Here’s a diagram of Sunflower’s known close genetic neighbors, as measured by marker mismatches in H. Huang’s RAPD study. The arrow points to Sunflower’s known progeny in the study. The maximum mismatches among all 36 cultivars is 22. The total number of error-free markers in this analysis is 45. The superscripts refer to sibling groups.
@JustPeachy , @Richard: The parenthood discussion of Primi 1216 and Pawpaw genetics studies is interesting. Satisfying curiosity is a common goal but I’m also wondering if there is any practical use for information regarding the parenthood of Primi 1216 or any other Pawpaw.
Breeding.
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As Richard said, for anyone interested in specific traits that COULD be inherited, knowing parentage is very important. I’m definitely interested in the discussion myself and have been following along. I have little to add to the conversation as genetics is not my background. It makes learning something new each day an easy task.
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This assumes one can isolate and identify the sequences responsible for flesh color (which usually correlates with flavor), color break, self-fertile, seed to flesh ratio, seed sack presence, overcropping tendency, astringency, phenolic flavor compounds, etc… etc… you could in theory accelerate the breeding process and probably remove 4-6 years off any pawpaw breeding effort should you have a specific goal in mind.
None of those responsible sequences have been identified. In fact, it’s only recently many of these sequences have been found for stone fruit, which has infinitely much higher interest and funding. Until someone fronts the funding, such identification is likely to be far off.
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That is one “angle” of investigation, which I’m currently pursuing with figs. Much of the needed preparatory work has already been completed by the community there.
Another angle though has been successfully pursued by N. Peterson and can be accelerated by discovering past unknown connections via high-resolution genetic distance. And the more specimens with known ancestry that can be incorporated the better. This is one of my motivations for inquiring about the ancestry of 1216 and others. As you will see in the upcoming article, I am planning on a new round of Pawpaw cultivar “fingerprinting”. Following that the research community might get interested in SNP investigations.
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True. The analysis will help establish relational distance. Finding the exact sequence will be a much harder endeavor (not saying it’s impossible). RAPD involves the amplification of random sequences, so you have as much chance to analyze a non-coding region as much as a coding region of DNA. And if you don’t have much confidence in the manner certain data was analyzed, you still have to have full confidence in the process and data collection methods to reanalyze that data.
I think it’s also partially complicated by the fact that no one as far as I am aware has done a complete map of A. triloba genome, such as with figs (another well funded industry) and stone fruit. We’re still looking at bits and pieces (random ones at that often).
Barring that map, in an ideal scenario you would have two know parents and produce hundreds/thousands of offspring (datapoints) whose phenotype is recorded and you can work backwards to sus-out some of the responsible genes with just raw statistical analysis from genetic variation.
It’s gets really complicated in some cases with polygenic traits. Peaches, for example, have two non -neighboring genetic regions responsible for acidity. In persimmon, a trait like astringency is even more complicated. Putting aside polyploidy, astringency is partially regulated by multiple regulatory factors, which is part of non-coding DNA sequences, which one would normally discount.
As it stands, we have no idea which traits are polygenetic. Everyone single one of these traits could be polygenetic for all we know. Hell, color break could be related to flesh color from some pleiotropic effect. To this day, we still get research papers published about malus genetics. The columnar locus apparently also effects trunk and branch geometry.
Agreed you need more known ancestry to help collated the information. This was what I was pointing out earlier. That information that Prima 1216 is a seedling of Sunflower. Even Blake’s book explicitly states “some sources say ‘Sunflower’ cultivar” in parenthesis. His sources are those pawpaw growers association members I mentioned - Ron, Cliff, Neal, Lehman, Woody, etc… etc… Depending on who you talk to, there might be someone with a different recollection about a specific cultivar’s history. Blake essentially created a quick pawpaw encyclopedia. There was at least one error I found for one cultivar, but if you open up a regular encyclopedia or wikipedia entry, there are loads of cases where there’s an error. Written history is oral history. When a human is involved, expect the possibility of an error.
So you disagree about the requirement for a metric for making all-to-all distance comparisons? Charles Dodgson knew this requirement.
Or perhaps you disagree that distance metrics applied to frequency samples are not valid unless the correlation matrix or tensor (consider multiple alleles) is non-singular. R. Fisher knew this. Nei might have too but he brushed it away as a “complicated” calculation. Expediency and publication were clearly more important to him than validity.
But maybe you still believe there is merit to Pomper’s genetic study. Well here’s his published data. If you click on this with an Android phone it will probably load straight into Google Sheets. The zeroes are missing data values. Only 3 specimens are error free, and one of the markers is predominantly errors. Further, the data as a whole lacks variance, even if the errors are ignored. And to add insult to injury, there are only 2 x 5 markers for 41 specimens - a completely under-determined system for anyone who took college algebra or freshman statistics.
I don’t want to hear about missing values being inevitable! It is only the result of practitioners who are too cheap to perform careful lab procedures with high-quality materials. There are studies and laboratories whose results are free of missing values - albeit sometimes it requires multiple trials.
Pomper 2010 SSR data (CSV format)
Neither. If N is the number of specimens, L the number of loci (marker locations for those reading along), and K the number of alleles per loci, then high resolution means L x K is much greater than N, and also the L have been determined by many regressions of heterozygosity, etc.
This is not the point of the analysis.
… for which the primer sequences are known.
- As I said in my post, I will rely on SNP studies to map characteristics.
- As of late, the assumption of non-coding is being thrown out.
- Figs are not a well funded industry, in fact they are a declining industry in the U.S. and per capita in developed nations worldwide.
- I am not an industry, grant funded, or salaried researcher.
Some researchers still do this but it is not the approach I’m taking.
You’ve mentioned that Blake was educated about Pawpaw by K. Pomper and associates. I believe K. Pomper received his knowledge as an intern of N. Peterson? And it was Peterson who placed H. Huang at the USDA research office in the Kentucky land grant orchard. I’d rather go back to the original source.
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We don’t need to rehash this. If you have more pertinent findings it will be borne out in future citations. It’s a simple as that. I am not disparaging the voracity of your approach or trying to start any sort of argument with respect to your endeavors.
The analysis is maybe not the ends, but it is the means to the ends if you’re trying to isolate and identify specific sequences.
True, but these then are focused regions of interest that express variation. It’s as simple as that. An area of interest with variation. It in no way has a guarantee to be tied to a specific trait.
Understood. That’s part of the assumption. Obviously that also means regularly factors are not accounted for.
Compared to pawpaws? Figs are very well funded. Or were very well funded. To date, pawpaw research has at no point been well funded… ever.
As it is, multiple organizations are pulling back agricultural research across the board, at the private and government level, so I certainly applaud your private efforts. I certainly never meant to imply you had any ulterior motive, and certainly not financial. Anyone posting on the GF is assumed to be here because of personal interest.
Blake can speak for himself, but it was my understanding that Pomper was not involved with the majority of the information that Blake compiled with respect to cultivar history. From what I understand, he had spoken directly with Neal, Cliff, Lehman, John. Jerry and John both had a specular memories about cultivar history. I often picked their brains about cultivars in years past. Their presence is sorry missed by all.
That said, there has been conflicting information regarding Prima. (@disc4tw’s information is slightly different to that of Blake’s) If it’s a particular interest to you, I’m sure you can reach out to Cliff or Neal to ask.
I’m unsure why there’s a specific fascination with Prima. I’m not particularly keen on it, from a consumption standpoint. If it’s just another data point, it might be worth asking Domenico Montanari directly, as Corwin is also no longer with us.
60 years ago.
I don’t know why you assume I’m fascinated by it. I used it as an example of why I ask about pawpaw ancestries.
I assume apples probably have the most cumulative worldwide and over time of all fruits. Vitus is probably next. I don’t expect figs to be anywhere near that or even in the top 10, but pawpaws are really the bottom of the barrel when it comes to research funding, which is why I think Neal, Woody, and others were concerned about the future existence of the germplasm repository at KYSU.
If that’s the case, it still might be worth reaching out to one of those I mentioned.
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The Kentucky land grant site is one of 5 USDA distributed Asimina triloba germplasm repositories under the administration of NCGR Corvallis. In terms of # of cultivars it contains a minority of the holdings. In addition, N. Peterson has a sizable collection at his breeding grounds.
Have you looked at Pomper’s 2010 data?
Peterson’s original plantings that were used to select his pawpaws are gone as far as I have been told. The land was repurposed I believe.
KSU has a decent selection. It’s not just named cultivars it’s also the existence of current breeding material. Blake has posted about this too. I know Neal has posted about this as well, but I do not recall his specific post. I think there was some discussion about selling off the land, which why there was concern. At the present time as far as cultivars go, Cliff probably has the largest selection in existence (at a single location). Next would be Ron and maybe Ken or Blake.
I have not looked at the raw CSV data, but I don’t think there is a need to rehash that. I do understand the points you make, particularly with Fisher and Nei (you have good points, but there are limitations too as you pointed out), and I simply believe this will be resolved via future citations if and when new findings are presented, whether they are yours or someone else’s. Moreover, I think to some extent we are talking past each other since you’re focused on analysis and I’m more concerned with the data generation and processes.
What do you know about the NCGR A. triloba sites?
I think you assume too much about me.
OK that’s enough of this particular debate. Let’s not sidetrack this thread. Thanks.
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This is where knowledge by way of oral history comes in. If you had only read the official webpage at Corvallis, mentions in other research papers, etc…, you would not know the current situation.
There are no specimen alive at Corvallis from the RVT. There exists a small faction of the original orchard at Wye. The Keedeysville was demoed a while ago. None of these were recent events. This is why Neal and Woody were both quite concerned with KYSU happenings.
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About pawpaw collections, Cliff England certainly has a lot of varieties and trees (I’ve been there many times, was just there 6 weeks ago,) but KSU has by far the largest pawpaw germplasm in existence or at least North America, currently. I have been there many, many times over the last 8+ years. I think a number of people on this forum have lots of things (good and bad) to say and assume about KSU’s operation but have never set foot on the property, never gotten to know the crews there, never discussed their work with them, or at best maybe went there one time for a couple of hours, which strongly limits their credibility, actual knowledge, and my ability to take what they say seriously. Not directing this towards you.
I would surmise from my last visit there last autumn that KSU has at least 75-100 numbered or named fruiting selections, as well as a couple hundred seedlings that are from the original planting in the late 90’s from collected seed and donated materials from around the USA. That planting is old now and in decline, and I think they have slowly been cutting it down. Most of that portion is pretty mediocre, but interesting none the less. It is the planting KSU Atwood came from.
Then they have their newest planting which is only about 3-4 years old and consists of a couple hundred of their newest crosses, and other acquisitions, some of which have come from our nursery. Those trees are small still but beginning to flower. Many were lost in the last 2 springs of very poor weather, 2022 being much better.
Our farm has around 30-40 named or numbered cultivars as well as a bunch of special seedlings which will bear fruit this year, for a total of about 200-250 pawpaw trees in ground total. Many are flowering this year and the oldest were seedlings planted in 2016. It’s a nice collection but I also have limited space, need room for other things, and it’s not a contest and their is no winner. Ron’s collection is large with lots of unusual material, but in decline and I don’t know about Ken’s. Jerry Lehman likely had the biggest collection next to KSU before he passed away. He had acres of pawpaws consisting of many of his crosses. We grafted a number of the best of those this spring.
Remember not to take pawpaws too seriously, folks. If you’re getting in arguments over it you’re probably doing just that. No thanks. 
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I knew Jerry’s collection was quite big. I have seen it, and I know that there were a bunch of NaFEX folks that collected material that was still WIP material. I have some of it as well.
Did John B. have a large collection? Do you know what became of it?
From that statement and other info I read I’m thinking the typical life of a pawpaw tree is 30 years so if it is grafted that will be lost with only rootsock root sprouts remaining. Is my assumption regarding age correct?
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I have READ that the expected life span of a grafted variety is 20-30 years, but there is nothing stopping you from grafting the same variety onto a root sucker that pops up 3 feet away from the original tree. Sure this adds another dimension to pawpaw maintenance, but that means for the average human you would have to RE-graft what, maybe 4 times in a life span max? That takes an extra hour of work per tree? I know peaches and other stone fruit only last 30 years or so as well, and they don’t grow their own replacement rootstock. So I guess it’s all relative.
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