When plants go polyploid

Sep 13, 2011 By Daniel Stolte
When plants go polyploid
A polyploid cultivar of Meconopsis, the Himalayan blue poppy. Credit: M. Barker

(PhysOrg.com) -- Plant lineages with multiple copies of their genetic information face higher extinction rates than their relatives, researchers report in Science magazine.

While duplication of hereditary information is a relatively rare event in , it is common in plants. Potatoes, coffee, , peanuts, tobacco, wheat, and , to name but a few, all carry multiple copies of their , in a condition called polyploidy.

In contrast, most animals including humans are diploid, meaning an individual carries only two copies of each chromosome, the carriers of , one from each parent.

"Scientists have been studying polyploidy for a century. It's one of the first genomic characters they were able to get a handle on because are visible with a microscope," said Michael Barker, an assistant professor in the University of Arizona's department of ecology and , who recently published a paper with several co-authors in Science magazine.

When plants go polyploid
Under a microscope, this cell of a polyploid Isoëtes quillwort, a group of fern-like plants, reveals multiple copies of chromosomes. Credit: M. Barker

The study settles a long-standing debate in evolutionary biology: In the relentless struggle for survival under the pressure of , what are the advantages – or disadvantages – of going polyploid by making multiple copies of the entire genome and passing them on to the next generation?

Analyzing more than 2,500 plant genomes with a computer-based, statistical approach, the researchers discovered a trend that sets polyploid plant apart from their diploid relatives.

"We find that plants that became polyploid in their recent evolutionary past are less likely to diversify into new species and face a higher risk of extinction compared to their diploid relatives," said Itay Mayrose, lead author of the study and now an assistant professor at the department of molecular biology and ecology of plants at Tel Aviv University in Israel.

Mayrose and Barker collaborated on this project while they were postdoctoral fellows at the Biodiversity Research Centre of the University of British Columbia in Vancouver, Canada.

"Our study suggests polyploidy is an evolutionary gamble," Barker said. "Duplicating its genome puts a plant lineage at a higher risk of extinction, but in those few cases where it does provide an evolutionary advantage, other analyses suggest that it could really pay off in the long run with significant increases in diversity."

In a previous study, Barker and Mayrose found that more than one-third of all existing plant species are polyploid. According to Barker, botanists have gone back and forth about whether having multiple copies of the genome is an evolutionary bane or boon.

Many argued that polyploidy makes it difficult for a plant lineage to diversify into new species because any mutations that might confer a new trait and a selective advantage over competitors would be masked by the remaining, unaffected copies of that particular gene, rendering the potential advantage invisible to natural selection and therefore useless.

"Many scientists believed that polyploidy is an interesting phenomenon, but probably not very significant in the great scheme of things," Barker said.

But according to Mayrose, things changed when recent genome analyses discovered that many plants are actually ancient polyploids whose duplicated genomes have diverged over millions of years to such a degree that they appear diploid.

"It turns out there are no existing seed plants that have never had their genome duplicated," Barker said. "Every lineage has undergone a genome duplication at least once at some point in its evolutionary history."

"Driven largely by these observations, researchers have come to view polyploidy as a key innovation that drives evolutionary novelty and diversification," Mayrose added.  

"So we set out to find out how polyploidy affects the evolutionary success of plants," Barker said. "We find that contrary to the popular opinion, just duplicating its genome doesn't instantly make a plant lineage successful."

According to the researchers, it is possible that polyploids suffer lower evolutionary success than related diploids over the short term because duplication events are likely to happen only in single individuals and therefore fail to establish themselves in a population.

In addition, competition with established, related diploid lineages renders polyploids susceptible to extinction. Over the long term, however, the fact that particularly fit polyploid lineages carry more variety in their genes to draw from may help them branch into new species.

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Isaacsname
not rated yet Sep 13, 2011
" According to the researchers, it is possible that polyploids suffer lower evolutionary success than related diploids over the short term because duplication events are likely to happen only in single individuals and therefore fail to establish themselves in a population. "

Key paragraph there. I could treat 1000 seeds with colchicine and have ~ 98% express identically.

Nanobanano
not rated yet Sep 13, 2011
Before I got to this paragraph, I kinda figured it was all some sort of "Junk DNA" fallacy nonsense.

Clearly, most of genetics is just flat out misunderstood by everyone. It's there for a reason, and it's likely the genes themselves are designed to function within and among massive redundancy to begin with.

After all, plants are different than animals, they can't move around and stuff. They have to bring all of their "tools" built-in, and they have to be able to recover from minor and even major catastrophes in their environment, without the luxury of self locomotion.

Highly redundant DNA would also appear to help prevent catastrophic negative gene expression, (think genetic cancers and dystrophies in humans).
Nanobanano
not rated yet Sep 13, 2011
According to the researchers, it is possible that polyploids suffer lower evolutionary success than related diploids over the short term because duplication events are likely to happen only in single individuals and therefore fail to establish themselves in a population.


I think it would be quite the contrary.

Consider if you have duplicate copies of any given chromosome, and one of them gets hit by a cosmic ray particle and mutates, then this could easily be advantageous. Why? Because the plant species gets to keep both versions of the chromosome.

If one of them is "bad" no big deal, it will be masked by the "good" ones, but on the other hand, exceptionally "good" genes on mutated chromosomes would eventually "bubble sort" to the top and dominate the weaker ones over several generations, BUT the plant would still have access to the old genes during this time, in case the new genes somehow mutate too much and become unfavorable.
Nanobanano
not rated yet Sep 13, 2011
Think about "phenotypes", the idea that the exact same plant seems to be able to adapt to two drastically different environments, often through different expressions of foliage and flowers, and changes in branching structures, etc.

Redundant chromosomes, with minor variations, explains a POSSIBLE genetic basis for phenotypes quite nicely.

It's like having an "Overloaded" function or operator in a computer program: You simply "call" the version of the function that works best for the conditions you are in. Gene expression isn't quite the same as a function call, but it's the same idea...

This would theoretically allow a plant species to adapt to multiple drastically different environments simultaneously, giving, as stated, observed "Phenotypes" of plant species which are actually "nearly" identical genetically.

The question these researchers need to uncover is how does the plant genome regulate itself in varying phenotypes know which genes to turn on and off and when?
Nanobanano
not rated yet Sep 13, 2011
What I'm suggesting here re. phenotypes, is the genetic equivalent of a "Switch" statement used to call the genetic equivalent of an "overloaded function".

The plant "somehow" determines the environment it is living in through receptors, and then certain genes would then be activated which determine which combination of genes should be expressed to give the plant the best traits appropriate to the environment it finds itself in.

This would explain how a forest of trees could grow in a novel, isolated, low-light environment such as the mouth of a colapsed cave, through expression and application of different traits, and yet stay genetically compatible with it's relatives growing nearby in an ordinary forest setting.

It's like two interent browsers, the problems which can't be solved by one might be solved by the other.

Again, this is purely speculative, BUT the phenotype issue is strong circumstancial evidence that it might be correct.
Nanobanano
not rated yet Sep 13, 2011
Ok, and without any access to the data, I thought of a way such plants could "probably" prevent genetic catastrophe, such as Down's syndrome.

Gene expression in plants could somehow be engineered so that these receptors and markers which control which version of the gene is turned may "somehow" be dynamically addressed, just as an operating system can handle the user adding any number of programs, up until your hard drive runs out of memory or you are out of RAM.

I'm not saying this is definitely happening, but it certainly seems plausible that the genetics of life could be that dynamic, and not just "static".

From that perspective, life forms could theoretically try all possibilities, why still keeping a version of the genome which works "well enough" just in case, and then keep what works best, in principle, it's a potential genetic algorithm for finding the best genes.
polygenomx
not rated yet Sep 14, 2011
For some insights into the 'bleeding edge' of commercial polyploidisation take a look at PolyGenomX.
sselig
not rated yet Sep 14, 2011
Might polyploidy be a response to viruses? Perhaps the plant's excess genetic material helps tip the balance in its favor by overwhelming that of the invader. This isn't my field; anyone out there who can debunk this hypothesis?

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