Karl
What do you consider being evolution then?
And for roses?
Don,
The term “Genomic Shock” was coined by Barbara McClintock and discussed in her Nobel Lecture, ‘The Significance of Responses of the Genome to Challenge’.
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintock-lecture.pdf
The general concept was discussed previously. The fact that many wild plants varied spontaneously when brought under cultivation was well-known in the 19th century. O. F. Cook (1907) called this aspect of the phenomenon ‘Neotopism’.
“Differences under New Conditions (Neotopism).—Variations induced by the transfer of organisms to new and unwonted conditions. Three stages of new place effects may be distinguished, (1) those in which there is merely a stimulation of growth, (2) those in which there is also a definite mutative change of the hereditary characteristics of the variety, (3) those in which the new conditions call forth a promiscuous mutative diversity.”
Clausen (1959) discussed an interesting example from Cooper (1954). The rye grass ‘Wimmera’ is a “highly purified” strain. But when the seed was sown in a heated greenhouse under continuous light, the plants varied dramatically as to the time of flowering.
http://bulbnrose.x10.mx/Heredity/Clausen/Clausen_wimmera.html
Durrant (1958) wrote of his experiments with flax. Seedlings of an inbred strain were treated to different combinations of chemical fertilizers. Not only did the various treatments produce alterations of the plants, two of the treatments produced changes that were inherited for at least 4 generations with no further application of fertilizer.
http://bulbnrose.x10.mx/Heredity/Durrant/Durrant58.html
This research was continued by Durrant, and later by Cullis (1973) who found that the “large genotroph” that resulted from the NPK treatment had 16% more DNA than the small.
http://bulbnrose.x10.mx/Heredity/Cullis/Cullis1973/Cullis1973.html
And more in 1986.
http://bulbnrose.x10.mx/Heredity/Cullis/Cullis1986/Cullis1986.html
And in 1991.
http://www.genetics.org/content/128/3/619.full.pdf
Henikoff (2002) provided more info:
http://www.plantcell.org/cgi/content/short/17/11/2852
And in 2005:
Yiming Chen, Richard G. Schneeberger, Christopher A. Cullis (2005)
A site-specific insertion sequence in flax genotrophs induced by environment
New Phytologist 167 (1), 171–180.
• A single-copy 5.7 kilobase (kb) DNA fragment, termed Linum Insertion Sequence 1 (LIS-1), has been identified and characterized. This is one of the DNA changes associated with the environmentally induced heritable changes resulting in stable lines termed genotrophs in flax (Linum usitatissimum).
• The insertion sequence and its insertion site have been cloned from genomic libraries and sequenced. PCR products across the insertion and surrounding regions have also been cloned and sequenced.
• The 5.7 kb DNA fragment is inserted into a 3.7 kb EcoRI fragment in the plastic line (Pl) with the generation of a 3 base pair duplication at the insertion site, as well as additional sequence changes. The identical insertion was also found in other genotrophs and flax varieties. The intact element was not present in Pl but appeared to be generated by a reproducible series of complex rearrangements or insertion events.
• LIS-1 is the result of a targeted, highly specific, complex insertion event that occurs during the formation of some of the genotrophs, and occurs naturally in many flax and linseed varieties.
Genomic shock is often (always!) accompanied by an overall reduction in methylation. This is what can release silenced transposons, as occurs in crosses with ‘Black Mexican’ sweet corn. In other cases, de novo methylation may occur.
New polyploidy can produce a shock of its own.
THE ROYAL SOCIETY Published online 15 May 2003
Do the different parental ‘heteromes’ cause genomic shock in newly formed allopolyploids?
Luca Comai, Andreas Madlung, Caroline Josefsson and Anand Tyagi
“Allopolyploidy, the joining of two parental genomes in a polyploid organism with diploid meiosis, is an important mechanism of reticulate evolution. While many successful long-established allopolyploids are known, those formed recently undergo an instability phase whose basis is now being characterized. We describe observations made with the Arabidopsis system that include phenotypic instability, gene silencing and activation, and methylation changes. We present a model based on the epigenetic destabilization of genomic repeats, which in the parents are heterochromatinized and suppressed. We hypothesize that loss of epigenetic suppression of these sequences, here defined as the heterome, results in genomic instability including silencing of single-copy genes.”
http://rstb.royalsocietypublishing.org/content/royptb/358/1434/1149.full.pdf
It has also been learned in recent years that aneuploidy can have “shocking” effects, even in humans. This was found in a rare case of monozygotic twin boys. One was “normal” while his brother had an extra copy of chromosome 21 and expressed Down’s Syndrome. The symptoms of Down’s previously thought to be due to the expressions of those extra genes. In fact, the chromosome provoked a genome-wide alteration in gene expression.
http://www.alzforum.org/news/research-news/downs-syndrome-loosens-regulation-entire-genome
Polyploidization also produces a genomic shock. Matsushita et al. (2012) also discussed the role of aneuploidy in regards to Arabidopsis allohexaploids.
“Despite the current lack of data explaining the underlying molecular reasons for phenotypic variation in the allohexaploid sibling lines, our analysis brings up several important points. First, we have shown that allopolyploidization in a cross between A. thaliana and A. suecica does not produce a single homogeneous population but leads to an aneuploid swarm that displays cytogenetic heterogeneity, phenotypic variation, and variability in individuals’ fertility. In a relatively short period of time, lines have begun to separate from each other, displaying typical new chromosome numbers and phenotypic characteristics.”
I suppose the aneuploidy would eventually subside in a wild population, but the temporary (?) phenotypic variation resulting from the aneuploidy could allow newly formed polyploids to find and settle into new habitats before stabilizing on “normal” chromosome numbers.
Song, et al. (1995) reported the accumulation of variability among the progeny raised from tetraploids bred from Brassica rapa, nigra and oleracea.
“Using synthetic polyploids, we have demonstrated that extensive genome change can occur in the early generations of Brassica polyploids. Genetic diversity accumulated among self-fertilized progenies, even when the starting materials were completely homozygous. We do not know whether these types of changes or this extent of change has occurred in the early generations of natural Brassica or other polyploid species. However, our molecular results, when combined with variation in fertility and other morphological traits observed in our synthetic polyploids and in previous studies (26, 27), suggest that rapid genome change in newly formed polyploids can produce many novel genotypes that would provide new genetic variation for selection. Thus, rapid genome change could accelerate evolutionary processes among progenies of newly formed polyploids, and this may, in part, account for the success and diversification of many ancient polyploid lineages in both plants and animals.”
http://www.public.iastate.edu/~mbhattac/bhattacharyya/Song.pdf
If you need more examples, I have a bibliography with some more interesting cases.
http://bulbnrose.x10.mx/Heredity/King/Acquired.html
The corn people capitalized on McClintock’s work starting very early on after she published her PNAS paper in the 1950’s. How can we rose breeders use the concepts in our efforts considering, too, that this idea of genetic shock has been superseded, really, by more specific, mechanistic explanations such as you point out like methylation, RNAi and other mostly control-type phenomenon?
Don,
“Superseded”? Changes in RNAi and methylation follow the shock, but my question is, What is being shocked? It seems that you are looking for a static explanation of a dynamic process.
As for applications, some of the oldest are still useful. In the early 19th century, Van Mons outlined his system of plant breeding. He collected UNRIPE fruit and allowed them to ferment before sowing the seeds in NOVEL ENVIRONMENTS (i.e., seeds from forest trees were sown in his nursery). The plants were grown somewhat CROWDED, closer than such plants are commonly grown. Shortening the LEADS. He emphasized the importance of FIRST FRUITS (and the seeds they contained), and the SUCCESSIVE SOWING, generation after generation without interruption.
Each of these items has merit, though not all involve a shock. For instance, crowded plants tend to produce fewer branches and to grow up more than they grow out. Shortening the laterals would also encourage this. And as it happens, maturity occurs first at the top of the plant. This is important to promote early sexual maturity, which is particularly useful when working with once-blooming species and varieties. Immature fruit also tend to produce earlier maturing plants.
Prokofyeva-Belgovskaya (1947) worked with fruit flies, but the hereditary principles probably apply to plants as well. She found that the percent of heterochromatin increased with age, and was partly inherited. That is, the offspring of old flies began life with a greater percentage of heterochromatin than did their older siblings raised from the same parents when they were young. She did not go beyond the first generation, differences in percent heterochromatin would be consistent with Van Mons’ observation that seedlings raised from first fruits were more variable than those from old parents.
P-B also found that percent heterochromatin and the expression of certain traits were influenced by environment. In one experiment eggs were laid at a standard temperature (25°C) then some were transferred to lower (14°C) and others to higher (30°C) temperatures.
“Under standard conditions (25° C.) the percentage of heterochromatization of the 1AB 1-20ABC region of the sc8 chromosome of this stock is 71. In larvae transferred to 14° C. after 6 hr. it is 33. Thus heterochromatization is suppressed when development proceeds at the low temperature. The high-temperature experiment gave very similar results. The percentage of heterochromatization in larvae transferred to 30° C. after 6 hr. was 37, and was thus again decreased.”
Again, she did not carry the experiment beyond the first generation. She merely assumed that the higher or lower temperature directly suppressed heterochromatization. The fact that the ancestors had been maintained at the “standard” temperature suggests to me that it was the CHANGE in temperature that provoked a “shock”, allowing an alteration in gene expression which would (if the experiment had been continued) have resulted in a different pattern of heterochromatin in high and low temperature strains.
Another shock can be produced by geographically isolated specimens of the same species.
Michurin (1932)
Already in the 1900’s, while working on hybrid varieties of yellow cigarette tobacco, the Kommunarka early-ripening melon and hardy grape seedlings—the first to be produced in those days—I was agreeably surprised, when selecting seedlings that completed their vegetative development earlier than others, to find that some of the seedlings that had germinated from seed later than others, namely, at about the beginning of July, managed to complete their growth and mature even earlier than those that had germinated in the middle or beginning of May.I made a note of this marked, and at the same time rather paradoxical, phenomenon, and in subsequent years I never failed to keep watch for similar manifestations in interspecific hybrids of other plants. It turned out that this phenomen is in most cases to be met with in hybrids from parents whose habitats were very far apart, and that, on the contrary, it is practically never encountered in simple seedlings or in hybrids from varieties of one and the same species coming from mutually close places of origin. This, of course, could only be explained by the fact that hybrids of parents of mutually remote places of origin are always far more susceptible to alteration of their properties under the influence of the environment than are simple seedlings or hybrids from parents whose birthplaces were not far apart. It is more difficult to find convincing reasons for the acceleration of the vegetative period in seedlings that germinate late from the seed.
Darlington (1958)
Two geographically separated varieties of > Hordeum sativum > give a vast array of segregation in their progeny which is not seen when parents with similar differences of form come from the same region.
Darlington rarely had a kind word for anyone outside his small circle, and was particularly hostile towards Michurin. He would be appalled to be quoted in agreement with Michurin.
Putting these items together, it seems likely that someone interested in breeding with species should start by crossing geographically isolated specimens of the species, collecting the hips before ripe, allowing the hips to ferment before separating the seeds. If possible, raise a second generation from the first fruits of the first. All this before attempting to mate the “softened” species with cultivated plants.
I should not that there is some evidence that mutations can provoke a degree of shock as the plants (or cells) scramble to accommodate the change. So, if the species usually has pink flowers, one might cross a white-flowered mutant with a geographically remote red-flowered selection. Or with a double.
On the other hand, if you want to skip the old methods and attack methylation directly, you might try methyl-antagonists like 5–azacytidine (a cancer drug) or ethionine (an analog of methionine, which is a methyl-donor).
Karl
PS. Adventitious shoots arising from root cuttings (or stems without buds) are also prone to “shock” symptoms.
Proceedings of International Workshop on Sweetpotato Cultivar Decline Study. Sept. 8-9, 2000. Miyakonojo, Japan
Mutations in Sweetpotato
D. R. La Bonte, A. Q. Villordon, and D. S. Fajardo.
“Fundamentally, preformed meristematic cells give rise to plants that are more genetically stable (Potter and Jones, 1991). Meristematic tissues provide strict control of cell division processes and minimize genomic changes (Sree Ramulu, 1987). Gould (1984) identified differences in the duration of cell cycles in meristematic and non-meristematic cells. The disturbance in cell cycles cause delays in DNA replication in heterchromatic regions (slower to replicate) and result in genetic variation (Lee and Phillips, 1988). Late replication of heterochromatin is hypothesized as the mechanism explaining chromosome breakage (Phillips, et al., 1994). Cells simply divide before the completion of DNA replication. Broken fragments that do not rejoin cause deletions while reunion of fragments lead to translocations, inversions, duplications, and deletions.”
Potter, R. and M. G. K. Jones. 1991. An assessment of genetic stability of potato in vitro by molecular and phenotypic analysis. Plant Sci. 76: 239-248.
Sree, R. K. 1987. Genetic instability during plant regeneration in potato: origin and implication. Life Sci Adv (Plant Physio.) 6: 211-218.
Gould, A. R. 1984. Control of the cell cycle in cultures plant cells. CRC, Crit. Rev. Plant Sci. 1: 315-344.
Lee, M., and R. L. Phillips. 1988. The chromosomal basis of somaclonal variation. Annual Review of Plant Physiology and Plant Molecular Biology 39: 413-437.
Phillips, R. L., S. M. Kaeppler, and P. Olhoft. 1994. Genetic instability of plant tissue cultures: breakdown of normal controls. Proc. Natl. Acad. Sci. USA 91: 5222-5226.
i am looking for R. macrophylla ‘Korolkowii’ (4x). Can anyone help me?
I am from Calcutta, India.
I read in Dr. Major C C Hurst work and hope this has potentials to give us roses that could grow in areas with heavy rainfall.
Please post your comment here or reply to me on my email biogrow@vsnl.net