Genetic Map

[mountainfigs]

Apparently about 6 years ago nearly 200 named figs were genetically mapped. The effort produced some interesting results, explained here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860561/

and pictured here:

http://tinyurl.com/zpkdrvd

Assuming I'm reading the information and genetic map right, I jotted some off the cuff thoughts:

(Others have commented on the science: http://tinyurl.com/hvoj4kx)

Some of these seem oddly listed as synonymous:
Lemon, Dokkar, LSU Everbearing, White Texas Everbearing, Kadota, Trojano.

Listed interestingly as close:
Ischia White and King (Desert King, I assume)

Oddly listed as close:
Alma and Encanto Brown Turkey, etc

Interestingly listed as synonymous:
Violet Sepor and Bourjassotte Gris

Interestingly listed as close:
Verte/Calverte to Paradiso, which is listed as synonymous with Ischia Green (in my experience Battaglia Green seems synonymous too)

Interestingly listed as perhaps somewhat close, these sweet late ripeners:
Ischia Green, Col de Dame, Sucrette, and Black Madeira

Understandably listed as synonymous:
Dark Portuguese, Sal's, Abruzzi
while interestingly listed as very close but not synonymous to "Hearty" Chicago (Hardy Chicago, I assume)

These Mt Etnas seem in the ballpark less interestingly with Brunswick, LSU Gold, Celeste, Genoa, and the late ripening St Jean but more interestingly apparently also in the ballpark with Becane, Aked, and Blanquette.

Understandably:
Mission listed as close to Noire de Caromb

Curiously:
Hollier listed as close to California Brown Turkey and several synonyms

Interestingly:
Excel listed as somewhat close to Mary Lane

Interestingly:
the very early dark Pastiliere listed as close to the very early light Yellow Neches (and both need the wasp?)

Interestingly:
Osborn Prolific listed among the reportedly most distinct or different grouping, which is mostly from Turkmenistan, farthest from the Mediterranean

Interestingly:
Adriatic and Lampeira are listed as synonymous

Oddly:
Deanna and 278-128 (aka Golden Riverside) and Orphan and Algerian Watts are listed as synonymous

Interestingly:
Gulbun and Jurupa are listed as synonymous

Interestingly:
Nero and Ischia Black are listed as close, and in the ballpark with Barnissotte

Interestingly:
Panachee is listed in the ballpark with Bourjassotte Blanche

Interestingly:
Italian 253 is listed as close to St Jean

Interestingly:
Italian 258 is listed as synonymous with Italian 320

Curiously:
LSU Gold listed as somewhat close to Brunswick (and synonyms)

[eboone]

Unfortunately the article is misleading without a full understanding of the genetic testing done. The researchers tested several loci on the genes and showed those loci were identical, but they did not test the whole of the DNA. So it is erroneous to say that varieties are identical or synonymous based on this testing - the best they can say is that they share some identical genes. If you take limited sampling of some loci on genes from a wide variety of people, you would find similar shared genes, but you could look and see the people were not identical. You would have to test the ENTIRE DNA of two varieties to prove they were identical or synonymous.

[mountainfigs]

I think the researchers can claim that the cases of "synonymy" are synonymous to the limits of their testing. I take the testing as basically a first approximation. Some of the instances where they find synonymy are of cultivars that have been widely noted to appear essentially identical anecdotally as well. (Makes sense: people for various conscious or unconscious reasons simply rename cultivars.)

In other instances of their tested synonymy, as with, say, Lemon and Kadota, I don't recall any anecdotal observations of synonymy, my own included. However, I can look anecdotally at Lemon and Kadota and see that they share a lot of similarities despite apparent differences.

Such first order approximations seem to show interesting relations or groupings of cultivars beyond those that evinced synonymy in the testing. For instance for a while I've wondered if Becane might be otherwise known as Gallo, a reputedly hardy, small, early yellow fig, a kind of counterpart to the Mt Etnas, so when I see that it tests out in close relation to the Mt Etnas, my curiousity and even expectations are piqued more. I've trialed most of the figs charted close to the Mt Etnas, but not Becane, Aked, Blanquette.

Disappointed that RDB, Palermo Red, Marseilles, Brooklyn White, Florea, Bianchetta among others were apparently not included in this study.

[AscPete]

Instead of being considered as synonyms they should probably be considered as 'Closely' or 'More Closely' Related.
For example in the OP the Condit Hybrids are lumped together but are know to be distinct cultivars some sharing the same or similar parentage.

[AscPete]

Thanks for sharing this document.
Since its release the consensus is as Ed, eboone pointed out, that there weren't sufficient markers tested and compared to be conclusive...

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860561/pdf/10709_2010_Article_9442.pdf

Note: Some of the Genetically "Close" proximity may simply be due to a shared lineage (possibly many times removed).

[mountainfigs]

As with human families, as with race, there can be or inevitably is a greater degree of difference within an extended family and race, and other groupings, than across family and race.

[ross]

So what from this genetic map can we actually use as truth? Or is it all just speculation?

[AscPete]

Ross,

The genetic mapping was performed at UC Davis by USDA National Clonal Germplasm Repository... All factual info no speculations they mapped "genetic polymorphism at 15 microsatellite loci..."

[Harborseal]

Humans and chimps share 96% of genes. These studies could have a fair chance of determining that we're synonymous. I don't know the literature well enough to be certain but to my knowledge the largest number of microsatelite loci used covered only 64% of the variation between their F carica specimens, leaving 1/3rd of the variation untested. If they tested all available F Carica varieties that 64% would almost certainly be smaller. Everybody gets to decide for themselves the value of these data

It's much more expensive to get the last 30% than the first 60% because there are many more genes contributing to the last 30% than the first 60%, in case anyone wants to know why they stopped at 64%

[Harborseal]

BTW, the example above about chimps and us demonstrates the general idea well but technically it's wrong. Because they target the variation they'd only be looking at the 4% difference. If they, like the UCD fig study, examined a limited sample of the genes that were different they might only get 1 or 2% of the variance.

[Darkman]

So they almost got to second base!

We all need to speak with our billionaire friends and see about getting the rest done. Seems like we should be able to get a government grant for this in the interest of truth in selling named varieties. look at all the crap they give grants too.

[Harborseal]

Right, except they're not 'out'. The next study can ignore those microsatellites and go for the next 10% of the variation and a few years later they can get the next 6% and on and on until they're done. The final 5% would probably cost more than the first 64% if they used the same methodology but by the time it's done it will cost your grandson in 5th grade $25 for his science project. That's in today's dollars, of course.

[Darkman]

Yes I understand but I don't see anyone moving forward to complete the mapping. I wonder what the real costs would be. It would be nice to know.

I was actually serious about the government grant money. I'm sure there are some amongst the fig lovers of the USA that could write some grant applications and get money to fund some of this. Our government gives away lots of money for some very ridiculous things. Does anyone really know how much the next phase would take?

[Kelby]

The mapping also operates on the assumption what they have is true to name. Much of the germplasm resource is from donations. If you go on the USDA website and dig around you can usually find the donor information. Bass has donated some, Encanto has donated some, and so forth.

Who's to say the Hardy Chicago donated is the same as the one in my yard?

[BC BYRON]

Thats the thing. You hit the nail right on the head. Richard is doing his testing but that only proves his sources. How many mislabeled trees are out there being traded around with differences being attributed to growing conditions and such when they are really just not the same plant. I think its an impossible quest

[Richard]

BC BYRON -
I am choosing major sources incl. AgriStarts, WillsC, etc. and in several cases I have the same cultivar name from each of them. I believe that tracking down genetic relationships and synonyms among the majority of figs in circulation within the U.S. is tractable. Further, for persons who cannot trace back the origins of their tree(s) to one of my sources: I believe that within 5 years they could submit a leaf sample and a few bucks to a plant service to determine its pedigree.

[Darkman]

As with any genetic mapping the name is not the important part at first. Just the maps and then the names are compared to the maps. I'm sure it will show that hundreds maybe thousands of figs are identical. The names will be sorted out by historical records. Oldest recorded name is the name assigned to a particular mapping. All others are footnotes. I'm sure there will be many hurt feelings but that is the only fair way to go about it. Of course this is all my humble uneducated opinion and your opinion may differ.

[Johnson1]

I look at the subject as guidance, one with limitations but possibly enlightening. Besides there have been significant advancements in the field of genetic testing since this was run.

Another good reason not to stick a new name on a fig that likely already has multiple names.
Rather than minimizing confusion it adds to it.

[HarveyC]

Jon, Sue, one other fig friend (forget her name now) and I were at USDA's office shortly after they finished this report. But, to be clear, it does not identify which varieties are identical. The use of SSR markers is less than ideal and only some markers were tested.

Someone referred to this report in a reply to one of you Youtube videos posted today. I posted a reply but then asked my friend who is an expert in the field to explain more accurately. She has extensive work in genetics and this was her post:

In many cases SSR markers can pick the difference. It all depends on how closely related are these figs. If there are just few minor DNA differences between them, the SSR markers will not pick them. The small changes may or may not contribute to the flavor or appearance or any other fruit or plant characteristics. With these markers, if you see the difference you can say that the cultivars are different. If you don’t see the difference, there’s no guarantee that they are identical. They could be identical, or they could be

[Richard]

p. 686.
"The cluster analysis (CA) revealed ten groups with 32 instances of synonymy among cultivars and groups differed significantly for frequency and composition of alleles for different loci."
...
"For example, figs with different names but identical multilocus fingerprint included: ..."

[Darkman]

Making sure I understand. In the "Smith" family there are mothers, fathers, sons ,daughter, aunts, uncles, and so on..... and non of them are identical yet all are in the Smith family. They all share familial markers and can be identified as family but they are not identical. So how does it work compared to say the "Celeste" family. Does Improved Celeste, Champagne, Black Celeste, O'Rourke, etc.... all bear identifiable familial markers while being unmistakably different enough to group others into their specific group i.e. Champagne and O'Rourke being individually identifiably and also identified as family from Celeste?

[Richard]

Darkman -
The blood relatives in the human Smith family are all in the same genetic clade.

http://dgmweb.net/DNA/General/Cluster_vs_Clade.html

The fig cultivar Celeste at NCGR Davis falls into a clade with these figs at NCGR Davis:
Abruzzi
Aked
Becane
Blanquette
Brunswick
Capitola Long
Celeste
Dark No. 1 Portuguese
Doree
Genoa
Genoa White
Hearty Chicago
Italian 215
Italian 253
LSU Gold
Nero Cesar
Pied De Boeuf
Rattlesnake Island
Red Italian
Sal’s Fig
San Pietro
St. Jean
White Russian aka Harvey Adriatic
Yougo #7

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860561/