The Rosa genome and insights into domestication of modern roses

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Peter Harris
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The Rosa genome and insights into domestication of modern roses

Post: # 67765Post Peter Harris
Tue May 01, 2018 9:42 am

The April 30, 2018 issue of [i]Nature Ge­­­netics[/i] contains a study which concludes (this is a very simple summary that I hope is accurate) that scent, recurrent blooming, and color are controlled by some genes that work in opposition to each other, and that breeders' emphases on color and recurrent blooming have sacrificed fragrance. The study reports discovering new candidate genes for recurrent blooming. By using these genes which are not antagonistic to fragrance, breeders may find ways to get around this trade-off of fragrance for recurrence and color.

The article is pretty technical. It's open access, so you may download a PDF if you wish.

https://www.nature.com/articles/s41588-018-0110-3

If you'd like to read a less technical rendering of the content, go to
https://www.sciencenews.org/article/ros ... -fragrance

Peter

Don
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67767Post Don
Tue May 01, 2018 3:12 pm

" We developed an original in vitro culture protocol combining fine-tuned starvation, cold stress and hormonal treatments to induce R. chinensis ‘Old Blush’ microspores to switch from gametophyte to sporophyte development. This approach allowed microspores to initiate divisions, form homozygous cell clusters and develop embryogenic callus from which homozygous plantlets could be regenerated"

They give the detailed procedure (!) which seems well within reach of amateurs who would then be able to produce homozygotes from pollen grains at will. This would give you the ability to assemble a tailored breeding population. This would be a powerful resource even in a conventional breeding program, and requisite for engineering approaches. If I had the resources I'd be all over this. If anybody from Ball Horticulture reads this please get in touch with me, I've got a proposal for you.

>> scent, recurrent blooming, and color are controlled by some genes that work in opposition to each other

That devil is in the details of Fig. 3: Inter-regulatory connections between color biosynthesis and some scent pathways.

We already knew that carotenoid-derived scent molecules like β-ionone were 'oppositional' simply because carotenoid pigments are their precursors and get depleted as they form. This figure shows the full story to be way more complicated than that. At early steps there is a regulatory ballet in which timing is everything. It's way more complex then the simple model of up-regulation/down-regulation and over-expression by particular genes where you would jigger a single gene to give you, say, more color by brute force.

They only mention the anthocyanins but it is clear from Figure 3 that carotenoids are also affected by the same genetic metronome. They do mention germacrine D with regard to opportunities for manipulating disease resistance.
What doesn't kill them makes them stronger.

henry kuska
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67768Post henry kuska
Tue May 01, 2018 4:49 pm

Another article, same topic:

http://www.bbc.com/news/science-environment-43950743

Since he states: "The rose and the strawberry are very close species," said Dr Bendahmane.", you may find this recent report about strawberries and viruses of interest: http://www.ijset.net/journal/2074.pdf
if you are interested in viruses in roses, I suggest that you do a search for the term rose in this article and see how many strawberry viruses also infect roses.

Karl K
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67782Post Karl K
Thu May 03, 2018 3:03 pm

Peter Harris wrote:
Tue May 01, 2018 9:42 am
The article is pretty technical. It's open access, so you may download a PDF if you wish.
https://www.nature.com/articles/s41588-018-0110-3
Peter
I can usually count on any paper of this kind I read contradicting others I've read. And often enough the authors will neglect relevant facts.
We focused on the modern Rosa × hybrida ‘La France’, which is considered to be among the first created hybrids combining the growth-vigor traits of European species and the recurrent blooming of Chinese species.
Really? What about 'Rose Edouard'?

'La France' is sometimes said to have been descended from a Bourbon, which makes this question relevant. It is also possible that the Tea parent (or grandparent) of 'La France' was descended from 'Blush Noisette' and 'Blush Tea-scented', a well as 'Rose Edouard'. Was there back-crossing to Rosa gallica in the HP line?

And do we know for sure that the Albas and Province roses had no part in the origin of the Monthly Roses?

And let's not forget that 'Old Blush' is also of fairly complex ancestry lost in the dim mists of time. The chromosome pairing is weak enough that it was not of much use for English breeders working in the open air. It bloomed well, but needed more heat.

Don
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67783Post Don
Thu May 03, 2018 3:34 pm

>> I can usually count on any paper of this kind I read contradicting others I've read. And often enough the authors will neglect relevant facts.

The import of this particular paper is still pretty impressive. I think a safe assumption would be that they did not publish all or even most of what they know based on the list of authors which is a who's who of the EuroAg biotech elite. What they did publish puts us on notice of what to expect from French engineers/breeders, in particular, in the future, their separation between public and private sectors being an oxymoron.
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Karl K
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67788Post Karl K
Fri May 04, 2018 11:31 am

Don wrote:
Thu May 03, 2018 3:34 pm
The import of this particular paper is still pretty impressive.
No doubt. But I can appreciate a paper for what it is, while dismissing what it purports to be, but is not.
1) Old Blush is an ancient cultivar, not a species. A homozygous derivative of Old Blush can be used as a reference without also pretending that it truly represents any one species.
2) Hurst regarded Old Blush as being derived (some generations later) from an old hybrid of R. chinensis Jacq. x R. gigantea Collett.
However, Jacquin's species was based on a pitiful fragment of a specimen. Maybe someone could extract a bit of DNA for analysis.
R. gigantea Collett. is also just a guess. There are other giant roses that could have contributed, such as the yellow-flowered R. macrocarpa.
http://bulbnrose.x10.mx/Roses/breeding/ ... t1891.html
http://bulbnrose.x10.mx/Roses/breeding/ ... a1932.html
in particular, in the future, their separation between public and private sectors being an oxymoron.
This is an interesting point that I have noticed through the 19th and early 20th century. The French had no apparent objection to a professional plant breeder like Louis de Vilmorin also commenting on scientific matters. In the U.S., by contrast, any academic scientist who had some interest in the works of Luther Burbank generally kept quiet on the matter.
Karl

Don
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67789Post Don
Fri May 04, 2018 1:49 pm

>> A homozygous derivative of Old Blush can be used as a reference without also pretending that it truly represents any one species.

They call it a progenitor of modern roses - is it?

>> any academic scientist who had some interest in the works of Luther Burbank generally kept quiet on the matter.

That had to do with valuing their reputations rather than any cultural public/private divide. Burbank was less than rigorous. European companies generally, and French ones particularly, are statist to the point of dependency.

>> There are other giant roses that could have contributed

Rob Rippetoe made the point to me when I wrote my 'Fun with Numbers' article years ago that I had omitted gigantea from the major descendency of modern roses. He felt that simple inspection made proved his point and I have to agree with him but it wasn't documented in any pedigree. Figure 2 in this paper seems to prove it along with giving interesting generalized origins for gallicas/damasks and Hume's/Old Blush.

https://www.nature.com/articles/s41588- ... /figures/2
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Karl K
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67790Post Karl K
Fri May 04, 2018 6:17 pm

Don wrote:
Fri May 04, 2018 1:49 pm
>> A homozygous derivative of Old Blush can be used as a reference without also pretending that it truly represents any one species.
They call it a progenitor of modern roses - is it?
'Old Blush' is a putative parent of 'Blush Noisette' and 'Rose Edouard', so I go with YES. Then we should consider the Minis, which spring largely (so to speak) from 'Old Blush'.
>> any academic scientist who had some interest in the works of Luther Burbank generally kept quiet on the matter.

That had to do with valuing their reputations rather than any cultural public/private divide. Burbank was less than rigorous. European companies generally, and French ones particularly, are statist to the point of dependency.
There was also the matter of Anti-Burbankitis (Hansen, 1905), particularly on the east coast. He was accused of fraud by the Rural New-Yorker for his Sunberry (renamed Wonderberry by Childs). They claimed that it was merely the old Garden Huckleberry under a new name. It was not. I have grown both, and the Sunberry is well worth having. I will never put another Garden Huckleberry in my mouth. There is also the matter of credibility. Some academic "scientists" of his time insisted that interspecific hybrids were necessarily sterile, and intergenerics impossible. Burbank proved them wrong "not once, but scores of times", and was accused of being "less than rigorous". I have even read accusations that Burbank never covered the flowers after he pollinated them. But he did. I saw him do it. Not in person, of course. But at the Burbank House they play a video showing him pollinating a lily. In practice, though, he usually did not bag them because, in his climate, any sort of covering increased the risk of fungal attack. (To the contrary, Percy Wright bagged his flowers to protect them from the drying winds.)
http://bulbnrose.x10.mx/Heredity/Hansen ... k1905.html
http://bulbnrose.x10.mx/Heredity/Burban ... berry.html
http://bulbnrose.x10.mx/Heredity/Burban ... amens.html
>> There are other giant roses that could have contributed

Rob Rippetoe made the point to me when I wrote my 'Fun with Numbers' article years ago that I had omitted gigantea from the major descendency of modern roses. He felt that simple inspection made proved his point and I have to agree with him but it wasn't documented in any pedigree. Figure 2 in this paper seems to prove it along with giving interesting generalized origins for gallicas/damasks and Hume's/Old Blush.
Good for Rob.
Gardening in China has ancient roots. To what extent were foreign (e.g. Indian, Burmese, etc) roses imported and added to the mix? A striking color from here, a semi-double from there, or a rare hybrid standing out among its cousins: all brought together in the royal gardens (perhaps). Drifting pollen, whether in the wild or in gardens, brought genes from R. luciae and R. multiflora , and others, together to give us the little Crimson China (which Slater did not import).

We have seen only a tiny fraction of the roses cultivated in China centuries ago.

China's biodiversity: a country study, pp. 185-186 (1998)
Weiping Zhang, China. Guo jia huan jing bao hu ju
"Because modern overseas rose cultivars are more preferred to traditional roses by Chinese people, old China rose cultivars are becoming fewer. During the 1950's, there were at least 200 Chinese traditional rose cultivars in gardens and parks (some 60 cultivars at Yanling, Henan Province) alone. Today, old cultivars are not commonly seen, only less than 100 traditional ones surviving. If not remedied or saved, the motherland of roses is becoming full of modern rose cultivars (from over 95% to nearly 100%) except for a few fine traditional cultivars."

The handful of "stud" Chinas that reached Europe are of great importance to the later development of modern roses. But we cannot assume that they were representative of what we did not receive. It was presumptuous to suppose that the Crimson and the Pink were merely color variants of a single species. And it was a confusion of common names that led to the myth that Parks just happened to carry home a yellow "variety" of the Tea-scented rose.

Having only a few examples of China roses, Europeans lumped them into a collective species based largely on rebloom.

Don
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67791Post Don
Fri May 04, 2018 7:27 pm

>> Today, old cultivars are not commonly seen, only less than 100 traditional ones surviving.

Hmm. I wonder if Quarryhill has any of them or if an organized effort exists to preserve them.
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RBaxter
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67793Post RBaxter
Sat May 05, 2018 2:58 am

Interesting paper. The genomics methods are bit beyond me, and I wonder why they didn't work with egg cells.

Even if we are talking non-species diploids, how would the genes from a homozygote produced from a pollen grain statistically differ from a self? (other than missing the mitochondria and chloroplasts)

I also think that most of us that have raised enough seedlings are already innately aware of the complex genetic competition between color, fragrance, and disease resistance, and would appreciate any help we could get.

I'm all for the advancement of knowledge. This paper looks to me like another nice step forward to the eventual use of tools like CRISPR/Cas-9 and future genetic instruments on our roses. I just hope those tools are not also used to build in sterility along with the positive advancements.
Katy TX Zone 9A

Karl K
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67845Post Karl K
Mon May 14, 2018 3:22 pm

RBaxter wrote:
Sat May 05, 2018 2:58 am
I'm all for the advancement of knowledge. This paper looks to me like another nice step forward to the eventual use of tools like CRISPR/Cas-9 and future genetic instruments on our roses. I just hope those tools are not also used to build in sterility along with the positive advancements.
It sometimes pains me to think of the plant breeders who have spent so much time and effort breeding roses (etc.) that are hardy and healthy, while also being pretty and fragrant. How many tens and hundreds of thousands of seedlings have been raised just to get a few worthy selections?

And when they give us something really terrific, there is nothing to stop us from using their triumphs to build our own.

But thanks to the wonders of gene-splicing, anything the does come out of the lab will be stamped with a patent that wll last until sometime in the next century. Not the cultivar, which is only entitled to a plant patent, but the gene itself. Intellectual property!

Imagine how wealthy would the Kordes. Meilland and McGredy families would be today if they got a royalty for every offspring, grand-offspring, great grand-offspring, descended from their patented roses.

Don
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67848Post Don
Tue May 15, 2018 1:41 am

>> Imagine how wealthy would the Kordes. Meilland and McGredy families would be today if they got a royalty for every offspring, grand-offspring, great grand-offspring, descended from their patented roses.

Conversely, if they had the full knowledge of the rose genome along with crispr then would we need to be breeding roses at all? At some point soon will we be flooded with designer roses?
What doesn't kill them makes them stronger.

Karl K
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Re: The Rosa genome and insights into domestication of modern roses

Post: # 67880Post Karl K
Sat May 19, 2018 9:51 am

Peter Harris wrote:
Tue May 01, 2018 9:42 am
The April 30, 2018 issue of Nature Ge­­­netics contains a study which concludes (this is a very simple summary that I hope is accurate) that scent, recurrent blooming, and color are controlled by some genes that work in opposition to each other, and that breeders' emphases on color and recurrent blooming have sacrificed fragrance. The study reports discovering new candidate genes for recurrent blooming. By using these genes which are not antagonistic to fragrance, breeders may find ways to get around this trade-off of fragrance for recurrence and color.
Peter
Le Grice also observed a correlation between color and perfume, even going so far as to speculate that the anthocyanin pigments could serve as catalysts.
Orris-violet is a perfume obtained from the dried rhizomes of some iris. Diluted by air, this gives an odour of violet and is present in a number of roses both as a predominant factor and in combination with the type called "nasturtium". Among those possessing an orris perfume it appears that the salmon colour in the petal acts as the catalyst. Because of the vast increase in the orange-salmon roses this has become a more usual although recent addition. It is a sharp lingering perfume often in combination. The strongest perfume may be found in Orange Sensation, while Salmon Sprite and Elizabeth of Glamis are good examples of this strong and penetrating perfume. Examples of damask-orris are My Choice and Dearest, while the very fragrant Blue Moon maybe described as lemon-orris.
Damask This is the strong, sweet, heady perfume which has been associated with roses as a whole. It is largely confined to reds and pinks with a magenta base.
http://bulbnrose.x10.mx/Roses/breeding/ ... rice3.html

Regarding the Nature Genetics paper, I see that chromosome 1 has two loci for GT1, the enzyme responsible for anthocyanidin 3,5-diglucoside. Assuming that there are at least two alleles for each locus, these alone at least 5 shades of red (allowing white as a shade). However, the authors don't mention whether the (at least) two forms of anthocyanidin 3-O-glucosyltransferase are derived from different alleles of the same gene.

Monoglucosides of anthocyanin pigments are common in roses, but those that appear only after the flowers open appear to be derived from the Chinas. 'Old Blush' shows a trace of this; the flowers developing a pale purplish flush. In shade, and in cool weather, this purplish tinge does not develop. The same is true of some dwarf polyanthas, such as 'Margo Koster' and 'Golden Salmon', that are clearer orange in shade or cool weather.

The more vivid examples of the light sensitive form of anthocyanidin 3-O-glucosyltransferase can be seen in the "chameleon" roses, such as 'Mutabilis', 'Emmie Gray', 'Color Magic', 'Mark Sullivan' and many otheres.
Karl

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