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Author Topic: some implied information about the origin of different citrus from DNA study  (Read 3048 times)

SoCal2warm

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I recently found an interesting DNA study done in Japan that could help provide more insight into the very far back origins of several cold-hardy Japanese citrus varieties.

Some things to bear in mind, this genetic marker analysis is not exactly indicative of precise ancestry percentages. It is only looking at certain markers, so this is only going to give us a very rough idea of the probable ancestry.


Apparently citron (C. medica) is nearly identical to Ichang papeda (C. ichangensis) in the DNA marker analysis, such that the study did not bother to differentiate them.
This means that wherever you see "C. medica" in the ancestry of these cold-hardy Japanese citrus varieties it is actually C. ichangensis.

The following percentages are not exact, they are rough estimates I copied from a visual graph:

C. ichangensis: 91.5% C. medica, 8% C. maxima, 0.5% reticula
Ichang lemon: 60% C. medica, 40% C. maxima
Yuzu: 99% C. medica, 1% C. reticula
Hyuganatsu: 26% C. reticula, 40% C. medica, 34% C. maxima
Kunenbo: 30% C. reticula, 65% C. medica, 5% C. maxima
Kunenbo (II) : 35% C. maxima, 65% C. reticula
Sudachi: 33% C. reticula, 67% C. medica
Kabuchi 33% C. reticula, 51% C. medica, 19% C. maxima
Kabosu: 34% C. reticula, 58% C. medica, 8% C. maxima
Kinkoji: 36% C. reticula, 0.5% C. medica, 63.5% C. maxima
Shiikuwassha 44% C. reticula, 56% C. medica
Keraji: 50% C. reticula, 16% C. maxima, 34% C. medica
Natsudaidai 52% C. reticula, 0.5% C. medica, 47.5% C. maxima
Satsuma: 25% C. maxima, 75% C. reticula
Hirado Buntan: 100% C. maxima


Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes,
Shimizu T, Kitajima A.
https://www.ncbi.nlm.nih.gov/pubmed/27902727


Some thoughts.

Yuzu is believed to share about half-and-half ancestry from C. reticula and C. ichangensis (or possibly even an earlier papeda species forerunner of C. ichangensis), so the fact that C. reticula barely showed up in the genetic analysis is a clear example of how imprecise the ancestry results of such an analysis are.
Yuzu probably wasn't just a simple cross of C. ichangensis with C. reticula; there probably had to be a few generations sexual propagation for the C. reticula gene markers to get bred out.

Apparently there are two very different forms of kunenbo, one with C. ichangensis ancestry, the other without. It looks like Kinkoji doesn't have any recent C. ichangensis ancestors, so it probably didn't descend from the kunenbo type in the study that showed C. ichangensis ancestry. The same is probably true of Satsuma as well.

Natsudaidai apparently doesn't have any close connection to Yuzu.
(Nansho-daidai I believe is Tiwanica lemon)

The overall ancestry composition in the graph is consistent with the theory that Hyuganatsu resulted from buntan getting pollinated by yuzu. However, if you look at the flow chart, the study inferred that Tachibana-B was one of the parents of Hyuganatsu. The graph shows Tachibana-B to be about 31% C. reticula, 69% "C. medica" (remember represents C. ichangensis here), so it may be that buntan (C. maxima) was pollinated by Tachibana-B, rather than yuzu. Although with that high a percentage of C. ichangensis I suspect Tachibana-B originated from a yuzu cross.

And the study does confirm the leading theory that Ichang lemon is a hybrid between C. ichangensis and C. maxima (though still doesn't prove whether it was a simple cross).

Keraji displays a surprisingly high percentage of C. ichangensis. It was my understanding that keraji originated, over a progression, from a triple backcross of Kunenbo with Shiikuwasha (C. depressa). It's possible that the C. ichangensis genes were positively selected for over time, since those genes conferred cold hardiness.

This isn't from this study but is just some things I've been able to put together from other studies, that may help you make some more sense of those varieties in that list:

Shiikuwasha x kunenbo = kabuchi; kabuchi x kunenbo = kikaimikan; kikaimikan x kunenbo = keraji
kishu x kunenbo = Satsuma; buntan x kunenbo = kinkoji ( kinkoji = Bloomsweet)
kabosu and sudachi are almost certainly hybrids from yuzu


Another DNA marker analysis done in China did not seem to show a connection between Changsha mandarin and C. ichangensis, which is interesting because the fruits/seeds of Changsha mandarin appear very morphologically similar to clementine-yuzu hybrid. The analysis did suggest Changsha mandarin might have just a little C. maxima ancestry though (maybe 15%)
Genomics of the origin and evolution of Citrus, Guohong Albert Wu, Javier Terol

Of course it's also possible the gene markers could have been completely bred out over numerous suceeding generations, since Changsha mandarin originated from growing in the wild.


A note about availability of these varieties in the U.S.
Most of these varieties on this list are fairly available to those in the U.S. The main exceptions are Kunenbo and Hyuganatsu.
Kabosu can be harder to find. Shikuwasa and Keraji seem to be fairly prevelent in Georgia and North Carolina, but I don't believe they can be found in the rest of the country. (Shikuwasa is sometimes written shikwasa, different spellings) C. ichangensis used to be more popular, but currently I don't think it is available from any mail order nurseries. It can still be found in Europe. Bloomsweet was introduced into the U.S. from Texas, so can be found in that part of the country.

Hyuganatsu isn't too difficult to get in Japan, it is sometimes sold as a seasonal specialty fruit. (I don't know whether it actually displays any exceptional cold hardiness traits) Kunenbo used to be the popular fruit in Japan hundreds of years ago before it was replaced by what is today called Satsuma. It's not widely available any longer but can still be found in some botanical and historical collections.
The UCR collection in California supposedly has one but apparently from the descriptions the type they have is not the delicious tasting one that exists in Japan, and in any case it's not available to the public.

Hirado Buntan isn't really that cold hardy but is more cold tolerant than other pomelos.


« Last Edit: April 21, 2018, 11:12:37 AM by SoCal2warm »

SoCal2warm

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According to the flow graph in the first study, they are inferring that kishu is one of the parents of natsudaidai, along with another mystery parent. Apparently kunenbo-A originated from a cross from kishu and another mystery parent, while kunenbo-B originated from a cross between sour orange and a different mystery parent. It would appear then that kunenbo A and B are not related, if this is correct. The flow chart also indicates that Kabosu resulted from a cross between Yuzu and kunenbo-A.

The kunenbo-A corresponds to the 35% C. maxima, 65% C. reticula
while the kunenbo-B corresponds to the 30% C. reticula, 65% C. medica, 5% C. maxima

It appears then that the "C. medica" here might actually indeed be C. medica (rather than C. ichangensis) if it's coming from the sour orange parent. (or possibly a mix of C. medica and C. ichangensis, since the other mystery parent is unnamed)
« Last Edit: April 21, 2018, 02:18:55 AM by SoCal2warm »

Ilya11

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A very misleading post, do not understand why you are mixing real scientific results with your unbased  prophetic revelations.
Best regards,
                       Ilya

Sylvain

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+1
To read the article is enough to understand.

SoCal2warm

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A very misleading post, do not understand why you are mixing real scientific results with your unbased  prophetic revelations.
I know there is a lot of information presented and being discussed here, but what are a few of the main things you find misleading about it?

I was just trying to condense a long study into an easy to read summary. And adding a little informed commentary to try to help facts make more sense.

To read the article is enough to understand.
It is good to have a plain-text version of this information. These downloadable pdf's have a way of becoming unavailable over time.

SoCal2warm

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Here's another interesting study and DNA marker analysis:

Citrus Genetic Resources Grown on the Ryukyu Islands, Japan
Yamamoto Yasashi, Kagoshima University
http://cpi.kagoshima-u.ac.jp/publications/occasionalpapers/occasional/vol-54/OCCASIONAL_PAPERS_54(pp9-15).pdf

It shows pictures of all these obscure citrus too.

Apparently kunenbo groups more closely with sour orange and pumelo, while Shikuwasa groups more closely with Tachibana, while yuzu and Ichang papeda group together in a separate group.

C. Tachibana may possibly be native to Southern Japan, Okinawa and Taiwan, and it appears to be very closely related to C. reticula, to the point it could possibly be regarded as a subspecies of C. reticula.
(Genomics of the origin and evolution of Citrus Guohong albert Wu, Javier Terol)
However, this fact does not make it show up as C. reticula in the DNA marker analysis inferring ancestry, so it's clearly not just a mandarin hybrid (i.e. it shows up as only 1% C. reticula in DNA ancestry)

Another study indicated Shikuwasa is probabably a hybrid of another unidentified mystery parent with Tachibana, or possibly some sort of backross with Tachibana.
« Last Edit: July 10, 2018, 04:15:12 PM by SoCal2warm »

Citradia

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Are medica and Ichangensis really the same?  I thought medica was the citron which was famous in the Middle East and not cold hardy. Ichangensis is cold hardy. What's up?

SoCal2warm

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Are medica and Ichangensis really the same?  I thought medica was the citron which was famous in the Middle East and not cold hardy. Ichangensis is cold hardy. What's up?
You are right. Citron ranks down there as one of the least cold hardy citrus species, with the exception of limes and C. micrantha from which limes are descended from. Citron is even less cold hardy than regular lemons, which in turn are a bit less hardy than orange.
And C. ichangensis is the most cold hardy known citrus species, besides from trifoliate.

Despite the vast difference in cold hardiness, citron shares a closer evolutionary similarity to C. ichangensis than to C. reticulata (mandarin orange). This results in a problem arising in DNA marker analysis, because apparently citron and C. ichangensis share some markers that C. reticulata does not, while C. maxima has its own markers that are unique enough to differentiate it. That's not to say a DNA marker analysis can't easily differentiate between citron and C. ichangensis, but the algorithm they employed, the same one to look at all these diverse citrus varieties, failed to do that.

It was because of the particular markers they were selecting for. They were not making much effort to try to differentiate C. medica and C. ichangensis.

If I remember correctly, the authors even made a note in the publication that they had intentionally decided to discard some markers because they were causing another problem in their data analysis, and speculated that doing this might have been what suppressed the differentation between C. medica and C. ichangensis.
« Last Edit: May 08, 2018, 02:08:44 AM by SoCal2warm »

Citradia

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SoCal2warm

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parentage of Sudachi
« Reply #9 on: December 27, 2018, 06:47:08 PM »
Sudachi is a slightly more regional citrus variety, used in Japan (more commonly used in Tokushima Prefecture) as a lemon similar to Yuzu except usually harvested while still green.

The Wikipedia entry for Sudachi states "Recent genetic analysis has confirmed its status as a hybrid, with one parent being the yuzu, and the other an unidentified relative of two native-Japanese cultivars, the koji and tachibana orange".

The entry under Yukou makes it a little more clear: "Genetic analysis has shown it to be a cross between the kishumikan and koji, a part-tachibana orange hybrid native to Japan.

Kishumikan is of course the ordinary kishu mandarin (sold in many nurseries, I have one, one my favorites, very small fruit size but effortless to peel).

Now, as for the koji, I had to look that up.

Useful Plants of Japan Described and Illustrated, by Dai Nihon Nokai, page 64, has an entry under Citrus nobilis, of which Koji-mikan and Koji are listed as synonyms.

Citrus nobilis is a somewhat broad category that primarily includes the citrus kunenbo, in fact the two are probably almost synonymous. (kunenbo isn't quite a single cultivar either but is actually a group, although there's a main cultivar of kunenbo)

Sudachi descends from the same koji-type parent that Yukou does. (Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes, Tokurou Shimizu, 2016 )

So, to put everything in perspective, Sudachi originated as a cross between Yuzu and a particular type of kunenbo that derived from tachibana (that is happens to have some tachibana in its ancestry).

This actually would make the parentage of Sudachi very similar to Satsuma mandarin (although the two fruits are very different). Satsuma derives from kishu x kunenbo. Sudachi derives from kishu x a type of kunenbo with some tachibana in it.

(kunenbo is a mandarin with some pomelo in its ancestry, maybe comparable to the family of citrus known as a tangor, and likely all existent varieties of kunenbo are pretty closely directly related, even if some have admixture ancestry from other citrus groups)

If you look at pictures of the Yukou, it looks pretty yellow, like something with a lot of pomelo ancestry or almost some sort of lemon. It wouldn't be very fitting to describe it as a mandarin.

(More information on that here, if you were really interested: http://www.tokyofoundation.org/en/topics/japanese-traditional-foods/vol.-11-the-yuko-a-native-japanese-citrus )

So how simply to describe the origin of Sudachi?

I might say that Sudachi is a cross between Yuzu and another semi-sour citrus related to Satsuma mandarin but which also has Tachibana Orange going back in its ancestry.

(It's worthwhile to put Tachibana in the description because Tachibana likely is conferring some genes for cold hardiness. Genetically, Tachibana is very closely related to mandarin, some taxonomists would almost consider it a subspecies under mandarin, but is a little cold hardier, enters into Winter dormancy more easily, and is a little cold hardier than ordinary mandarin. Tachibana is also a bit more sour than the ordinary sweet varieties of mandarins people are familiar with)

SoCal2warm

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drew up ancestry diagrams








« Last Edit: December 27, 2018, 10:11:48 PM by SoCal2warm »

Millet

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SoCal2warm, interesting about your article of citrus grown on the Ryukyu Islands.  I believe your article is correct, however the interesting thing to me is that I lived on the Ryukyu Islands for two years (Okinawa) and I never seen a citrus tree.

SoCal2warm

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SoCal2warm, interesting about your article of citrus grown on the Ryukyu Islands.  I believe your article is correct, however the interesting thing to me is that I lived on the Ryukyu Islands for two years (Okinawa) and I never seen a citrus tree.
They may have originated there several hundred years ago, but I think today they are nearly extinct in the wild and almost no one grows them, since people in modern times are less dependent on self-sufficiency and less in touch with agriculture and growing things. (Also I think citrus imports from foreign countries have displaced the use of native varieties)
Okinawa is not a big island, and I'm sure there has probably also been a lot of deforestation compared to hundreds of years ago.
It is kind of paradoxical that in the origin regions of some of these citrus cultivars very few of the people now living there even know what they are.
All across Asia the old culture, and many of the unique agricultural cultivars that went along with that traditional culture, have slowly died off. There are attempts being made to preserve them.

Radoslav

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SoCal2warm, interesting about your article of citrus grown on the Ryukyu Islands.  I believe your article is correct, however the interesting thing to me is that I lived on the Ryukyu Islands for two years (Okinawa) and I never seen a citrus tree.

Annual production of shikuwasha mandarins is several 1000s tons in Okinawa. For example 3 139 t in 2009.
There are over 200 Shiikuwasha (Citrus depressa Hayata) cultivars and varieties reported.
Another indigenous citruses like kabuchi, or oto are produced only in amounts of severa tons per year.

Major  Shiikuwasha cultivars:

カーアチ  (Kāachi)
伊豆味クガニ (Izumi kugani)
勝山クガニー (Katsuyama kugani)
大宜味クガニ (Ōgimi kugani)
仲本シードレス (Nakamoto seedless)

SoCal2warm

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One DNA marker study found that Shikuwasa (C. depressa) and Tachibana clustered closely together and seemed to be related.
(Phylogenetic Relationships among Selected Citrus Germplasm among Selected Citrus Germplasm Accessions Revealed by Inter-simple Sequence Repeat (ISSR) Markers, Dequiu Fang, UC Riverside, 1998 )

Although it's not a direct relation, so it's not as if Tachibana is the actual parent of Shikuwasa.
(Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes, Tokurou Shimizu, 2016 )

Both of these varieties are indigenous to Taiwan, so they may have shared some common ancestor in the past or evolutionary diverged from the same line.
The latter study also indicated that Shikuwasa appeared to have either C. medica and/or and C. ichangensis (analysis wasn't very precise on this point) ancestry going back in its line, in addition to the relationship with Tachibana.

So some of these distant origins remain somewhat of a murky mystery.

(Nanshodaidai doesn't appear to show any relation to either of them in these studies, rather appears to have mandarin and pomelo ancestry, but that may not necessarily preclude the possibility of something else in its ancestry going distantly back)
« Last Edit: December 28, 2018, 04:41:34 PM by SoCal2warm »

SoCal2warm

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Related the first post in this thread, looking at the bottom there was another bar graph, from a different analysis of the markers, that did a better job differentiating between citron and C. ichangensis. They seemed to identify a group of genes that was more unique to C. ichangensis, while the C. medica (citron) was not entirely unique to citron but also shared to some extent by C. ichangensis. However, this category of genetic markers associated with C. ichangensis also seems to be shared (in great part) by three different Tachibana accessions.
( Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes,
Tokurou Shimizu, 2016 )
 
That could either suggest a relationship between C. ichangensis and Tachibana (but I read in previous genetic studies Tachibana seemed to just be a subspecies of C. reticula), or possibly they might just share in common a certain set of activated cold hardy genes. I don't know, this certainly seems mysterious and inexplicable.

What was particularly interesting here is the study indicated that Shikuwasa definitely doesn't seem to have any C. medica (so that would preclude the idea it could have been derived from some sort of lemon or sour orange).

(Taking the two different graphs together, I think we can assume that Shikuwasa has either some C. ichangensis or yuzu genes, since it showed up with "C. medica" markers in one analysis, where C. ichangensis did but Tachibana did not, but showed up with overwhelming C. ichangensis / Tachibana markers in the other analysis where lemon did not.)

Going back (and I don't want to dwell on this too much) to the mysterious connection between C. ichangensis and Tachibana, one theory could be that C. reticula and C. tachibana simply branched off from C. ichangensis/yuzu early on, and then C. reticula went off to lose these genes. Perhaps C. tachibana kept them because it was growing in a colder area (in the Japanese islands). Another possibility could be genetic introgression (but it would have to be very strong in this case), where perhaps yuzu (C. junos) imparted its genes onto the ancestral line of C. tachibana, possibly before it even arrived in the Japanese islands. I don't know, both of these ideas seem a little far stretched.
« Last Edit: January 25, 2019, 03:24:36 AM by SoCal2warm »

SoCal2warm

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If I had to draw a relationship of the different cold hardy citrus together, the diagram would look like this spatially:




SoCal2warm

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I'm looking at a map and the Chinese city of Yichang seems just a little further north of Changsha, about 320 km northwest.

That would lead me to believe that, while they may technically constitute separate species, the Changsha mandarin may just effectively be a natural evolutionary progression on the branch off between Ichang papeda and mandarins, which are native to the region a little bit further to the southeast.

I read an article in an old encyclopedia that stated that Ichang lemons [referring to Ichang papeda here, do not want to cause confusion] were actually cultivated (only in personal yards) in that area and sometimes were used by the inhabitants (or sold in markets) as lemons (probably inferior to ordinary lemons but that must have been all they had in that area), although they could also be found in the wild.

It's also possible there could have been genetic introgression at some point into the Changsha species from cultivated mandarin varieties, which also would have contained a small amount of pomelo ancestry.
I do not have any way of convincingly supporting this but I suspect the combination of pomelo genes to mandarins was able to increase the level of cold hardiness (even though pomelos are native to the region much furth south), perhaps because pomelo genes were able to provide more vigor to overcome cold damage. (suggestive evidence being the hardiness of Taiwanica lemon, many varieties of sour orange, and the fact that grapefruit varieties were able to be bred in Florida that were more hardy; furthermore I have grown many types of different seedlings and the Oroblanco pomelo-grapefruit hybrids appear to be the most vigorous and fastest growing, followed by pure pomelo)
I know this is very speculative.

If that's the case, Yuzu might ultimately be an evolutionary progression as well and constitute its own very closely related species.
Ancient Chinese texts refer to "oranges" (thought by modern scholars to be Yuzu) growing on the upper banks of the Yangtze river, and that area runs between the Yichang and Changsha area (much closer to Yichang than Changsha).

I would theorize that this may be a very closely related family of species, that had been developing and evolving in isolation in this area for a long time, and thus are not simple hybrids.
This region of Asia has a lot of localized biodiversity, due in part to the high productivity of the wet Summer season and long growing season.



In case you're wondering why pomelo genes might be able to add more vigor, and mandarins never independently evolved that, I found this:
"Water use for grapefruit and lemon is about 20 percent higher than that of oranges, while water use for mandarins is about 10% less."

I hypothesize there may be a trade-off between drought tolerance and vigor. As one goes further north in China there is less precipitation. So because the species needed to be able to survive rare years of drought, they were not able to take advantage of the full cold hardiness that would have come with more vigorous growth genes.

(A bit unrelated, but despite the higher water needs, pomelos can still tolerate higher amounts of sun than mandarins, which is not surprising either since pomelos are native to a region closer towards the equator)
« Last Edit: April 14, 2019, 12:09:06 AM by SoCal2warm »

Ilya11

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I enjoyed  your disclaimers 😈
Best regards,
                       Ilya

Ilya11

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I do not have any way of convincingly supporting this but I suspect the combination of pomelo genes to mandarins was able to increase the level of cold hardiness

I know this is very speculative.

Best regards,
                       Ilya

Radoslav

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More vigor grow means more cold tolerant?
Have you ever heard about vegetation zones?  More cold areas or higher level under sea means plants are smaller and leaves are repleced by needles.
And influence of citrus maxima to mandarins? As far as I know, citrus maxima is as old as citrus reticulata. They are together with citrus medica considered as  ancestors of all citruses.

SoCal2warm

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And influence of citrus maxima to mandarins?
The relationship being referred to would be artificial, due to human cultivation.
There was genetic introgression into the genepool of cultivated mandarins. I believe the humans noticed that some of these mandarins had better flavor and seemed to grow a bit better (hybrid vigor, if you want to look at it that way) and these mandarin cultivars gradually disseminated their way up North.

Perhaps citrus Taiwanica was one such mandarin-pomelo hybrid cultivar that escaped into the wild and became naturalized in Taiwan, undergoing some degree of further evolution. Taiwan has plenty of precipitation so lack of drought tolerance would not have been a problem there, but the island does have fairly severe freezes that come along about every 40 years, so there would have been natural selection for the most cold tolerant progeny.
We are talking in much older times, I doubt Taiwanica exists in the wild on the island anymore.
« Last Edit: April 14, 2019, 02:25:01 PM by SoCal2warm »

SoCal2warm

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Here's another proposed grouping of hardy citrus types


SoCal2warm

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I enjoyed  your disclaimers 😈

I am just coming up with very speculative theory, based on scant available evidence.

We have DNA marker analysis that can point out some relationships, and some historical records.
I'm just trying to combine those and make some sense out of this all.

 

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