Why plant clones aren't identical.......

[Oregonism]

They were using Arabidopsis [which has been covered here before] but I was looking for thoughts?

How can this pathway be expressed chemically?

Why Plant 'clones' aren't identical - University of Oxford
29 Jul 11
A new study of plants that are reproduced by ‘cloning’ has shown why cloned plants are not identical.
Scientists have known for some time that ‘clonal’ (regenerant) organisms are not always identical: their observable characteristics and traits can vary, and this variation can be passed on to the next generation. This is despite the fact that they are derived from genetically identical founder cells.
Now, a team from Oxford University, UK, and King Abdullah University of Science and Technology, Saudi Arabia, believe they have found out why this is the case in plants: the genomes of regenerant plants carry relatively high frequencies of new DNA sequence mutations that were not present in the genome of the donor plant.

The team report their findings in this week’s Current Biology.

‘Where these new mutations actually come from is still a mystery,’ said Professor Harberd. ‘They may arise during the regeneration process itself or during the cell divisions in the donor plant that gave rise to the root cells from which the regenerant plants are created.

http://www.ox.ac.uk/media/news_stories/2011/110729.html

 

[Avinash.miles]

interesting read, kool that they are still studying this.
thanks for sharing

 

[dizzlekush]

Im just gonna point out that they're talking about plant tissue culture regeneration as "cloning", not the simple rooting of cuttings most of us do. Id imagine why cannabis clones can get what some have dubbed "genetic drift" is due to simple phenotypic plasticity, not whats being discussed in this thread.

Here's the study referenced in the article:
Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes
Caifu Jiang, Aziz Mithani, Xiangchao Gan, Eric J. Belfield, John P. Klingler, Jian-Kang Zhu, Jiannis Ragoussis, Richard Mott, and Nicholas P. Harberd
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162137/

And a notable excerpt from the discussion:

There are two possible nonexclusive explanations for this observation. First, callus phase growth and/or in vitro regeneration from tissue culture might be inherently mutagenic. This first explanation may be supported by previous observations that somaclonal variant phenotype frequencies increase in proportion to the duration during which cells are maintained in tissue culture [25]. Second, mutations in regenerant plants might reflect somatic mutations that existed in the cells of the initial root explant prior to in vitro regeneration, with these somatic mutations comprising a molecular mutational spectrum differing from that of spontaneous “germline” mutations. This second explanation may be supported by the observation that somatic mutation rates are characteristically higher than germline rates in multicellular organisms [26] and has important particular potential consequences for the evolution of plants, given that they frequently adopt life cycle strategies that involve regeneration from somatic tissues.

And the same thing in rice, except that there was ~250 FOLD greater mutation rate found in this study:

Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing.
Miyao A, Nakagome M, Ohnuma T, Yamagata H, Kanamori H, Katayose Y, Takahashi A, Matsumoto T, Hirochika H. Source

Somaclonal variation is a phenomenon that results in the phenotypic variation of plants regenerated from cell culture. One of the causes of somaclonal variation in rice is the transposition of retrotransposons. However, many aspects of the mechanisms that result in somaclonal variation remain undefined. To detect genome-wide changes in regenerated rice, we analyzed the whole-genome sequences of three plants independently regenerated from cultured cells originating from a single seed stock. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were detected in the genomes of the regenerated plants. The transposition of only Tos17 among 43 transposons examined was detected in the regenerated plants. Therefore, the SNPs and indels contribute to the somaclonal variation in regenerated rice in addition to the transposition of Tos17. The observed molecular spectrum was similar to that of the spontaneous mutations in Arabidopsis thaliana. However, the base change ratio was estimated to be 1.74 × 10(-6) base substitutions per site per regeneration, which is 248-fold greater than the spontaneous mutation rate of A. thaliana.

 

[Avinash.miles]

even better, thanks DK

 

[vapedg13]

I dont know about all that scientific BS..... I can tell ya I have been growing this strain since 1993 and it is just as good today as it was 20 yrs ago.

I believe that just as long as the mother or doner plant is healthy and shows no issues that the clones will always be the same .....over 100 times clone of a clone

 

[dizzlekush]

I dont know about all that scientific BS..... I can tell ya I have been growing this strain since 1993 and it is just as good today as it was 20 yrs ago.

I believe that just as long as the mother or doner plant is healthy and shows no issues that the clones will always be the same .....over 100 times clone of a clone

View Image

No offense buddy, but you're posting in the wrong sub-forum then. This sub-forum is all about the "scientific BS".

 

[SeaMaiden]

Oregonism, let me find the thread on genetic drift. I got some learn on there.

https://www.icmag.com/ic/showthread.php?t=248249&highlight=genetic+drift

 

[Crusader Rabbit]

Yeah, that "genetic drift" thread. In that thread were referenced the above article about mutations after separating tissue from the donor plant. SeaMaiden referenced an article that showed genetic variability between tissues in different parts of Cottonwood Trees. This could result in differences between cuttings from the same donor. I posted a link to an article about how stress induced epigenetic change has explained the phenotypic differences between populations of Poplar Tree clones.

Here's my link

http://blogs.discovermagazine.com/8...pigenetics-makes-clones-diverge/#.UM9T-mdefEU

What ever is going on, I'm not sure that "genetic drift" is the proper term for this situation.

 

[purple_man]

yepp folks, listen to dizzlekush! they are speaking about in vitro cultures of callus (totipotent stemcell "clumps"), which when regenerated to a shoot, rooted and grown will have a high probability of being different then the motherplant. also different cultivars are differently prone to somaclonal variation.

blessss

 

[Granger2]

"Scientific BS?" Hhrumph!

I don't know what the proper terms are for the variance I've experienced. Twice I've seen dramatic change with cuttings from Nirvana Bubblicious. Once, with no apparent inordinate stress, a cutting finished distinctly and beautifully blue. All others since then have been normal and more potent than the blue individual.

The other, which I attribute to stress from Root mofo Aphids, was sex reversal. This was not a hermi, it was a shonuff male. His twin sisters, stressed also, were shonuff females. These plants were seriously stressed, healed, and finished as healthy females. I didn't allow the male to finish, but it was loaded with nanners and nanners only. -granger

 

[Avinash.miles]

check dansbuds entry in the yogurt cup challenge
got a crinkley leaf mutation thats a considerble drift from its mother that he has pics of ... it happens, not to all strains in all conditions, but genetic drift happens 4sure

 

[Oregonism]

Actually I did notice that it was alluding to cell culture and not specifically stem cloning. It just interested me and I really wanted the people asking questions about cell culture to look at it as well.

Basically, what I gather is that a recessive gene was[were] always present and then were expressed later on in a more adult form.

I put this up, as I thought this was the OPPOSITE of genetic drift and that was the original curiosity.

 

[Oregonism]

I still have doubts about the concept of "genetic drift" especially in polyploid species.

Drift is their future's existence, the ability to "drift" by using multiple sets of genes, inherited from both Ma and Pa.
Isn't genetic drift and perpetuation the same, more so in polyploids?

 

[SeaMaiden]

For me to participate in this part of the conversation, I think I need to revisit my own understanding of what genetic drift is, and isn't. Basically, I have come to understand genetic drift as something different from sexual reproduction, where two different sets of genes are 'married' together vs the (epigenetically induced?) changes that occur outside of sexual reproduction. The difficulty in grasping well is further inhibited by differences between what is observed (phenotype?) vs what is possible (genotype?).

 

[Crusader Rabbit]

Genetic Drift refers to a change in the frequency of alleles within a population due to random factors. Genetic Drift is specifically not driven by the process of Natural Selection.

 

[Oregonism]

Overall that is my argument CR, Natural selection = random factors. A single polyploid plant cell has the ability to "genetically drift" thru natural selection in my mind. [Which is another can of worms altogther]

A system @ homeostasis that is dominated by natural selection is also a random occurence is it not?

However, I do get your point, a mutation could be caused by a random factor and is not a natural selection hence a mutation.

 

[Hash Zeppelin]

I knew someone that grew the same 3 strains in a room for 15 years and claims they drifted towards each other in similarity until you could tell much difference. Like after a while it became it's only mini land race. I never saw this so i have my doubts, but it is what he told me.

 

[NotSoNewbie]

It is not that uncommon for a cutting not to be genetically identical

They are called sports
http://en.wikipedia.org/wiki/Sport_(botany)

Many common agricultural plants are derived from sports such as nectarines ad ruby red grapefruits.

Although since indoor MJ growers tend to grow in very small numbers, even in what people here would consider a large grow, we are fairly unlikley to see one in our hobby

 

[Green_science]

I have seen a plant develope loss of vigour over many years, almost like it developed some kind of virus

 

[foaf]

I don't know in any one situation why a clone would be different, but the most likely explanations are and Ive never personally seen a mother produce dramatically different offspring but...

epigenetic variations. http://en.wikipedia.org/wiki/Epigenetics

and variable expression of otherwise identical genes secondary to different environmental exposures

mutations are much less likely but possible and could be induced by viruses, random, or UV light.