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Author Topic: some implied information about the origin of different citrus from DNA study  (Read 2037 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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