Diversity? Desirable or not.

[DarJones]

This thread is intended to get some folks to sound off about the benefits and failings of diversity in corn specifically and in plants in general.

I'll start out by saying that the objective of any breeding program is to reduce diversity. How so? Well, consider, a breeding program tries to eliminate undesirable genetics. The net effect is to reduce diversity.

Because genes are linked into chromosomes and because eliminating just one deleterious gene may wind up eliminating an entire chromosome or some part thereof, the end result of breeding to get rid of that unwanted gene is that you lose diversity.

DarJones

[robertb]

I think reasonable diversity is a good thing, depending on the purpose of the crop. Obviously, if it's a vegetable you want them all to be a reasonable size, taste good, and so on. you don't want that much. At the same time, if you're a gardener, you don't want the whole crop ripening in the same week. If you're a farmer, or you're growing for a show on a specific date, you may want less diversity. It's probably a good thing if we don't try to grow the same varieties as agribusiness!

[blueadzuki]

This is actually a very complicated question. The real problem is that the answer differs not only depending on whether you are a home grower versus a commercial one, but also on whether you are growing what you grow for money, for eating/use, or for the propogation of the species (like a seed bank has to) if the last then you really have an obigation to keep EVERY possible gene combination, desirable to humanity or not, on the grounds that you never know what trait will be the one that a crop will need in the future and that you are in a way simply the plant's stewards not thier masters. In an ideal world this would simply stratify we would have some sort of universal seed banks above us charged with keeping all possilble diversity intact, and then us below free to select which groupings of genes are the best for our usage. However since despite the efforts we make such a absolute universal bank is probably not only impossible to create, but impossible to even come close to, there is a certain onus, if you think of it, to do all one can in ones small way to keep diversity at the absoutle maxium whether it is to your advantage or not. I remember a story I read once about a seed reasarcher in sout America who saw an old indian woamn collecting corn seed to save for the next years planting. He noted that she was taking a few kernels from all the cobs even though they were mostly very sicky and barrnen with a few really good cobs thrown in. The reasearcher point out to the old lady that, if she focused on saving the seed from the best cobs, her crop would likey imporve next year. The woman replied that corn was a gift from the gods, if man did something so presumtuious as to try and improve it just becuse they could, the gods might get angy and take the gift away again.
The real irony is that if we truly wish to make the best selction for the plant we would probably have to consistently select against any trait that made the plant usable by us, after all the best state for any plant to be in from a survial standpoint is probably the wild form, the one that requires no help at all from anyone and has the maxium defense agains all prdators that might want to consume most of its bits (like us).

[Joseph Lofthouse]

Mar 22, 2010 15:49:00 GMT -5 blueadzuki said:

The real irony is that if we truly wish to make the best selection for the plant we would probably have to consistently select against any trait that made the plant usable by us

If I were a member of the Zea maize species, and if I had
feelings or thoughts, I bet that I would consider it a great
bargain to have been domesticated... The wild teosintes of
Mexico always seem to be flirting with extinction.

How about the Navel Orange? In exchange for giving up it's
ability to propagate itself it has become one of the most widely
distributed species on Earth.

Regards,
Joseph

[canadamike]

I disagree that breeding means reducing the genetic diversity. In many cases, it is exactly the opposite. An example could be »Astronomy Domine, were Alan, a few others and I have included seeds from all over the world in it. That is re-introducing a lot of diversity...as for selecting, it is never neutral nor should it be....nature does it all the time....it is rainy here in summers, want it or not, the survivers will be accustomed to rain....Painted Mountain loves my cold spring but prefers dry summers.....over the years it will select itself for that criteria, even if I do not want it to happen. And mutations do occur too, and we can notice them.

Tom Wagner does include a lot of different species in its taters, that is ADDING, not substracting. I will do the same this summer with lots of taters, mixing in genes from andigenums and other species....

This ''reduction of genes'' theory work well from a gene '' accounting standpoint'', but in reality the genome is a fluid, a river or sorts, and it moves all the time. Breeders are but a few of the boulders its waters will hit while moving towards the sea...

[blueadzuki]

Mar 22, 2010 18:07:57 GMT -5 Joseph Lofthouse said:

Mar 22, 2010 15:49:00 GMT -5 blueadzuki said:

The real irony is that if we truly wish to make the best selection for the plant we would probably have to consistently select against any trait that made the plant usable by us

If I were a member of the Zea maize species, and if I had
feelings or thoughts, I bet that I would consider it a great
bargain to have been domesticated... The wild teosintes of
Mexico always seem to be flirting with extinction.

How about the Navel Orange? In exchange for giving up it's
ability to propagate itself it has become one of the most widely
distributed species on Earth.

Regards,
Joseph

That true if you are thinking in terms of a world where you can count on who or whatever you gave up your independence for staying around (in the case of the above, us); I on the other hand was thinking in terms of what happens when whatever it is stops being there. Fact is, if we weren't around both corn and navel organges would be gone in a few generations, they're dosmeticated to the point where their co-dependent it sorta a question of which is better, you and your descendents living forever on the verge of potential extinction, versus living in comfort but with the knowedge that, if anything goes wrong, you extinction is certain.
Then again there are plants in this world that seem to get along quite well with virtually no diversity at all . From what I understand mangosteens are all basically natural clones of each other (the pollinated embryo is always outgrown and killed by somaclonal ones and natural random mutation does not seem to occur much).

[DarJones]

Canada Mike and Others. I'll repeat. All breeding programs result in reduction of diversity. This is DIRECTLY opposite to what you posted about Astronomy Domine.

When you crossed the many different lines into Astronomy Domine, you HAD to include genetics that are not adapted to a given area. The result is that nature will severely limit reproduction of those plants and will enhance production of the adapted lines. End result is a LOSS of diversity.

The only way to increase diversity in a plant species is to dramatically increase the number of plants. Look closely at tomatoes and you will see part of what I am getting at. The domestic tomato is severely restricted from a genetic standpoint. It came through a genetic bottlenect a few thousand years ago when man started cultivating them and the result is a plant that lost over 95% of its diversity. Fast forward to today and plant breeders are going to the wild species of tomato to introgress genes for disease tolerance and climate adaptation and hundreds of other traits. The only reason this can be done is because the wild species are available. If we had to rely on the cultivated tomato, we would have nearly zilch for disease tolerance.

Now I will repeat my assertion. The result of all breeding programs is reduction of diversity. I challenge you to prove otherwise. Only nature truly increases diversity.

DarJones

[canadamike]

This is a pointless argument, you're coming from one place and me from another. Of course selection means losing some genes, we all know that. It is like saying that the guy''was still alive 2 minutes before dying''.... what's the point?? You're looking at gene acccounting, starting from the point of vue of the ''whole'' species living in nature, although for corn it is not truely a wild plant.

I am looking at my plot. We introduced loads of corn to each other to create diversity then we will reselect. At the end of the day, at 1220 Landry road, there will a lot of corn genetic diversity...way more than before. and I sure will not argue that nature is our main genebank...

[nuts]

I think you have to see the development of cultivated species as a coevolution of 'wild' species and humans.There is a interdependence comparable with the coevolution of flowers and insects,This is nature at work.

This evolution has resulted in an incredibly diversity of cultivated plants(and animals).As long as the natural mechanisms keep their place in the proces ever more diversity is created.

The proces of increasing of genetic variation is only partly explained by the scientific genetic models,these models tend to easily explain how genetic material is lost,but they don't easily explain the creation of diversity.

Nevertheless the existing biologic diversity is a proof enough that natural evolution creates diversity.In the case of cultivated plants the development of diversity is even multiplied by the human diversity.

As so far I completely disagree with fusionpower.

But fusionpower is completely right that modern,insdustrial age seedbreeding is going the opposit way.
Not is this only a result of the the lack of understanding of natural mechanisms,
The decreasing diversity comes forth by the economic imperatif to make seedbreeding a profitable enterprise.This has gone so far that for european seedlaws for longtlme genetic diversity of cultivated plants was considered as ennemy nr1 to be shot down.

Modern industrial genius cosiders that we don't need evolution and genetic diversity anymore.They will do the job and not anyone else then the professional seedcompanies has to worrie about anything. because they keep the diversity in their freezers.They are smarter than the creator...

Yes,seedbreeding by farmers that are able to create diversity and modern industrial engineering,that are two different worlds.

[silverseeds]

Theres a few points Id like to make.....

when we take a wild species, and select for cultivation we DO lower the genetic variability.

but as breeders among the things we can do, is reintroduce the base genetics, or differing variables of the mutations and the like that have resulted since.....

for all species that we still have the wild versions, we have in my opinion increased diversity. Through our selection over the Milena, and centuries, weve ended up with variations and mutations, that simply were not happening in the wild cousins. so the tomatoe example above becomes really interesting...... we now have tomatoes doing things they did not before, and its true we took the tomatoe through a bottleneck....... so what other possibilities lie in the non cultivated tomatoes? the non cultivated grains? The wild fruits.........

when we select and adapt, a species and new possibilities emerge, how is this not a expansion of genetic variability? when you have the base genetics still....... If something happens to tomatoes that makes them unable to grow in their native regions...... There will be people growing them well, in a dry cool mountainess place perhaps..... or some other variable...... because through selection, which was a reduction of genetic diversity in theory, we adapt things to new areas. but there are also mutations it seems. either way on the crops where we still retain the base genetics, selecting, and thus limiting genetic variability, can in a sense be increasing genetic variability, at the same time....... especially when your talking about something you breed or adapted to a new place, and climate.......

Personally Id love to see much longer term breeding projects as well...... Adapting fruit and nut trees, especially to new areas......both through breeding, and also using the base wild versions, to select, and adapt from as well...... I think there is a lot of long term potential in that.

[DarJones]

In reply to the argument that "cultivation increases diversity", please consider the following. The domestic tomato has 12 genetic changes that make it what it is. This is just 12 - count them - very minor changes that cause a plant that produced a tiny fruit to produce a large fruit with large seed locules. Can you actually argue that 12 changes incorporated into the cultivated tomato by human action is more important to diversity than the thousands of genes that were lost as a result of that cultivation?

Here is a specific example of a 'lost' gene. Tomatoes have all the genetic machinery to produce anthocyanin, the stuff that makes blueberries blue. Every single piece is there, all the genes are present for a complete bio pathway to produce anthocyanin, but ONE gene (chi) is turned off in the domestic tomato. The result is that domestic tomatoes produce lycopene and carotene, but not petunidin. The loss in this case was the turning off of one single gene.

Go back to that statement I made above that the only way to increase diversity in a plant species is to dramatically increase the number of plants. This statement is arguably true, but in an agro dominated industry, all of those plants are going to share most of their genetics. Using corn as an example, the genetic base of the corn grown on millions of acres around the world today is narrower than at any time in the past. Granted there are exceptions, granted that significant breeding work is being done with gene bank accessions, still, the overall direction is moving toward LESS diversity.

Taking Astronomy Domine as an example again, the only way you can argue that it is an increase in diversity is if you can dramatically increase the number of plants. That means you need hundreds of growers propagating it.

DarJones

[silverseeds]

who said the adaptations in tomatoes or other foods, is MORE important then the genetic diversity in the wild species? do you really want to eat only the wild versions of foods we eat now? Most are not to tasty. Of course the diversity in the wild, is key. In fact I am convinced, besides just what we call breeding today which among other things incorporates attributes from wild species, we SHOULD start adapting the same and other wild species to be edible crops in the future. I can think of a few wild grains, and a gourd which likely could be whole new crops as large as wheat or squash....... with better benefits, if only they tasted like food.

Which is more important? well if I was to be placed on a new planet, and had to choose the base genetics, or the selected varieties, and I knew my descendants 2would have to live with my choice, Id choose the wild stuff surely.....

Loosing the base genetics would be worse, then loosing our cultivated ones in many ways......

but in cases where we have the base genetics, AND the ones weve adapted, and or saved mutations of, we have things they can exist in ways, and in places they simply could NOT before..... this IS a increase of diversity, in a real sense, and YES it took a selecting within the original genetics to get there, but how else could it be?

I know mathematically tomatoes able to grow in places they could not ARE less diverse, being a selection of a selection from wild types, that is true, no one can argue with that. but at the same time, now the tomatoe and so many other things are able to grow in ways they simply could not before.....

what do you make of tim peters rye and wheat work then?? Taking the annual species weve selected since the beginning of farming, and crossing it to wild perennial cousins, of the annual ones weve had selected all these years...... the wild perennials always had smaller seeds, which is why our ancestors domesticated the annual versions instead..... so from our selections of annual grains over the milennia, selecting the larger seeds among other things, and the wild perennial cousins, we now have perennials with large enough seeds to make people care....... Is this LESS genetic variability in your eyes? the wild perennials wheats still exist, the heavily selected annuals are all over the pace, but now we also have essentially a new plant as well........ Mathematically Im not sure if it is more diverse then either of the base parents..... but I would assume so.......

[blueadzuki]

Mar 24, 2010 20:17:17 GMT -5 DarJones said:

In reply to the argument that "cultivation increases diversity", please consider the following. The domestic tomato has 12 genetic changes that make it what it is. This is just 12 - count them - very minor changes that cause a plant that produced a tiny fruit to produce a large fruit with large seed locules. Can you actually argue that 12 changes incorporated into the cultivated tomato by human action is more important to diversity than the thousands of genes that were lost as a result of that cultivation?

Here is a specific example of a 'lost' gene. Tomatoes have all the genetic machinery to produce anthocyanin, the stuff that makes blueberries blue. Every single piece is there, all the genes are present for a complete bio pathway to produce anthocyanin, but ONE gene (chi) is turned off in the domestic tomato. The result is that domestic tomatoes produce lycopene and carotene, but not petunidin. The loss in this case was the turning off of one single gene.

Go back to that statement I made above that the only way to increase diversity in a plant species is to dramatically increase the number of plants. This statement is arguably true, but in an agro dominated industry, all of those plants are going to share most of their genetics. Using corn as an example, the genetic base of the corn grown on millions of acres around the world today is narrower than at any time in the past. Granted there are exceptions, granted that significant breeding work is being done with gene bank accessions, still, the overall direction is moving toward LESS diversity.

Taking Astronomy Domine as an example again, the only way you can argue that it is an increase in diversity is if you can dramatically increase the number of plants. That means you need hundreds of growers propagating it.

DarJones

Selective breeding can increase or decrease diversity, it all depends on what you are selecting for. In theory, artificial selection can increase diversity, by allowing one to propigate new genetic mutations that may occur that might not naturally be preserved if left out in the wild population (if they offer the plant no immediate comparitive advantage or even a compartive disadvatage at that time (imagine a plant that had a genetic mutation that allowed for better drought tolerance, but which happened to grow in a year that was unusally wet) such new genes might be lost over time in natural selection.) In pratice however selective breeding tends to reduce diversity becuse of the reason fusionpower stated, whne you are actively selecting, you are usally doing so with an end in mind, and bioteleology usally does work out to promoting some gense while supressing or eliminating others.
Addionally there is the fact that, statistically, when you are selectively breeding a crop, a lot of the genes you are trying to preserve/promote tend to be those that are normally recessive since a lot of the trats that are good for the plant (being rich in toxins, having seed propagules that shatter when ripe etc.) are bad for us, from an agronomic viewpoint. so you often shooting for mostly double recessive, by defintion this promotes genetic homozygocity and the elmination of normally dominant traits. This is why cultivated plants, while usually less gentically diverse, often look like they are more diverse than the wild ones; most of the genes you see in the culivated crop are present in the wild population but dominance and natural selection tend to keep them supressed and in the minority. And let's face it; until fairly recently a lot of the selection work we have done has required a visual cue as to results; we can see right away if a corn plant has red or yellow kernels or grows giant, but we don't know if it has cold tolerance until we actually subject it to a cold snap which, until recently was largey someting that was beyond our power to do on our own.
Actually that change in what we can control is one of the core bits of why modern agriculture has moved so far towards near clonal crops; the maount we can change in the enviroment (or at least we think we can) is now in some way suplanting what would normally be the plants own methods. if the soil turns poor in nutrients, we no longer try and select those plants that make more efficent use of what there is, we simply dump more nutrients in. If there is a new pest around we dont pick the plants that best resist that pest, we dust the area with herbicides (in fact we do this so much that we've had to create crop plants that can tolerate the pesticdes we like to dump, because otherwise they would die as well) We're so use to getting what we want, that, when what we want becomes rather more difficult to do, we come up with rather outlandish and extreme ways of continuing to get what we want, rather than sitting down, and wondering if what we want is waht we should want, or even if we have a right to want or act on our want, for anything.
I think the modern tendecies in seedbreeding are tending towards reduced diversity. and that this will get even worse as soon as we make next big scientific breaktrough in genetic engineering, to waht I have always called "gene assembly" (the difference between gene spicing (which is what we do now) and gene assembly is that in splicing you take a big existing chromasome or strand of DNA and you stick little bits of outside DNA in it so that the resutling thing is still mostly the natural DNA of whatever you started with. Gene assemby however would be where, using a genetic model of whatever it is you are trying to make (a corn plant, for example) as a you put together the chromasomes entirely from scratch one gene at a time artifically so that you have a completely artifically assembled genome (and on the postive side a lot more control over which genes get where, as well as the ability to insert large numbers of foreign genes simutaneously (since they all would be tecnically foreign) the stage after that, incidentally would be "gene creation" where our knowledge of how genes interact becomes so complete that we no longer need existing natural models for creation, basically where we reach the stage where we really do know how to create life from scratch and can basically make whatever lifefroms we want; where we can play God literally.) I'm not saying that I think any of this is a good thing (I belive all genetic engineering to be a perfectly neutral thing; whether it is good or bad depends solely on how we use it.) but I do believe it will, in the fullness of long time, happen. (thought I admit I am a little apprehensive of waht could happen, I cant help remembering the fact that, in the book and TV show, the Triffids were the result of selective breeding, as was Audrey Jr. (in the orginal black and white movie not the musical).

[Alan]

I don't really know how to say this fusion power but you aren't seing the forrest for the trees.

Yes, breeding and selecting by it's very nature decreases genetic diversity, is it a big deal, in some crops yes, in others not nearly as much.

As was mentioned by someone above teosinte was pretty much a useless two row grain. Great in the wild probably, always close to extinction, useless to us for the most part until we came along and did our thing to it.


Genetic bottlenecking and inbreeding and wide crosses between types of corn gave us access to genetics not obviously present in this (in my eyes) most sacred of plants. While the "wild" diversity has been bred out of modern corn, in times prior to the green revolution we discoved some new and very divese traits; High protein, High oil, sweet, super sweet, sh2, dent, flint, flour, drought tolerance, cold tolerance, disease tolerance.

Fairly diverse traits, particularly to have come from such a basic ancestor. The simple fact is that as an inquisitive/exploitive/intellectual/exploratory beast we could not and would not have existed on this planet without interfering to some degree with the natural cycle of plants and animals.

If you would go and read your history regarding the breeding of corn and the early hybridization experiments you would find that even the early hybridizers said that F1 hybrids were only a temporary solution, that population selection retaining as much diversity as possible while centering in on a couple of worthwhile traits was much more desirable in the long run.

So what hae we here with this Diversity desirable or not conversation? Well we have 8,000 years of human selection of Zea Maize and various subspecies and a great but now dwindling diversity of types and genes and mutations of genes to work with. Sure, I could select Astronomy Domine down to and ideaotype so strict that the diversity could be bred out, but I haven't and don't plan to, what I have been doing is reintroducing diversity which would otherwise have been lost, selecting for a few traits here and there while trying to maintain others, in time my selection will be different from others and won't be as diverse but michaels will differ from mine as will Johno's as will the version growing in the desserts surrounding Palestine and Israel, all of them will be selected for differing and diverse traits. This argument is one for arguments sake and not for actual intellectual digestion in my opinion.

From Astronomy Domine we have isolated new and very diverse lines of sweet corn, we have indeed created diversity, no not by adding new genes into the genetic coding of corn, but instead by re-introducing genes into the pool, genes which may or may not have ever intereacted with one another, we have facilitated the culmination of evolution in the corn species just as corn breeders have done for 8,000 years and we have maintained diversity by spreading F1, F2, F3, and F4 material as well as various plant type, kenel color type, and cullinary type selections all around the world.

You tell me, what is your definition of diversity because mine is different from yours. That said, I believe firmly that wild material should be preserved as it's use from an eco-logical standpoint, the role it plays in the wild is absolutely invaluable as well as it's use in future breeding endeavors.

Painted Mountain and Astronomy Domine are probably the two most genetically diverse corns on the planet, what more could you want in diversity?

That said the other side of your argument is that your always selecting against the traits which make for a stable and reliable line which once again is not true as is provable by the work done with painted mountain. It is very possible to select for a handful of traits while maintaining the diversity of the corn through population breeding, constantly adding and subtracting those genes you want or need, invigorating the stock with new genes. This is not your fathers nor your grandfathers plant breeding. If you have Native American ancestory it might be your great, great grandfathers version of plant breeding.

Also two things to point out:
1. I didn't go to school for any of this and though it didn't occur in this thread I don't like being told I don't understand the genetics of corn when I damn well do and already have varieties available to the public domain.
2. For reference to all involved in sweet corn breeding SU and SE not only travel on the same chromosome they are the same gene, SE is a mutation of SU which is why no isolation distance is required.

[DarJones]

Well taken points Alan, and arguably the best points so far in this thread.

There is however a weakness in your position. Diversity is not a requirement of a breeding program. It may be desirable for other reasons, but from a general standpoint, it is not required. The primary objective of a breeding program is to select desirable genetics and to propagate them to the exclusion of any and all undesirable genetics. If you will take a few moments to think through the background of Painted Mountain, you will see that it has been highly selected for survival in a very harsh environment. This in and of itself means that it has lost genetics that were otherwise present. Granted that it is a highly diverse corn population, but if you consider the diversity of all the parent lines that went into it, then it will have lost diversity in that measure.

Virtually all man originated breeding programs are 'inclusion' programs. They are based on picking specific desirable genetics and propagating them to the exclusion of all else. Corn in all its current diversity is the result of an 'inclusion' breeding program.

How does nature do it? Nature uses an 'exclusion' breeding program. The only genetics that do not survive are those that are unadapted. Because climate is such a variable, some genetics that help with survival in a dry year will be a liability in a wet year. This is the origin and meaning of 'survival of the fittest'.

Why is corn such a diverse species? This has to do with the sheer number of plants being grown. Corn is arguably the most mutable plant on earth. When the population is large enough, there will be mutations at such a high rate that diversity will develop. Consider that every single corn plant has at least 2 mutations that were not present in either parent. Now multiply that by the billions of corn plants grown each year.

The Indian method of saving corn for seed was highly effective. They picked the best ears and kept them over for the next year and they got to define what was the 'best'. Corn was grown over virtually all of North, Central, and South America. Adapting to the various climates took time, about 8000 years, but still, just a cosmic eyeblink. Most of the adaptation took place in the last 1000 years.

Now I'll pose a simple question. Your Astronomy Domine corn, is it more diverse? or less diverse? than the parent lines from which it derived.

About breeding an se open pollinated line. Inbred lines have been developed and crossed to make hybrids since the se gene was popularized in the 1970's. Most of the early hybrids were a combination of se crossed with an su because of problems with vigor, germination, etc. The key in this is that there are homozygous lines that are pure se and they are readily available. To develop a population that breeds true for the se gene would require crossing a homozygous se with an op line that is genetically diverse and then selecting from the offspring. I know that you know how that would have to be done.

Any time you are 'damned well certain' you understand something about genetics, nature will teach you that you don't. Corn breeders thought they understood corn genetics until someone figured out transposons. As soon as someone is certain they understand corn genetics again, there will be another 'transposon' paradigm. That does not prevent us from trying.

Please read this with a bit of humor. The most I ever learned in my life was from a man who totally challenged everything that I thought I knew.

The purpose of this thread is simple, to develop an understanding of diversity. Some is needed. But not too much. Think about it, not the way I think, but the way you think.

I am part Cherokee. I have a strong heritage from 3 separate Amerindian ancestors.

DarJones