Rose Genome and the Possibility of (almost) Inseparable Traits

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RBaxter
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Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68347Post RBaxter
Sun Sep 23, 2018 11:51 pm

If we assume that Mother Nature prefers to use the formerly called "junk DNA", non-protein coding sections of the DNA as breakpoints during gene swapping as chromosomes align and swap chunks, then it stands to reason that by proximity some traits would be harder to separate than others. If that holds water, that might explain a lot of our difficulties.

If I'm restating what has already been posted I apologize, but this just dawned on me tonight as I was harvesting achenes. I've always wondered why the long stretches of non-coding DNA exist. It makes evolutionary sense to me to use those as safer "scissor points" instead of important coding sections.

Any thoughts on how this seems apparent in our roses?

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RBaxter
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68348Post RBaxter
Mon Sep 24, 2018 12:15 am

it's been over forty years since I took a biology class, but this would explain the importance of bringing species roses back into the gene pool. Over time, in different species, I can see how both desirable and undesirable genes could become either more or less "separable".
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Jwindha
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68354Post Jwindha
Tue Sep 25, 2018 2:42 pm

What you're referring to is called "linkage". The closer two genes are on a chromosome, the less likely it is that they will be separated by recombination. "Linkage Drag" occurs when a lot of unwanted genes are passed on to progeny due to their close proximity to a desirable gene.

johannesp
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68355Post johannesp
Tue Sep 25, 2018 4:59 pm

Since for the most part modern breeders are using tetraploids in rose breeding it makes it harder to recover recessive genes. A similar result but different cause.

Karl K
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68360Post Karl K
Wed Sep 26, 2018 3:09 pm

RBaxter wrote:
Sun Sep 23, 2018 11:51 pm
If we assume that Mother Nature prefers to use the formerly called "junk DNA", non-protein coding sections of the DNA as breakpoints during gene swapping as chromosomes align and swap chunks, then it stands to reason that by proximity some traits would be harder to separate than others. If that holds water, that might explain a lot of our difficulties.
I won't go into detail, but much of the so-called "Junk DNA" contains little snippets of DNA that are transcribed as very small but useful RNA segments. This is part of RNAi (RNA interference), and includes small interfering (siRNA) and micro interfering (miRNA), which do different things related to gene regulation.

Then there are the RNA transcripts that are tiny "weapons" in the battle for conquest between euchromatin and heterochromatin. As I understand the process (no bets as to compete accuracy), each type emits (so to speak) RNA bits that encourage the other type to convert. Eu-Het boundaries are famously unstable, and it has long been known that B chromosomes (i.e., "fragments") are heterochromatic, and their presence in the cell increases the percentage of heterochromatin in the other chromosomes.

This also relates, just a bit, to the matter of apparent linkage between traits. It would be better to call this business "correlated expression", because the "linkage" is due to structural similarities between RNA transcripts of the genes rather than proximity. In other words, the interfering RNA bit (which is very small) might find a matching segment of RNA transcripts from two very different genes, and block (or promote) both together.

I started to draw an analogy with telephone party lines, then realized that I was dating myself.
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68367Post Karl K
Thu Sep 27, 2018 12:50 pm

A little clarification:
Biochem Soc Trans. 2008 Dec;36(Pt 6):1224-31.
How do microRNAs regulate gene expression?
Cannell IG1, Kong YW, Bushell M.
Abstract miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3'-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing. The exact mechanism of miRNA-mediated translational repression is yet to be fully determined, but recent data from our laboratory have shown that the stage of translation which is inhibited by miRNAs is dependent upon the promoter used for transcribing the target mRNA. This review focuses on understanding how miRNA repression is operating in light of these findings and the questions that still remain.

Don
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68369Post Don
Fri Sep 28, 2018 1:58 am

So do we know which traits are linked in roses, mechanisms aside?
What doesn't kill them makes them stronger.

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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68370Post Karl K
Fri Sep 28, 2018 12:18 pm

Don,
Before starting on your question, I need to mention statistical correlations. Two traits may not be linked at all, but still appear to be loosely linked because they were derived from the same ancestor. In the first several generations the two traits may often show up together unless that has been deliberate selection against their association.

For example, it was long believed that Rosa foetida had a particular susceptibility to blackspot. Further observation revealed that Foetida is a short season grower that naturally goes dormant by summer. Thus, it normally would avoid BS by dropping its leaves.

The association of short-lived leaves with a long growing/flowering season might have been disrupted much earlier, but Pernet-Ducher lived in a region where BS was not a problem.

The tendency of Foetida-derived roses to suffer from "winterkill" is not proof of an inherent sensitivity to frost. Rather, some of these are too anxious to start growing in late winter ... like their ancestor. Unfortunately, these Pernetiana/HT derivatives inherit the thick, succulent new growth of the Tea and HP ancestors rather than the very slender, pithy Foetida canes.

As for useful linkages, I think there has not been enough research. There are people who grow seedlings on a large enough scale to get good data. But they are too busy selecting commercially valuable selections to pay for all their efforts.

The people who might be interested usually don't have the scale or operation or statistical tools needed to identify linkages and/or correlations.

Some groups of apparently linked traits were identified almost a century ago by C. C. Hurst. Critics refused to look at his data because they were convinced (without evidence) that ALL traits must re-assort without restriction. But it is amusing to note that one of Hurst's harshest (and least rational) critics was C. D. Darlington, who later discussed in Rubus precisely what Hurst had described in Rosa. Of course, Darlington never acknowledged Hurst's priority.
Karl

Don
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68371Post Don
Fri Sep 28, 2018 1:55 pm

>> For example, it was long believed that Rosa foetida had a particular susceptibility to blackspot. Further observation revealed that Foetida is a short season grower that naturally goes dormant by summer. Thus, it normally would avoid BS by dropping its leaves.

I missed this paper. Do you have a citation or can you send me a copy?
What doesn't kill them makes them stronger.

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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68373Post Karl K
Fri Sep 28, 2018 3:00 pm

The Rose Manual (1933) 265-268
J H Nicolas
Rose Infections
Summer defoliation is not always due to disease, although diseases will precipitate it. Summer defoliation did not bother our fathers before the introduction of Austrian Briar blood. Austrian Briars will lose their foliage early because it matures early. It is the nature of the beast that nothing can change, and all their hybrids inherit that character in a greater or lesser degree. When the foliage is mature, the "cortex" or film of corky material that heals the pores where the leaf is attached to the branch begins to form, the leaf receives less and less nutrition from the plant and drops at the least provocation, spray or dust notwithstanding. Some varieties when plants are healthy will push on new leaves at the top as fast as the bottom ones drop and the plant retains its "activity," but if the defoliation is premature and accelerated by disease faster than new foliage can be produced the plant goes dormant. Pernetianas are at best in regions of long vegetative season, like southern France, the birthplace of the race, divided in two distinct growing periods — an early spring and a long springlike autumn intervened by a hot summer, because there is enough growing weather when they awake from their summer rest enforced by natural defoliation to come again to a useful life, and the new growth has time to mature before winter, if winter there is. Pernetianas are out of place as autumn bloomers where the season is short between a late spring and an early winter.

Black Spot starts from the inside, but is induced and spread by outside atmospheric conditions. As proof of this Cochet offers the argument that black spot always attacks the older leaves as they mature. If it did start from outside it would attack the soft new foliage just as mildew does, but the moisture inside young foliage is in rapid motion to and from the roots and has no time to mold even when inoculated until that motion slows down in the process of maturity. Black spot is intimately related to the innate persistence of foliage, as above stated; long-lived foliages, such as pure Teas and species evergreen in their native habitats are immune. As Lambert said, "Have you ever seen black spot on bracteata, sempervirens, Cherokee?" When Pernetiana foliage has reached near maturity and the weather is humid, the moisture inside the leaves is not evaporated fast enough nor reabsorbed by the plant, and a fungus or mold forms just as clothes fresh from the aseptic laundry process will mold if put away moist.

Although black spot starts inside, the fungus fruits outside through punctures, and infection spreads rapidly to foliage already in process of maturing, there finding a fertile ground even if weather conditions were then normal for proper evaporation of excess moisture in the leaf tissues. This foliage has to be kept insulated by some medium. They do not like dust over there [in Europe] but prefer copper sprays. Another point brought to me to support that theory is that true Hybrid Teas do not take the spot until very late (if they do at all), when part of their foliage has naturally matured, which process is much later than Austrian Briar hybrids. Where summer weather is normally sultry, stick to the old line Hybrid Tea.

A Rose Odyssey (1937)
J. H. Nicolas
p. 12
Pernet was also well aware that his Pernetiana strain was not as universally adaptable as the Hybrid Tea. He did not expect it to conquer the world. He often remarked that he did not recognize his roses in Paris, less than three hundred miles away. He was an artist working primarily for his own enjoyment. The climate or atmosphere of Lyons is what we might call "anti-black spot." Why, I do not know, but I suspect that soil alkalinity has something to do with it. He never knew what the accursed disease was until I showed him an infected leaf which it took me hours to find. This may be the reason why Pernet stuck so closely to his own original strain. I received today a catalogue from another firm at Lyons. In the rose-growing instructions the catalogue mentions mildew and rust, but not black spot. Happy country!

pp. 157-158
Lambert believes that black spot starts as "an old age infirmity", because Austrian briar, which is on one side of the family of most susceptible varieties (Pernetianas), is a species of short-lived foliage. He says that the foliage gets prematurely old, ceases to function properly and becomes diseased. The spores then spread to younger foliage and defoliation occurs if the climatic conditions are propitious to the multiplication of spores. Lambert, corroborated by Father Schoener, claims that a strain of immune roses can be produced from species with long-lasting foliage, as experience has proved that evergreen and ever-growing types such as R. bracteata, R. longicuspis, R. glomerata, R. gigantea macrocarpa, etc., are absolutely immune to leaf diseases. He also believes that a careful selection of breeders in the mixed Hybrid Tea and Pernetiana classes would help in bringing about a more resistant strain.

Karl K
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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68442Post Karl K
Wed Oct 10, 2018 8:51 pm

I almost forgot to add this note. It shows that the loss of foliage can be inherited, without regards to disease.

The Rose Annual pp. 106-113 (1972)
The Development of Modern Yellow Roses
E. B. LE GRICE
I would like to pause here, as a personal experience might help the reader to appreciate the difficulty still besetting the raiser in his search for color-consistency combined with satisfactory growth. My first true yellow was 'Yellowcrest', '35. It was a true, shining gold on a fairly strong plant, but with very thorny wood. It promised to be thoroughly good and then, without warning, after its first flowering it shed its leaves (as I have seen 'Austrian Yellow' do). It broke into growth once more and flowered freely in the autumn only to repeat the process.

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Re: Rose Genome and the Possibility of (almost) Inseparable Traits

Post: # 68454Post Ophiophagus hannah
Sat Oct 13, 2018 12:59 am

RBaxter, I guess those "junk DNA" are like "Motherboard socket".

According to the theory I have learned, there is nothing random about any portion of evolution. And the evolution of Plants is related to their consciousness. The Genetics we learned is not complete (and partially correct). We now have no ability to understand the "complete one", because it is Involving different levels of time and space.

I guess the "Inseparable Traits" may not exist, for consciousness can change "Reality".

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