[vj_tu (OP)]

Why not using monoploid, triploid or tetraploid to identify gene function?

[WylieE]

Hi,
 Here is just a quick answer. . . basically, monoploid would be ideal, and these can be generated from tissue culture for some plants, but they have some issues.  So if you want to look at a "normal" plant, your choice would be diploid or more. . . . For a diploid plant if you wanted to see what happens when a gene is disrupted the first step would be to get the disruption to a homozygous state- where both alleles of the gene are disrupted.  Since there are two alleles of the gene in a diploid plant, a heterozygous plant (one with a disruption in one of the copies of the gene) crossed to another heterozygous plant (or itself) will give homozygous offspring 25% of the time.  So if you look at 4 plants you have a good chance of finding one that is homozygous. 

  If you were working with a tetraploid plant it would give homozygous offspring on average for only one in every eight plants.  This keeps going up, if you were working with hexaploid wheat plants, it would only be one out of every 64 plants on average that were homozygous.  And this is only an average, usually you look at about twice as many as you would expect on average to be sure to find one homozygous plant.   

So it is much simpler and you have to screen fewer plants if you work with a diploid plant.  However, there are many important crops that are not diploid and people do work with them, it just involves more screening of plants. 

[chris]

Thanks Colleen

can you please explain why plants are polyploid in the first place - water lillies, for example, can be something ridiculous like 40-ploid can't they? How does this happen, why and how is it compatible with life?

Chris

[WylieE]

Hi Chris,

Yes, plants can certainly tolerate polyploidy well- some estimates are that 40-50% of angiosperms are polyploid.  But WHY do plants tolerate genome duplication so well?
 
I sent this question to our resident genome duplication expert, but while I wait for an educated answer back from him, I'll give my wild speculation.  I think you'll be sorry you asked.

Remember, this is just total speculation but here's my thoughts:

I think there are two reasons that plants can tolerate these huge duplications. 

1.  Energy abundance:  Plants are, in general, not energy limited (as least not as much as animals).  Often throughout evolution there is strong selective pressure on most animals to use energy as efficiently as possible.  However, plants are often faced with problems of how to divert excess sunlight away to protect their proteins. Since this energy limitation is not as strong in plants they can afford to spend a bit more on things that might seem frivolous or too expensive to an animal, such as an enormous genome or multiple copies of the same genome. 

 My terrible analogy is this:  when a grad student goes to buy car insurance, money is really tight, they are faced with barely enough money to pay rent, groceries, and gas and so will probably get the insurance with the highest deductible so that the monthly payment is lower and in the event of an accident they will just have to scramble to come up with the money or will have to get by without a car for awhile, but if you don't have the money, this is a sacrifice that has to be made.  It's more important to spend the little available money on immediate needs (Beer) than on potential problems that may or may not happen.

Compare this with a tenured professor: they have enough money to pay rent, buy food, and even a new tweed coat every so often.  So, when they go to buy car insurance, they spend a bit more every month, but get the comprehensive insurance with a low deductible.  This way if there is an accident, they are better prepared and less inconvenienced and since they probably have kids to get to school and other obligations the loss of a car for a few days might have a greater impact than to a grad student who can just ride their bike for awhile. 

So what does car insurance have to do with plants?  Well, actually nothing but . . .

 Often, particularly in response to stresses, plants behave like a professor.  They have everything prepared in advance, they spend a little more to be prepared for the worst.  They go through the effort to make all of the proteins necessary for a response.  For example, the plant ethylene response system is poised and ready to go and the only thing stopping it is an inhibitory protein that is rapidly degraded when ethylene is present.  If no ethylene is present the plant wastes some energy making the proteins, but it is ready when ethylene shows up.  Similarly the maintenance of a large (or duplicated) genome is a huge expense- energy is required to maintain and duplicate it with every cell cycle.  It has some advantages. . .duplicate genes allow for divergence of the functions of proteins and if the plant can afford to keep the extra copies, it probably pays off.  Animals, however, since they can't just sit around all day and soak up the sun to get energy, have to weigh the cost vs benefits and pinch their pennies a bit tighter.  For animals that have to find the energy they need, the cost of maintaining and duplicating all that extra DNA baggage for the off chance that they might get a gene with a new function probably isn't worth it.     

There are some examples of the "be prepared" (or Boyscout) approach in animals, I can think now only of NF-kB, but here the extra cost of producing everything "just in case" is worth the expense. 

If you haven't had enough wild speculation yet. . . here's the second reason I think plants can handle this:

2.  An elaborate RNAi system.  Plants have an elaborate RNAi system that includes both transcriptional and post-transcriptional gene silencing.  Duplicate copies of some genes could be harmful directly or indirectly in the cost of producing proteins from them.  It would be important for a plant (or animal) suddenly finding itself in possession of an extra two copies of all genes to be able to rapidly shut down production of proteins that could either be potentially harmful or costly to produce.   Plants are well prepared to deal with this, they have several RNA dependent RNA polymerases, four Dicer proteins, several Argonaut proteins, all designed to keep proteins that aren't needed from being produced.  Perhaps the plant-specific RNAPolIV is one reason plants can handle polyploidy better. 

Now. . How to test this crazy speculation . . can PolIV mutants handle polyploidy as well? If plants are light-starved to they start shedding copies of their genome? After several generations will couch potatoes start becoming polyploid?

Are you sorry you asked?   []

I'll post the real answer to this question when I find out what it is. 

Colleen

[another_someone]

Thanks Colleen for some interesting speculation, which even if the speculation may be the wrong reasons, nonetheless does seem to raise even more interesting questions about the premisses for that speculation.

some estimates are that 40-50% of angiosperms are polyploid.  But WHY do plants tolerate genome duplication so well?

So, what is the situation with non-flowering plants?

1.  Energy abundance:  Plants are, in general, not energy limited (as least not as much as animals).  Often throughout evolution there is strong selective pressure on most animals to use energy as efficiently as possible.  However, plants are often faced with problems of how to divert excess sunlight away to protect their proteins. Since this energy limitation is not as strong in plants they can afford to spend a bit more on things that might seem frivolous or too expensive to an animal, such as an enormous genome or multiple copies of the same genome. 

Firstly, this seems at face value to imply that blanks are deliberately inefficient at energy conversion, and this could have an impact in their long term use for biofuels (either their conversion efficiency could be manipulated, or we might yet develop artificial solar energy conversion mechanisms that might exceed the conversion efficiency of plants).

Secondly, with regard to the specific speculation you are making, does that imply that fast growing plants are less polyploid than slower growing plants?

2.  An elaborate RNAi system.  Plants have an elaborate RNAi system that includes both transcriptional and post-transcriptional gene silencing.  Duplicate copies of some genes could be harmful directly or indirectly in the cost of producing proteins from them.  It would be important for a plant (or animal) suddenly finding itself in possession of an extra two copies of all genes to be able to rapidly shut down production of proteins that could either be potentially harmful or costly to produce.   Plants are well prepared to deal with this, they have several RNA dependent RNA polymerases, four Dicer proteins, several Argonaut proteins, all designed to keep proteins that aren't needed from being produced.  Perhaps the plant-specific RNAPolIV is one reason plants can handle polyploidy better. 

This sort of gene silencing sounds like it might be a useful viral protection scheme.

One other aspect I think may be the case (maybe you might comment) is that the species boundaries between plants is less sharply defined than in animals, hence it is easier to cross breed between plant species than animal species.  This would imply that plants are better able to tolerate alien genes (consistent with your arguments above) than animals are, but still take something useful from the alien chromosomes while suppressing anything toxic within them.  This too, I believe is one of the ways in which higher order polyploidism is introduced into plants species.

[WylieE]

Hi George,

Thanks Colleen for some interesting speculation, which even if the speculation may be the wrong reasons, nonetheless does seem to raise even more interesting questions about the premisses for that speculation.

Well, it's always fun to speculate when you don't have to come up with the proof to back-up the ideas []

So, what is the situation with non-flowering plants?

I don't know, I was wondering about this too. 


Funny this whole topic came up just now. . .Hot of the presses an article in Cell today:

The Evolutionary Consequences of Polyploidy
Sarah Otto

Polyploidization, the addition of a complete set of chromosomes to the genome, represents one of the most dramatic mutations known to occur. Nevertheless, polyploidy is well tolerated in many groups of eukaryotes. Indeed, the majority of flowering plants and vertebrates have descended from polyploid ancestors. This Review examines the short-term effects of polyploidization on cell size, body size, genomic stability, and gene expression and the long-term effects on rates of evolution.


The article goes on to suggest that there was an ancient event in the ancestors of angiosperms- and possibly all angiosperms had a polyploid ancestor (although this is hard to prove).  So maybe it isn't so much that it is easier for angiosperms, but that it just happened earlier.

The neatest thing for me from the article were two points:

1.  Polyploidy happens in animals, just not in birds and mammals so much.  Fish, insects, amphibians, and others all have events early in their lineages (so it's not just  a dead end when it happens)

2.  The failure of polyploids in mammals and birds is not a result of complications from sexual determination- This was going to be my other point for why it happens in plants more than animals, but I guess that is wrong.  So their point is that problems from polyploidy aren't due to confusion in sexual identity, but rather more general developmental problems.   

Firstly, this seems at face value to imply that blanks are deliberately inefficient at energy conversion, and this could have an impact in their long term use for biofuels (either their conversion efficiency could be manipulated, or we might yet develop artificial solar energy conversion mechanisms that might exceed the conversion efficiency of plants).

There is a wide range of energy efficiency usage in plants- so I would certainly agree either manipulation or selection of plants that are efficient users of energy (Miscanthus) for biofuels is an important area to consider. 

Secondly, with regard to the specific speculation you are making, does that imply that fast growing plants are less polyploid than slower growing plants?

This would be a cool question to address!

This sort of gene silencing sounds like it might be a useful viral protection scheme.

Plants do use gene silencing as a viral defense.  Again, just wild speculation on my part, but I wonder if this isn't why plants and other animals maintain such an elaborate system, but mammals don't- perhaps mammals have replaced the need for this with their immune system. 

One other aspect I think may be the case (maybe you might comment) is that the species boundaries between plants is less sharply defined than in animals, hence it is easier to cross breed between plant species than animal species.  This would imply that plants are better able to tolerate alien genes (consistent with your arguments above) than animals are, but still take something useful from the alien chromosomes while suppressing anything toxic within them.  This too, I believe is one of the ways in which higher order polyploidism is introduced into plants species.

I wonder about this, it would certainly seem possible.  It does seem that the species line is blurred more in plants- but my hesitation here is just that I am not sure how good we are at defining a "species."  For example. . . if you were just looking at the wide size range of dogs, you might not think that they were the same species, but we know they are and one piece of evidence for that is that they can mate and produce viable offspring, but how about two plants that can do the same, but also look wildly different- are they the same species?  The whole "what is a species" debate is tough and way out of my area of understanding - I'm not even sure some of the students here are all the same species (especially this weekend- it's the Michigan vs Michigan State home game- they are all wacko sapiens- especially the ones from Michigan!)

Interestingly, that article on ploidy talked about a similar thing- the acquiring of alien genes.  They mentioned that the success rate of taking up foreign genes is much higher when the entire genome is duplicated, as opposed to just parts of it.  The idea here is that possibly it is easier to maintain the "balance" issue if everything is duplicated rather than just part.  Or another possibility is that cells are used to differences in ploidy (when cells divide) so it isn't such a stretch to carry that on throughout the whole cell cycle.

There is a lot more interesting in that article, I need to figure out what I can post here from it and what has copyright issues (and I need to do some work today).  So this weekend I'll try to summarize some of the other cool things from the article or post them directly if allowed.

Thanks for the light-hearted speculation, George, Fun!

Colleeeen

[another_someone]

At the risk of overloading you with questions, but to each answer there is always another question, and the answers are indeed intreguing (so, thank you again for that).

1.  Polyploidy happens in animals, just not in birds and mammals so much.  Fish, insects, amphibians, and others all have events early in their lineages (so it's not just  a dead end when it happens)

2.  The failure of polyploids in mammals and birds is not a result of complications from sexual determination- This was going to be my other point for why it happens in plants more than animals, but I guess that is wrong.  So their point is that problems from polyploidy aren't due to confusion in sexual identity, but rather more general developmental problems.   

My first instinct was that fishes, like plants, do not (as a generality) directly impregnate their mate, but release their sperm into the environment, and so risk have the sperm potentially fertilise the egg of a different species.

If this was the issue, it would not explain insects (which generally mate on land, and so do directly impregnate a specific female).

So the issue would seem to be between cold blooded and warm blooded animals (I know the line between the two is not absolute, but that line is drawn around the point where polyploidy becomes more difficult).  It would be interesting to know how it affects some of the larger fishes (such as tuna), that are bordering on being warm blooded, and give birth to live young (and thus must become directly impregnated).

In other words, it does seems likely that animals that have difficulty with polyploidism are likely to be animals that impregnate in mating, as a defence against accidental polyploidism, but is not the reason for abandoning polyploidism, but the constraints of warm blooded metabolism seems to make acceptance of alien genes more difficult.  This would seem, in my speculation, to be a logical conclusion to the greater specialisation of the enzymes in warm blooded animals (that the enzymes are designed to operate in very narrow environmental constraints, tight constraints that are maintained within the body of a warm blooded animal, but constraints that make the system far more vulnerable to disruption by being in alien conditions).

One other aspect I think may be the case (maybe you might comment) is that the species boundaries between plants is less sharply defined than in animals, hence it is easier to cross breed between plant species than animal species.  This would imply that plants are better able to tolerate alien genes (consistent with your arguments above) than animals are, but still take something useful from the alien chromosomes while suppressing anything toxic within them.  This too, I believe is one of the ways in which higher order polyploidism is introduced into plants species.

I wonder about this, it would certainly seem possible.  It does seem that the species line is blurred more in plants- but my hesitation here is just that I am not sure how good we are at defining a "species."  For example. . . if you were just looking at the wide size range of dogs, you might not think that they were the same species, but we know they are and one piece of evidence for that is that they can mate and produce viable offspring, but how about two plants that can do the same, but also look wildly different- are they the same species?  The whole "what is a species" debate is tough and way out of my area of understanding - I'm not even sure some of the students here are all the same species (especially this weekend- it's the Michigan vs Michigan State home game- they are all wacko sapiens- especially the ones from Michigan!)

The issue about dogs is interesting, but still pales into insignificance with regard to the species issues in insects (which rank in your article as being an animal that is to some extent more tollerant of polyploidism).

One of the arguments about the high variability with dogs is that, while they are not polyploid, they do have a large chromosome count in comparison to most animals.

There is a lot more interesting in that article, I need to figure out what I can post here from it and what has copyright issues (and I need to do some work today).  So this weekend I'll try to summarize some of the other cool things from the article or post them directly if allowed.

I look forward to whatever you have to offer.

[WylieE]

Hey George,

I haven't forgotten about this. . .It's been a super busy week- I'll think about some of your questions and come up with some good (or crazy) opinions on them.  Meanwhile, here is the table that shows the number of polyploids for a few organisms:

From Otto, S.  "The Evolutionary Consequences of Polyploidy" 2007, Cell 131:452

Table 1. Polyploidization in Insects and Vertebrates      

Reproduction	Insects	Fish	Amphibia	Reptiles	Birds	Mammals	Total
Parthenogenesis	89	9	3	15	0	0	106
Sexual	2	23	26	1	0	1a	54
?	0	18	1	0	0	0	19

A summary of data on the number of polyploidzation events. (Data derived from Otto and Whitton, 2000, online Table 1; and Gregory and Mable, 2005, Table 1). Mode of reproduction of the polyploid is specified, where known.

[a] The only reported case of polyploidization in mammals involves the related red and golden viscacha rats (Gallardo et al., 2004).


Then I thought the model from that paper was a cool description and visualization of the cost vs benefit of polyploidy:

 [ Invalid Attachment ]

Figure 3. Polyploidization Decreases Mean Fitness at Equilibrium

By doubling the number of gene copies, tetraploids undergo twice as many mutations as diploids. This can be visualized as doubling the flow rate from nonmutant individuals (top tanks) to mutant individuals (bottom tanks). Ultimately, the flow rate out of the mutant class must equal the flow rate into it; this balance of flow rates is accomplished by a higher equilibrium level of mutant individuals in tetraploids (bottom right tank), resulting in twice the number of deaths due to mutation (“mutation load”) in tetraploids compared to diploids.

[another_someone]

The table is certainly interesting, because again it shows that animals that mate on land (and thus animals that directly impregnate their mate, rather than mating externally) are very unlikely to polyploidize through sexual reproduction (only 4 cases).  This does I suppose make sense.

Again, I suppose when we are talking about parthenogenesis, one of the limitations of parthenogenesis is the difficulty in achieving genetic diversity, so I suppose that resorting to polyploidization might seek to offset this limitation.

All very interesting - if maybe sending one's mind wondering down all sorts of tracks.

[WylieE]

Hi George,
 I didn't forget about this discussion, but I have been super busy (but still thinking about it). 

To get the discussion kick-started again- the warm blooded / cold blooded difference idea- seems like the real divide is between mammals and non-mammals.  Is this also the divide between warm/cold blooded?  I'm not sure exactly where this divide is- or as you say, if it is even firm.  But like you say for warm-blooded, maybe there is something specific to mammals that makes it tough to tolerate polyploidy. 

Your point about parthenogenesis makes sense, if one is not mixing the gene pool perhaps polyploidy provides a means for accumulation of mutations that allow for the maintenance of genetic diversity- I wonder if this is actively regulated?  The odd thing about this is that parthenogenesis is not very common in plants, where (as the start for this discussion) we know polyploidy is very common. 

Again, fun to speculate when I don't have to do the experiments to prove it

[another_someone]

Hi George,
 I didn't forget about this discussion, but I have been super busy (but still thinking about it).

[]

To get the discussion kick-started again- the warm blooded / cold blooded difference idea- seems like the real divide is between mammals and non-mammals.  Is this also the divide between warm/cold blooded?

No - my thoughts were deliberately otherwise - warm blooded normally refers to mammals and birds.  Your table includes a single mammal and no birds that are polyploid.

Even the case of the one mammal (red and golden viscacha rats) seems to be talking about (if I understand what I am reading in Wikipedia) a transient historic phase, rather than contemporary polyploidism.  On the other hand, what is interesting is mention that the human liver is polyploidal, and the human liver is one of the few organs in the human body that can regrow.

Your point about parthenogenesis makes sense, if one is not mixing the gene pool perhaps polyploidy provides a means for accumulation of mutations that allow for the maintenance of genetic diversity- I wonder if this is actively regulated?

Again, looking at wikipedia, it mentions that one of the common consequences of polyploidism is sterility - so the question has to be to seperate cause and effect (is parthenogenesis a consequence of sterility brought on by polyploidalism, or is polyploidism  a way of getting around the limitations of asexual reproduction).  Ofcourse, one aspect of this is that, is that there are (according to your table) plenty of fish and amphibians that that are not sterile polyploids (one question is whether, even if not sterile, do the species retain the ability for asexual reproduction?).

The odd thing about this is that parthenogenesis is not very common in plants, where (as the start for this discussion) we know polyploidy is very common.

Maybe technically true, but for practical purposes, is it relevant?  Plants regularly reproduce vegetatively, if not by strict parthenogenesis.