Is a non-astringent American-Asian hybrid persimmon within reach?

Fusion_power · January 16, 2023, 8:45pm

Here is another thought that needs to be considered. With a hexaploid genome and not knowing for sure how the chromosomes will pair up during meiosis, there is a possibility the genome would tend to prevent the desired combination. Here is an example.

In JT-02, we believe the genetics are hexaploid(nA, nA, nA). In wheat, there is a very specific genetic construct that stages the hexaploid genome so that it reproduces correctly. I don’t know if there is such a construct in persimmon. If not, it is possible the pairs could be hexaploid(AA, nA, nn). In this case, it would never be possible to get an nnn zygote. It would always be A(A or n)n. I’m not saying this is correct. I am just pointing out that there are a ton of things we don’t know about the persimmon genome.

jrd51 · January 16, 2023, 10:42pm

Two questions:

Where in “the literature” do you read this? Can you give me a reference?
How do you reconcile your specific statements about the persimmon genome (and how those genes are expressed) with @Richard 's assertions that we basically know nothing about it?

jcguarneri · January 16, 2023, 11:32pm

I think @Fusion_power is enumerating all the things we don’t know about persimmon genetics that could throw a big ol’ monkey wrench in breeding efforts. What he’s saying is very consistent with @Richard 's assessment.

jrd51 · January 17, 2023, 12:05am

Right. So I freely admit that I know nothing about how the 3 N and 3 A alleles in the JT-02 genome would get sorted into oocytes. Maybe you can give me a clue. . . .

In my prior thinking, I assumed that the pairings would be random. And I think my arithmetic (3/6 x 2/5 x 1/4) is correct given this assumption because the selection of one allele would not affect the probabilities for the other alleles. For example, the selection of an A allele does not disqualify an N allele. In this model, metaphorically speaking, three alleles are “selected” in succession at random from one big “bin” initially containing all six alleles.

You assumed above that the pairings would be very orderly (i.e., nA, nA, nA). So I think (if I’m understanding you right) that in your model, the selection of one allele disqualifies its paired allele. For example, the selection of an A allele disqualifies the paired N allele. So you get 1/2 x 1/2 x 1/2 (which still works out to 12.5% not 25%). In this model, three alleles are “selected” in succession at random, one from each of three separate “bins” each containing 2 alleles.

I agree with you that there are hypothetical orderings of the 6 alleles that would make a NA hybrid impossible. I just don’t see any reason why the arrangement of chromosomes in persimmon should be constrained.

I appreciate your observation that wheat has “a very specific construct that stages the hexaploid genome.” But wheat is allopolyploid – it is constructed from genes from different species, and I can readily imagine that the contributions of the different species must remain somewhat stable. Persimmon is, I believe, an autopolyploid – it is constructed from genes from the same species. So I can imagine that the arrangement of the chromosomes can be more flexible.

What reason do we have to believe that the assortment of the alleles follows any specific pattern?

p.s. This paper argues (as I suggested above) that the “very specific constraint that stages there hexaploid genome” in WHEAT does have the specific purpose of not creating disorder among the genes from different species that are combined in the allopolyploid. This constraint would have no purpose that I can see in a autopolyploid such as persimmon.

jrd51 · January 17, 2023, 12:22am

@jcguarneri – Maybe. I’m willing to acknowledge difficulties, not least the large number of crosses that must be evaluated before we have a hybrid that is not only non-astringent but also cold hardy, tasty, early ripening, whatever.

But I don’t want to be inappropriately pessimistic. I want to include only the obstacles that truly apply. It seems that he may be extrapolating from what he knows about the allopolyploid species wheat to the autopolyploid species (plural) persimmon.

Perhaps Richard can weigh in as to whether he agrees with Fusion_power’s logic. From what I’ve seem. Richard doesn’t agree that there is a single gene that causes NA in Japanese kakis. Fusion_power not only says that there is a single gene but also asserts that the NA trait is expressed if either 5 or 6 such genes are present. He’s being way more specific and definitive that Richard ever has.

tonyOmahaz5 · January 17, 2023, 12:59am

Here is a breaking news from Cliff England. He has 2 PVNA hybrid persimmon trees and both are siblings that fruited . He is selling the scions. Exciting news.

Tony

Fusion_power · January 17, 2023, 1:16am

No, I’m not confusing wheat with persimmon. I specifically stated that wheat has a genetic construct that maintains the hexaploid genome in balance. I don’t know that the same is either true or untrue for hexaploid persimmon. Your numbers are wrong. Look at it closely and figure out why. I showed the number of possible gene combinations are 8. Also, I do NOT subscribe to the theory that only one gene results in PCNA. This IMO is unproven though there is some literature that suggests a single gene is in play. We need a good persimmon genome to determine yea or nay and we need some serious test crosses to find the mechanisms. As an example, I could see this as 2 genes interacting where one is recessive and the other dominant. A single copy of the dominant gene with 6 copies of the recessive would result in PCNA fruit. This must be proven. It is not something that can be done by you or I from current literature.

Where does 25% come into play? because that is exactly two times the 12.5% probability based on raw numbers. Under the very best conditons, 1/4 of the seedlings could be PCNA. Under worst conditions, 6.25 out of 100 would be PCNA. This allows for the inexact conditions under consideration. Until we know more about the genome, any other statement would be premature. Quit asking people to do due diligence for you. You are perfectly capable of digging out the existing documents and of figuring out the genetic odds presuming a single gene causes PCNA. If you had read the literature that has been posted on GF over the last year, you would have read about the 5 genes PCNA phenotype.

What throws a monkey wrench into this? We don’t know enough about the differences between D. kaki and D. virginiana. There is an excellent chance that the two genomes have differences that could significantly affect outcome in any crosses.

Richard · January 17, 2023, 2:32am

I agree with this:

I will also add that you appear to only skim the explanations that Darrell and I have provided and your replies are solely defensive in nature – doing nothing to further the conversation.

jrd51 · January 17, 2023, 3:33am

Sorry, I was trained as an academic. The modus operandi is that the author (1) makes a statement, then (2) supplies evidence, including references. I’ve tried to follow that pattern here.

So I find it unacceptable for someone to say “the literature says X” then refuse to supply proof. Even worse to tell the reader to go look it up. The burden should not be on the rest of us to verify an author’s assertions.

It’s too easy for someone to misunderstand or misremember what he read. If that’s what happened, none of us will EVER find the promised support. So it should be up to the author to point out the specific evidence that supports a claim. Then we can all assess whether the evidence cited says what is claimed.

So point me to the 5 genes PCNA phenotype.

Fusion_power · January 17, 2023, 4:44am

I am an engineer, not an academic. I read and study and develop my own knowledge without relying on people who don’t do due diligence to prepare it for me. I pointed you toward the simple math error you made and so far have not seen any acknowledgement that there is a problem. You haven’t even studied it to see if there is a problem. More important, you haven’t studied the underlying genetic issue.

This is just arguing, not in any way advancing anyone’s knowledge or understanding. By your own admission, you are good at coming up with projects for other people to tackle. Instead of talking, grow some persimmon trees!

There is an issue that needs to be understood. Does persimmon have a way to manage the chromosomes such they they always pair up as (nA,nA,nA) in a DK X DV cross? If they don’t, the odds are dramatically worse for developing a PCNA in the F2. Wheat has it with a structure that looks like a 6 arm octopus to manage the chromosomes. Without such, persimmon breeding for a PCNA cross goes down to 3.125% chance in a backcross to PCNA. A friend from beekeeping circles is a wheat breeder for one of the big AG companies. I might send him an email to see if he has any information about the way it works.

jrd51 · January 17, 2023, 3:49pm

Whatever your background, there is no excuse for refusing to supply references that you know exist and that you rely on in your argument. Do all of us a favor – substantiate what you think you know.

Meanwhile, I am very willing to read and I did not treat your comments casually. See how I responded to your comments based on the genetics of wheat. See how I confirmed my suspicion that wheat (allopolyploid) is different from persimmon (autopolyploid). I investigated, trying to learn more. That was the point of asking you for references.

And FWIW, I am not merely sitting in my armchair. I am growing persimmon trees. I’ve got at least a dozen at various stages. Just two days ago, I ordered scions for Morris Burton so I can see for myself whether it loses astringency early, as claimed.

What I’m not doing is breeding. That’s partly because I’m well aware of the work involved and the land required. I have neither the time nor the land nor the climate.

I agree 100% that the challenge of developing a PCNA hybrid is huge. My assumption is that persimmons do not have a mechanism to order the chromosomes. So as you know, I estimated the chance that a backcross of JT-02 x Taishu produces a NA offspring at 5% (see the OP).

That’s the main reason I started (and continued) this thread. Like many of us, I believe that a non-astringent Asian-American hybrid could be very special – not only NA but also cold-hardy, early-ripening, and great tasting. HOWEVER, I see many growers here attempting crosses that have zero chance of producing that result. They will probably produce hybrids that are cold hardy. But they will not produce hybrids that are non-astringent because they are fighting the genetics.

So my contribution, such as it is, would be to help point amateur breeders who hope to produce a non-astringent hybrid in the right direction, which appears to be a back-cross of JT-02 x Taishu. I’m not suggesting that it will be easy. It just seems the best choice. My rationale is simple:

1, Most likely, the J-PCNA trait is is controlled by a single gene that is recessive. This means that all 6 chromosomes must have the gene. [You say 5 are sufficient but I’m still waiting for the evidence. Richard says that we don’t know anything for sure, but that’s not gonna help us decide what to do.]

So any breeder who wants to produce a non-astringent hybrid IN THE NEXT GENERATION must figure out a way to ensure that the hybrid has 6 NA genes.

I made a constructive suggestion – back-cross JT-02 x Taishu. I’m not saying that success is assured. As JT-02 is 50% D. Virginiana, we can’t be sure how it’s genome will interact with NA genes from D. Kaki. But this uncertainty is inherent in any effort to breed a NA American-Asian hybrid.

I’m certainly open to other ideas. Maybe you and Richard could set aside your quibbles and doubts and offer your own suggestions. If an amateur grower wants to make a serious attempt at breeding a non-astringent American-Asian hybrid persimmon, what should we do?

Fusion_power · January 17, 2023, 9:10pm

The only “excuse” that I need is that I don’t put up with people who refuse to study a topic to understand as much as possible how it works. Do due diligence to learn more about genetics. As for what “you” should do, the first and foremost is grow some trees. By now, you could have had Taishu and JT-02 growing in your yard. I have plans to get Dar Sofiyivki growing later this year. Maybe I’ll get Taishu and JT02 as well.

jrd51 · January 17, 2023, 9:55pm

I’m not refusing to study. I’m asking you to tell me what to read, which is what you refuse to do. Make just a small start – tell me, finally, where you read that 5 NA genes are sufficient. Otherwise I have to conclude that you made it up.

Where do you get off assuming that I’m not already growing trees? What do you really know about me? FWIW, I’ve already got JT-02 growing in my yard. I even published a picture of the fruit. If you can tell me where to get Taishu, please do. But Taishu seems very unlikely either to survive the winter or to ripen fruit here. So I don’t get why you would suggest it.

You wrote, << This is just arguing, not in any way advancing anyone’s knowledge or understanding. >> I couldn’t have said it better.

Fusion_power · January 17, 2023, 11:26pm

The easiest way to get an answer on the internet is to post the wrong answer and then watch as 400 people gather around to tell you you are wrong, why you are wrong, how you are wrong, what part of wrong you don’t understand, experts are called in to harrumph and give their opinion and in the end a thorough answer is provided.

jrd51 · January 17, 2023, 11:40pm

<< The easiest way to get an answer on the internet is to post the wrong answer and then watch. . . . >>

Are you suggesting that I should learn by trolling?

Meanwhile you side-stepped my query. You are “not in any way advancing anyone’s knowledge or understanding.”

Sprout_It · January 18, 2023, 12:48am

Do you have any other information about these two siblings?
Cold hardiness, fruit size, flavor, and when does it ripen compared to jt-02?

tonyOmahaz5 · January 18, 2023, 2:01am

I spoke with Cliff England at nuttrees.net. He stated the siblings were the offsprings of Costata X Rossyanka. One is Astringent and one is a PVNA. He labeled them separately. The male parent was Rossyanka then it is pretty hardy because he had these tree since 2013. You can email him from the website or call his number. Here is the photos again.

Tony

jrd51 · January 19, 2023, 1:59am

@Fusion_power – Throughout this thread, you belittled my 5% calculation as a math error (though I think you went back and edited out the most critical statement). You came up with a variety of other estimates.

Please see Table 1 in the attached article. The table give the “Ratio of the PCNA phenotype in F1 (%).” Looks in the column Hybridization (non-PCNA genotype x PCNA genotype) for the row AAAaaa x aaaaaa, which would represent JT-02 x Taishu. Now look at the column for an Autohexaploid species. The calculated % of PCNA is given as 5%.

2327-9788-article-p59.pdf (615.1 KB)

Furthermore, you insisted that persimmons with 5 NA alleles would display the NA trait. See Table 2. It lists dozens of non-PCNA varieties, each with between 1 and 5 NA alleles. None of these persimmons is non-astringent. Only persimmons with 6 NA alleles are non-astringent. This is why scientists in this field label the J-NA trait “recessive” and the A trait “dominant.”

Fusion_power · January 19, 2023, 4:08am

You finally did some reading and some digging in the details. Unfortunately, you missed the really important parts. Did you learn anything about Cunningham’s Law?

“These results indicate that only Mast is linked to the ast gene among the four alleles in the cultivars, and that non-PCNA cultivars possibly have many ast genes. The sequence analysis for Mast showed single nucleotide polymorphisms among the cultivars. We designed the primer sets (forward: PCNA-A1F and reverse: Co-A1R) by amplifying the Mast fragment specifically using the conserved sequences among the cultivars (Table 3)”

This section details that they found 4 separate alleles associated with the chromosome section connected with PCNA phenotype. Only one of them results in PCNA offspring. A separate section states that non PCNA cultivars have multiple occurrences of the non-PCNA marker meaning that it occurs more than one place in the genome. This is highly suggestive that PCNA is a result of multiple deletions in the persimmon genome. The results also strongly correlate with hexaploid persimmon NOT having a chromosome control array which means the number of possible PCNA offspring is much lower than standard inheritance would yield. That is arguably the most important piece of information in the article. Pachytene pairing in persimmon must be a beast! The actual number of PCNA offspring in a cross of JT-02 X Taishu would be 3.125%. But you can relax, nobody would be able to detect the difference between 5% and 3.125% without making tens of thousands of crosses.

One more thing that will eventually be important, most plants went through chromosome doubling about 70 million years ago. I’m betting there was a chromosome doubling event for persimmon and later there was an event that resulted in diploid progenitor persimmon turning into hexaploid and tetraploid modern species. This would have occurred millions of years ago, it could not have been recent.

One very very important thing to keep in mind is that they were using primers which means they were NOT using the actual persimmon genome. They were searching for a piece of DNA either in front or behind the gene that gives PCNA offspring. It is kind of like saying you have a box with a few strings and one of them has a special purpose. They know approximately where the special string is in the box.

It is a chromosome deletion, not proven, but the results are highly suggestive
Persimmon chromosomes randomly align during pachytene pairing
They were working with markers to detect the mutated gene
The probability of a cold hardy PCNA persimmon from JT-02 X Taishu would depend on how cold tolerance works

Overall, I would put the numbers at about 1% of the offspring of JT-02 X Taishu being both PCNA and cold tolerant. That suggests a need to grow out at least 1000 seedlings to have 10 to pick and choose from.

jrd51 · January 19, 2023, 7:36pm

I’m not a geneticist but I know bullshit when I see it. You have an extraordinary talent for piling it high and deep. I won’t speculate on your motives. except to say that one of your objectives must be to block the view of how you have already misled and confused us:

You still have not documented why you insisted that persimmons with 5 PCNA genes would display non astringency. The published research (above) says that you are wrong. A persimmon with 5 PCNA genes is astringent.
You still have not acknowledged that your extrapolation from wheat to persimmons is invalid because wheat is allotropic and persimmons are mostly autotrophic, as indicated in the published research. All your earlier commentary that depended on persimmons being like wheat is misleading.
You still have not acknowledged that 5% is the correct first-order estimation of the proportion of non-astringent offspring from a cross of (a) a variety with 3 NA alleles (like JT-02) x (b) a variety with 6 NA alleles (like Taishu). I grant the uncertainty created by DV heritage; for simplicity I’m assuming that the hybrid behaves like a kaki. Notably, you have quietly given up your earlier various wide-ranging estimates, which ranged as high as 25%. But you insist now that the proportion would be 3.125% – even though the published research tells you that it is 5%. You could at least tell us why the published research is wrong.

Then you make a big deal of certain facts as if they support your case:

“Only one of [the alleles] results in a PCNA offspring.”

Yes, exactly. It’s pretty simple.

“This is highly suggestive that PCNA is a result of multiple deletions in the persimmon genome.”

Yes, at least 6 deletions – one AST gene missing on each of 6 chromosomes.

"The results also strongly correlate with the hexaploid persimmon NOT having a chromosome control array. . . . "

Yes, exactly, persimmon is not like wheat.

Then you throw in some irrelevant commentary, presumably just to add confusion:

“. . . and later there was an event that resulted in diploid progenitor persimmon turning into hexaploid and tetraploid modern species. This would have occurred millions of years ago, it could not have been recent.”

OK, no shit! You are merely describing how a polyploid comes to exist. But for the purposes of this discussion, it’s ancient history.

All the following, true but not problematic:

<< - It is a chromosome deletion, not proven, but the results are highly suggestive

Persimmon chromosomes randomly align during pachytene pairing.
They were working with markers to detect the mutated gene.
– The probability of a cold hardy PCNA persimmon from JT-02 X Taishu would depend on how cold tolerance works. >>

“Overall, I would put the numbers at about 1% of the offspring of JT-02 and Taishu being both PCNA and cold hardy.”

Ok, I can live with that. It introduces a different trait but it’s not far off from what I said earlier myself.

Now tell me: Would we as a community endorse a project to produce 500 offspring of a cross of JT-02 x Taishu, given that roughly 5 offspring would be both PCNA and cold tolerant. ABSOLUTELY!

I would have stopped this dialogue a while ago except I can’t abide the way you sow confusion and take our eyes off the prize.