a low COI is usually promoted as a good thing these days, with COI being pursued by some as a breeding objective in itself, but as discussed previously, COI is just a probability. These tests help to reveal if there is genetic evidence of heterosis to support a particular low-COI mating. If there is not, there might be little to recommend a mating that was chosen primarily for its COI.

Someone wishing to import a dog where pedigree information is lacking can also use this test to find out if the dog is similar or different. Without doing the test, we don't know if the dog carries cards from the familiar suites of clubs and spades, or perhaps has a more exotic hand containing elephants and snakes.

With thanks to Natalie Green Tessier and Jane Rowden
The new SPD is available from PHR

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