Actually PCR will work on DNA from any ploidy as it amplifies specific DNA or RNA sequences regardless of how many copies of chromosomes/DNA there are per cell. How accurate PCR is can be highly variable depending on many factors, but ploidy or the source of DNA (e.g. any kind of apple, orange, bacteria, human, etc.) are not among those factors introducing variability. If done correctly PCR can be highly effective and distinguish between two very closely related individuals, like siblings or parent vs. offspring. Results from a reputable lab should be trustworthy.
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This is false.
Horticultural PCR is far from being correct. For example, they never examine the contents of the amplified sequences.
What horticulturalists consider trustworthy is considered wishful thinking by genetic experts.
As I think back to that day of grafting in 2019, I recall dropping some scions & not sure I retrieved all that had been dropped. So…
Now I am pretty sure someone brought a mislabeled scion & I, in the heat of the moment, grafting and fumbling pieces, switched the Twenty Ounce scion for the mislabeled one. Thus, Something Else, which turns out to be likely a Fameuse/Snow offspring I had labeled wrong, adding to the confusion.
My first time (with documentary evidence!) wrongly applying names. Since the WSU results (by whatever method You wish to call it, Richard; you be the expert) tell me Twenty Ounce grows in my yard, I will do my level best to care for it & see how it can do. It was the one I most wanted that year.
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I’ll jump in here, albeit a bit late, to share my experience with DNA testing through Washington State. Over the last two years, we’ve submitted 330 tests to WSU, and I’m also part of the Historic Fruit Tree Working Group with Cameron.
The way the DNA dataset works is based on consensus. A cultivar (like HoneyCrisp, Baldwin, etc.) has to accumulate 10 points to be added to the dataset, which future tests are then compared against. I don’t remember all the details, but Cameron gave a presentation about it at the 2024 Maine Apple Camp. Basically, a cultivar can get 1 or 2 points for a test from an individual, something like 5 points for a test from a collection (USDA, MEHO, MORP, etc.), a number of points for phenotypic accuracy, historically accurate based on parentage, etc, etc.
There are a few caveats. For example, if SSE (where I work) submits a test, but we don’t have source info on the tree (where we got it from), it won’t necessarily get 5 points. The point system can also be challenged, and points can be revoked. For example, if an old tree from Maine comes back as Zusoff, but we know that Zusoff wasn’t historically grown in that area, it opens up a discussion, either among the involved parties or at a Historic Fruit Tree Working Group meeting about the accuracy of what’s labeled as Zusoff in the dataset. So in that example, the “Zusoff” results would be in a holding pen of sorts until a resolution is reached. It’s my understanding that there’s also some level of cooperation between different labs, and they share data to some extent (look up MUNQ codes).
Essentially there are layers of checks to make sure the results are as accurate as possible. WSU doesn’t just do DNA testing; they also gather information and confirm results with historians and growers, to the best of their ability. That’s not to say there couldn’t be inaccuracies here and there; I don’t have the technical knowledge to comment on that. In terms of their process, what I do know is that the current method is using SNP testing, and a few years ago, they were using SSR before switching to SNP.
One important note: The current DNA tests can’t distinguish between bud mutations, so keep that in mind. Also, I believe the current wait time for receiving results after submitting a sample is between 8 and 12 months.
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@jhanson
There are three problems with “fingerprints” they’ve assembled. The first is the 35 year-old laboratory method used in horticulture. They do not examine the contents of the chemically extracted short DNA sequences. Instead they obtain a coarse estimate of the length. Several length estimates are obtained for each specimen. If all the length estimates between two specimens match, the investigators believe the two specimens are the same. However, highly accurate full DNA sequences of apples in the WSU database have been obtained in the past five years. They demonstrate that chemically extracted segments from the same locations with the same estimated lengths can have different contents. Further, there are chemically extracted segments from the same locations with different estimated lengths having the same contents.
Second, there is a statistical problem with the these types of “markers”. Basically, they don’t have enough resolution to distinguish between all specimens – even if they were to examine the contents. Worse, it is intractable to use enough markers per specimen to obtain sufficient resolution.
Third, DNA markers of celled life forms were designed to determine dissimilarities – not similarities. Using them for the latter purpose is nothing more than extrapolation.
I can concur with your last paragraph. Sometime in the past decade I saw a DNA list for the Royal Horticultural Society (pretty sure that was the list) collection in Great Britain. Queen Cox, which is a bud sport of Cox Orange Pippin, came out as COP from their tests.
That caught my eye since that is how Queen Cox was described elsewhere, and I had bought that tree and planted it. (It couldn’t hack near-desert conditions here & produce edible fruit.)
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My demand as a casual grower is not absolute accuracy.
The inability to detect bud mutations with the currant affordable ID systems is an issue. I suspect bud mutations are far more frequent than we think.
Knowing whether a tree is diploid or triploid is obviously a huge issue for a small backyard grower. The Mammoth Black Twig/Paragon/Arkansas all being thrown together as the same apple is frustrating since it is not known if the Paragon or Arkansas are different or if they’re diploid. If the Paragon is a different apple, has the same qualities, and is diploid, then this apple should be the preferred apple, not the Mammoth Black Twig.
I’m seeing pics of MBTs on this forum that don’t look like any MBT I’ve ever seen. The MBT has a Red Limbertwig parent. It’s conical/oblate. MBTs tend to look like Winesaps with about 50% of apples having the RLT silhouette, but much larger. MBTs also have a fair amount of green with a red wash. They’re not dark or near solid red.
Back to square one. Are there any experts on the Paragon/Black Twig issue? I desire to learn more as well.
This is a very easy and cheap test that you can have done
Detecting bud sports is essentially asking for absolute accuracy. Sports differ by literally a couple genes from the parent, those couple genes may make a big difference in fruit quality, but it’s extremely hard to detect and would require very expensive equipment and long test times
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If you can accept gross inaccuracy then horticultural PCR marker tests are for you.
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