Breeding Beans

[jim]

Sadly those resistance genes haven't been very durable, and are breaking down.

[Joseph Lofthouse]

May 4, 2012 19:20:32 GMT -5 jim said:

Sadly those resistance genes haven't been very durable, and are breaking down.

I would think that the horizontal and QTL resistances would be getting better as the more susceptible cultivars and individuals succumb. Or perhaps the growing strategy there is like it is here: Grow susceptible cultivars and spray them prolifically to kill the whiteflies that are the transmission vector? Thus preventing the development of multi-allele resistance.

[jim]

Resistance rarely gets better Joseph...the virus evolves even faster than the genes in our plants. Resistance genes are slowly overcome by the pathogen...we are always in a race against the pest to get a different resistance before the older one is overcome.
Multiple QTL might help, but even then a specific strain or race of the pathogen might be able to infect a "resistant" plant.
QTL does not mean horizontal...a QTL could be involved in vertical resistance too....Vertical resistance is much easier to breed with, obviously...
Jim

[Joseph Lofthouse]

May 4, 2012 21:47:32 GMT -5 jim said:

Resistance rarely gets better Joseph...the virus evolves even faster than the genes in our plants.

When I observe the world around me I come to a different conclusion: Because if viruses tended to evolve faster than plants, then there would be no plants and only viruses. But that is not what I see when I look around me... I see a balance: The plants and the viruses more or less in equilibrium with each other...

Historically there have been tremendous losses when a new pest gets into an essentially cloned mono-crop like potatoes in Ireland, or corn in Africa. But some portion of the plant population survived, and developed suitable defenses. Beans in the tropics are doing the same thing in the fields of traditional farmers. The technocratic heavy equipment operators might be having a harder time of it with their essentially clonal monocultures, but that's the karma to be paid for growing highly inbred genetically fragile monoculture crops.

May 4, 2012 21:47:32 GMT -5 jim said:

Vertical resistance is much easier to breed with, obviously...

It's not at all obvious to me... I go for incremental multi-allele resistance every time rather than seeking out a single allele. And multi-allele resistance is incredibly simple for observant farmers to achieve on their own land with their own seed: It's how farmers have been maintaining their crops for 10,000 years.

I'm pretty much a disbeliever in Mendelian Genetics as taught by the public school system... It seems absurd to me: The idea that there is one allele that turns a trait on or off by being either dominant or recessive... I think that a more accurate model would propose that there are dozens or thousands of alleles that affect every phenotypic trait, and they are just as likely to be penetrant as they are to be either recessive or dominant. Then add epigenetic traits into the mix and things get really unpredictable really quick.

[raymondo]

In some cases, there is simple dominance. And as a teacher of genetics in the public school system I'd have to say that Mendelian genetics is a very useful model for a number of things we see around us, several human ailments among them. The course I teach includes both qualitative and quantitative genetics so the students are certainly exposed to the idea of multiple genes contributing to phenotype. They even get to hear about pleiotropy. Of course, I'm talking about public education in Australia, not the US.
I think that perhaps from a farmer's perspective, you may be right Joseph. It seems reasonable to me that if you are growing large numbers of things regularly, it would be far easier to be selecting incremental improvements, whatever they may be.

[Drahkk]

Joseph, I spent several years teaching Genetics and Biology at the high school level (thinking seriously of going back to it soon, but that's another story), and you're absolutely right. Mendel was a pioneer in a very complex field, but he chose the specific traits he did his research on because they worked predictably with his system. We now know that they only worked because those few traits really were controlled by a single gene, and the peas he was working with were diploid. The truth is, he was very lucky to identify multiple single gene, 2 allele traits in the same organism. The overwhelming majority of traits are controlled by multiple genes, usually a dozen or so, but sometimes hundreds. (Fruit shape in pepos, for example!) Most of those genes have more than two possible alleles, and dominance or recessiveness is rarely complete. Add polyploidy to the mix and you have more than two alleles per trait. A single gene diploid cross may have 4 possible outcomes, but a single gene tetraploid cross would have 36. And as we mentioned, single gene traits are rare.

I think it was Johno who started the thread earlier today about the complexity of plant genetics. I don't envy people who work in that field professionally.

Mike

[jim]

Obviously you are not going to be convinced Joseph...and I don't really care if you are...but, there actually are simply inherited traits controlled by a single gene with dominant and recessive interaction...there are many, many, many examples.
Mendell was lucky, but that does in no way reduce the value of his observations and that he was the first to look at this critically and worked out the models he did.
Are most phenotypes Mendellian, Absolutely not!
Your argument keeps moving....Horizontal resistance is important, and so is vertical resistance. There is a theory that what you consider "horizontal" alleles for resistance were once "vertical" and have since been overcome, and there is pretty good evidence to that. When you break down the interaction between pathogen and host...you will see why this makes sense.
Are smallholder farmers supposed to maintain poor yield and resist vertical resistance for some philosophical reason?
Since the pathogen and host coevolve, as long as the host can stay one molecule ahead, it can resist...
No need to be overdramatic...obviously plants can keep up...most of the time....
Jim

[oxbowfarm]

There's more to think about than breeding here. Virulent viruses are taking advantage of a set of specific circumstances, large numbers of hosts in close proximity is usually the big one. Instead of thinking about ways to genetically engineer a crop to resist a virus, how about redesigning the circumstances to favor avirulence. Most viruses evolve towards avirulence, HIV is deadly in Homo sapiens but is avirulent in the African monkeys we caught it from.

[Joseph Lofthouse]

May 5, 2012 22:15:00 GMT -5 jim said:

there actually are simply inherited traits controlled by a single gene with dominant and recessive interaction...there are many, many, many examples.
...
Are smallholder farmers supposed to maintain poor yield and resist vertical resistance for some philosophical reason?

I have a fundamentally different view of the world. I can't think of a single phenotypic trait that depends on only one allele. As far as I can tell, every trait depends on hundreds of alleles coding for all sorts of proteins, and metabolic pathways, and etc... And in most instances the only populations in which Mendelian phenotypic segregation can be readily observed are in extremely inbred fragile cultivars for example in "elite" germplasm, or in radical inbreeders like peas.

As far as I can tell on my own small farm, and with my own eyes, my mongrel landraces with their multiple allele resistance yield better than any commercial strain that can be purchased, and they taste better. I believe that single gene resistance should be avoided by every clever farmer for the philosophical reason that single gene resistance is futile.

And for the practical reason that single gene resistance is typically owned by mega-corporations, but multiple allele resistance is available to every seed saver.

In my fields, a pest would need to overcome tens of thousands of corn genomes in order for my corn crop to completely fail to produce seed for the next season. In a highly inbred monoculture field it only needs to overcome one.

[jim]

I definitely have a different frame of reference from you Joseph...and I certainly respect your methods.
I have, however, studied genetics in considerable detail....and can tell you that there are Mendelian traits whether you, yourself, see them or not. Modifying genes? certainly.
But what you are considering "horizontal" and "vertical" is the same exact thing, originating in the same exact way. And, they are used by both private and public breeders...yourself included.
Jim

[castanea]

Dec 9, 2011 3:42:00 GMT -5 Hawk said:

Hey Holly!

We would get along just great... The "M" word and GMO's give me the creeps...

It is funny that you mentioned pole beans because that is what I had in mind. My Papaw (Grandfather) has always told me to stick with pole beans. His favorite pole bean was a white greasy cutshort bean that may not exist anymore. I am on a quest to find this bean if it still is around. My grandparents said it had the best flavor and yield of any bean they have grown. They said that this bean had white seeds. Their second favorite bean that they still grow is Kentucky Wonder. I have always been a serious gardener. Breeding plants is of high interest to me. I enjoy watching things grow and paying attention to the details. No laboratories in my backyard!

There are certainly a few white greasy cutshorts available. I think I have one or two. They are generally only available from regional seed companies that specialize in Appalachian or southeastern plant varieties.

[DarJones]

But what you are considering "horizontal" and "vertical" is the same exact thing

This is a correct statement but should be clarified a bit to make sense. Horizontal resistance is implied to mean a single phenotypic expression resulting from multiple genetic traits. Vertical resistance is implied to mean a single phenotypic expression resulting from a single genetic trait. Joseph's position that relying on a single trait is a fools paradise is amply proven by the rust resistance genes that were trialed in African maize crops yet failed miserably so long as only one resistance gene was involved. I very much agree that the terms Horizontal and Vertical are misleading. I would rather say "single trait" vs "multiple trait" resistance.

Potato is a good example for this discussion since it has developed multiple copies of the R gene group which convey late blight tolerance. Several variants convey tolerance to a single strain of P. Infestans yet are susceptible to all other strains. By stacking R genes into a single plant, it is possible to achieve resistance to multiple variants of late blight. However, this resistance is based on single traits and the probability of a given strain of late blight overcoming a single trait is 100% given enough time. So in this case, stacked single traits do NOT convey broad tolerance to the disease because it is based on a 1 trait 1 strain of late blight model. An analogy would be a door with a dozen locks, but if you release any one of the locks, the door is open and the disease can enter. The way we need it to work is to put a bunch of locks on a door, then each individual lock must be released one at a time before the door will open.

Joseph is very accurate in condemning monocultures. The 1970's corn disease scare occurred because of using a single highly susceptible parent with cytoplasmic sterility. This single line made essentially the entire world wide corn breeding programs of the time susceptible to a single devastating disease. We are not doing more to maintain diversity, rather, the large companies like Monsanto rely more and more on monocultures.

Joseph states that he has thousands of genotypes in his fields. I state that even so a single disease organism has the potential to find an achilles heel that would allow it to wipe out all of his corn. Look closely at the rust devastation in Africa and you will see that one plant here and one plant there survived. That may be great from a breeding perspective because it means there are tolerance genes to work with, but it is lousy from a human perspective since people starved to death because of the crop failure.

Is GMO totally bad? My answer is no, it is not. I have reason to believe that genetically modified food crops will in the end be the key to feeding an expanding world population. But it will not be because of efforts of the plant breeding companies like Monsanto who want to lock up the results of gmo work and it won't be based on the current shotgun methods of inserting genes into organisms. GMO will only reach its true potential when we can completely construct a genome from scratch with the desired traits. We are very very close to this capability. An example I would use is to suggest combining the nitrogen fixing abilities of cowpeas with maize so that a maize crop would produce most of the nitrogen it needs. This is not possible with today's GMO techniques, but it is feasible in a constructed genome. The implication is we need a LOT more knowledge about genetics than we have today.

One thing I see often on this board and that bothers me immensely is an attitude that because someone got several dozen different varieties of corn (pick your crop, corn is just a good example) and planted them together so that they inter breed that something great has been achieved. Far from it. True genetic improvement comes in the following generations where a crop is selected and reselected by both natural and artificial means until it becomes a truly outstanding crop in a given environment. That is the point where a composite breed becomes an adapted breed and the value of diverse germplasm becomes evident. If you move that adapted breed to a different environment, it might be an utter failure. Consider Joseph's adapted corn which if grown in my climate would probably be devastated by corn smut and other fungal diseases.

I get pretty torqued up when an outbreeder like corn and an inbreeder like tomato and a clonal group like potato are all lumped together and treated like they can be managed the same way, i.e. get a bunch of varieties together and select the best adapted. The advantage of getting a bunch of varieties together and selecting the best only works when sexual reproduction is involved. If you want to improve potato, you will have to start breeding potatoes, saving seed, and growing those seed to find better producing potatoes for your growing conditions. If you want to work with tomato, you are going to have to cross a lot of tomatoes and find selections that work in your environment. This can be done with natural crossing since tomatoes typically cross 1 to 5 percent of the time, but it means that selecting an adapted tomato landrace could take 100 times as long as for an outbreeder like corn.

Selection pressure has to be directed toward survival and production. There is a reason why wild crops are rarely useful in cultivation and it has to do with economics. As Kapuler noted, when you plant a cultivated crop in a naturalized environment, pests tend to destroy the crop because it is just a nice convenient snack for them. Consider teosinte, it makes a wonderful fodder, but it is hopeless to expect to eat much grain from it. When Mesoamericans started selecting teosinte for agronomic traits, the result was corn as we know it today. You can use corn for fodder, but it excels as an economic grain producing crop. This is all because 5 critical genetic variations were recognized and propagated, not because someone grew a lot of varieties together.

I should write a lot more, but it is late and I am tired.

DarJones

: corrected spelling

[steev]

Well, yeah. One can play the lottery, or one can punch in at the factory. The lottery is enticing, but the factory is a living. I plant lots of varieties to see what works in my conditions and on my plate. Lots of failures, not always or often the plant's fault. In time, I will amass a file of plants/varieties that work for me/have characteristics I want. Then I may start breeding. I don't see any end to this. That's what I really want: work that has no "end", so I always have stuff to figure out and work on. What else would I do, learn to play Bridge?

[12540dumont]

I'm with Steev on this one.
How can I expect to start breeding even one crop, let alone the 30 that I think I need for the farm, unless first I trial many varieties to see what works.

Let's take my artichoke example.
Year one, I planted Globe artichokes and planted them. I got 3 artichokes (all tough and stringy) and the gophers ate all 12 plants.

Year two, I put in cages and planted another strain of Globe artichokes and learned when to pick them. I got 20 artichokes.

Year 3, I did nothing and the same 12 Globe artichokes gave me about 50 artichokes.

Year 4, Some one sent me some Violetta artichoke seed and I planted them. I got a bumper crop of mini chokes and about 75 Globe artichokes. Right then I decided that mini chokes were not for me and I wanted bigger artichokes.

Year 5, the gopher ate a hole in the irrigation and so, I got about 30 dry stringy artichokes.

Year 6, I pulled the whole mess out and started again. I tried finding artichokes from all over the world. Unfortunately, it came down to either hybrids or 4 varieties. I'm not happy about this. There's an artichoke fly that devastates artichokes, and I'm not sure that my artichokes have any resistance. All 4 new varieties came to me from Europe, Alan Kapuler sent me his own artichokes as well. Unfortunately, only 2 of 12 germinated of his varieties. Susan Ashworth also sent me hers, but too late to do anything with this year.
So what do I have 36 artichokes that I do not know yet if they will meet any of the qualities that I'm looking for. Larger! Tastier, a little more drought tolerant? In the meantime 4 artichokes spontaneous sprouted up in the garden, a cross between the violetto and the globe.

What have I learned? Artichoke breeding takes a long time. Germplasm is hard to find. Of the 50 or more known types, I can only find 4. That sucks. I'm 1/2 hour from the artichoke capitol of the world, what do they have to offer? Hybrids.

What about the cross between the violetto and the globe? Don't know yet. So much time already gone. I probably will have purple hair by the time I get decent artichokes.

What about potatoes? Dar is right on here. I have saved the same clonal potato year after year and watched the vigor and yield decrease year after year. I have high hopes for TPS. Maybe there will be something there? Once again, only time will tell.

What about the onions? Ditto.

What about the beans? I have to grow them out so that there is enough to even experiment with. So far I have at least 6 beans than have more protein than a pinto. More time needed to access yields, diseases, and of course the variations in weather.

What about the carrots? Still working on it.

Everyone of these things boils down to time. Who will take up the work that I started when I'm too old? Will it matter if the carrots I worked so hard on are only good here in San Martin?

Now, I'm totally depressed.

Vanity of vanities, all is vanity. What profit has a man of all his labor which he performs under the sun? One generation passes away, and another comes: but the earth remains.

[DarJones]

There is a vanity which occurs on earth, that there are just men to whom it happens according to the work of the wicked; again, there are wicked men to whom it happens according to the work of the righteous. I said that this also is vanity.

Good things happen to bad people, bad things happen to good people. But in this case, I think Holly just needs someone to help her plant beans.

DarJones