2022-02-07T08:00:00Z
Julia D
Whenever I read about epigenetics, I wonder they are talking about endophytes instead. Ok think about it… heat, cold tolerance and various stress tolerance in the second generation, and inconsistent results based on the researcher. If some researchers are sterilizing their seeds, they could lose anything that looks like epigenetics, just like the sterilized basil lost resistance to fusarium, while other researchers who don’t get good results. Not sure how that could explain sweet potatoes, maybe it does?
Mark R
The two are a bit confusing to me as well but I think that epigenetics and endophytes are very different things. Epigenetics deals with, for lack of a better word, spontaneous changes in how genes are expressed where Endophytes deals with a symbiotic relationship between organisms. In my garden I think it’s unlikely that sweet potatoes, a tropical perennial could have picked up appropriate endophytes allowing them to morph into a productive annual.
It’s just speculation of course but I think it’s more likely some epigenetic change took place instead. Only that, to me, can explain how such a rapid transformation took place. Especially since sweet potatoes are already known for a high incidence of spontaneous mutation.
Mosty just fun stuff to think about, the beauty of landrace breeding is all you really have to do is observe it, full understanding is optional. 
Actually, now that I’m thinking more on it, I think I’m kind of relying on epigenetics, for example to trigger greater cold tolerance in my brassica project. I know the larger plants going into last winter fared better than the smaller ones going into this winter. Maybe with greater stress these smaller ones will undergo some change that makes them even more tolerant and eventually I can harvest fresh produce in increasing colder periods.
If I can add in even greater vigor by encouraging endophytic relationships that will just be icing on the cake.
Lauren Ritz
I planted five varieties of cabbage late last summer. Three of the plants survived over the winter and got small heads. When I leave here I’m going to take them with me (if the soil is soft enough) and hopefully get seeds this year.
Mark R
I think we do have wild brassicas, but I don’t know what species or how to really how to identify them, I’ll be looking into that though.
I suspect that, and without much real evidence that if a change happens very quickly it may be more likely that epigenetics is involved. If an overall improvement in vigor, tolerances and production occurs over a longer period then endophytes may be playing a role.
I think my best shot for meaningful experiments with endophytes is in corn and beans. I have many wild grasses, both perennial and annual and a native wild bean, all of which are easily accessible as sources.
What I don’t have is space to run a lot of experimental and control plots simultaneously.
Mark R
I could try that with brassica I reckon. Sterilizing anything has not been my practice for a long, long time. If I do sterilize some, I guess in theory they may fare poorly in comparison.
Not with sweet potatoes though. Although I now have reliable TSPS (true sweet potato seed), and they have reached the point that they even volunteer, there are several reasons I can’t add new experiments with them. I’m still in the process of backcrossing the best of each year (by cloning) to the new seedlings each year. This is an effort to genetically “distill” for lack of a better word, a line of seed that has all of my desired traits basically locked, while at the same time still being diverse in other traits.
The space issue is a big factor here too, just not enough room to take on more ventures until I have my elite seed line established better. It’s been close to ten years but I’m getting closer to the goal of an annual seed grown sweet potato that makes a good crop (from seed) in 100 days or less.
Ray S
I think the two (endophytes and epigenetics) are intimately connected - the knee bone is connected to the thigh bone and all that. The French seed grower Pascal Poot has been allowing his plants to do their own thing for many years now. He grows in a climate with hot, dry summers, rarely irrigates, never weeds and so on. He talks about his pants learning how to survive his rather harsh gardening style and passing on what they’ve learned to their offspring. I think his results are due to a combination of epigenetics and an improved, localised seed microbiome, and perhaps numerous other things we know nothing about as yet.
I think it would be a mistake to believe that one or the other is solely responsible.
Christopher W
I wonder how frequently endophytic infection triggers epigenetic effects and it would be impossible to claim it’s one or the other.
Mark R
Or the opposite of that. How often an epigenetic switch enables an endophytic relationship. Fortunate that actually knowing isn’t really necessary. All we have to is observe and encourage improved vigor, tolerance or production by favoring seed from superior plants. It’s fun to learn and speculate but to me the actual mechanism of improvement is largely irrelevant.
Julia D
Both make sense to me… this for example on epigentics causing an endo. relationship?.. JW talks about the corn that takes a 2-5 years to “relearn” how to associate with microbes (after being bred for high yields/syn N) . I was grilling him on if this is a selection process, or something else that causes this re-learning process, he couldn’t tell me.
Lowell M
I live in Tallahassee, FL which is zone 8b and about 5 years ago I grew Austrian winter peas from seed and have saved their seeds for about 3 generations (there was a gap in which I was gone and didn’t plant). The seed I have today is completely different from the seed bought from the company. Their seed was perfectly round, all uniform, and had two very slight brown color variations. I have not noticed any types of pollinators attending the flowers and plants are often spaced far apart as they are interplanted within our field and some make it in with row crops. The seed I have now has multiple different colors of light golden brown to dark brown, some with very detailed markings and others plain, some are large and dented seeds, some smaller and round or also dented. Anyways, there is an incredible variety of genetics showing up in the seed that was not at all present in the initial seed. I even purchased some more from the company recently and it is very distinct from my saved seed. It is possible some of our very small pollinators are not catching my eye and exchanging pollen, or that when I was not looking the bumble bees have been exchanging pollen. I thought that perhaps these changes are reflective of the new environment which would include our clay soil, large temperature fluxes between frosty winters and hot temperatures as it goes to seed in April and May. It was clear to me that the genetics were changing and I attributed this to either an epigenetic process or perhaps the seeds contained diverse genes that were inactive in the climate it originally grew and were more active here. I thought a lot about how genetics are influenced by environment from making tempeh and working with aspergillus cultures. For example, protases and amylases work better at specific temperatures, protases at cooler and amylases at warmer. Thus to some extent you can control if more protein or starch is broken down by temperature control. Perhaps plants experience a similar situation. Higher temperatures during seed formation may make it more difficult for protein synthesis and so less protein content is expressed in the seed which then makes sugary or starchy genes become predominately expressed which then may also have secondary expression in color and shape of the seed. This is all hypothetical. I do not know if higher temperatures inhibit protein synthesis for some plants. My point is speculative about how the genetics of these peas work and changed since I do not suspect they exchanged pollen and their seeds are very different from their parents. Adding endophytes to all of this seems essential and yet also make any claim more uncertain.
Julia D
Interesting. Have the pea plants also changed the way they grow? Are they any more or less vigorous now then when you bought them?
Lowell M
Not that I’ve noticed. It has been a few years too since I last planted them and this year I plan to make make more observations. At some point I may trail separate plots of original seed and my seed for comparisons.
Lauren Ritz
Certainly let us know what happens. There is a huge amount of what scientists call “junk DNA” which they say has no purpose. I personally think the simplest organisms are far more complex than modern science admits.
Because of the industrial revolution, we (as a culture) are used to thinking of things as disconnected. Put everything in its box and that’s all there is. But the natural world doesn’t work that way.
Julia D
@Mark I asked James White this question about endophytes and epigenetics. Just posted his response. Maybe you can tell me what he actually means?? Like a real world example. It’s in the Optional topics, Epigenetics. [now in the Microbes course]
Mark R
Goodness, I don’t know, I’m anything but an expert on this. I only heard the term for the first time a few months ago. From what I can gather it’s like Dr. White said, that genes can switch on and off or express in different ways. From what I’ve read before, various things like temperature or disease stress can cause that to happen but that when it does happen it becomes inheritable in offspring.
I think it might be also that sometimes genes simply have no value in some situations so go unnoticed but are not actually in a switched off state. That might be the case with a tomato I got from Joseph. It isn’t completely disease proof but at least as resistant as any others I have. The gene for that had no use in Joseph’s arid environment but it comes in real handy in mine. Probably overall, about 30% of tomatoes I got from Joseph resisted disease just fine even though they had no need for that ability in his garden, so I doubt this is a case of genes switching states. I suspect they were doing their thing all along but the diseases they resist aren’t present in the high desert, so it wasn’t obvious.
Another possible example is a tomato I call Particularly Productive Rutger. It just showed up one time in the Rutger patch. It was more productive and determinate than the others. It wasn’t a cross because its offspring did not segregate. Maybe it underwent an epigenetic change or maybe it made an endophytic friend or maybe both, I’ll never know.
Right now, I’m watching my brassica plants. Out of the couple hundred I started with this winter I’m down to about twenty. This is an example of where I hope epigenetics might come into play. Maybe some extra hardy genes are in there in one or more of those twenty that will get switched on.
I like Dr. White’s summary where he says it’s more of a philosophy. I think that is especially true outside academia and extra true in my little gardens. If for example one or more of these little brassica plants survives better than others I will never really know why. It might be purely genetic; it might be due to epigenetics or to endophytes or to some combination.
So, my philosophy for a long time has been to keep my garden as natural as possible. Lots of plant material gets added to rot, nothing except produce and seeds, not even diseased tomato vines ever leave.
I’ll never know the real scientific basis of it, but I theorized a long time ago that the micro life in the soil is supposed to be there and it was a good idea not to mess with it by using chemicals of any kind. Even things you might not think of as toxic might be toxic to the bacteria or funguses that live there.
Of course, like Dr. White mentioned not all things are of those things are good. That’s where, I think a lot of common garden advice and practice goes wrong. It makes the assumption that they are all bad or at least that the bad ones are so bad that it’s worth killing them all.
I think that’s why the landrace practice works so well. All I have to do is observe. When good plants show up, I can speculate that they had epigenetic changes or that they have new genetic makeup from being crossed but fortunately I don’t have to actually know. All I have to do is replant their seeds.
Now that I’m learning about endophytes I can again, just speculate, that maybe they have made microbial friends that help them along and that protect them from the bad microbes. That the endophytes themselves as well as the plants can also undergo epigenetic changes just adds a whole new twist but still, all I have to really do is observe.
Julia D
Interesting stuff coming out aboutt how mutations are not actually random… which Joseph has often said,… 'plants will figure out how to deal with the bugs, diseases…" which I took non-literally, --ie the past prevailing science mindset said changes will be random, then Nature selects the strongest, then we select our favorites of the strongest. BUT, I think this means that genes will more often recombine in more beneficial ways in future generations, so the plants are literally figuring out how to survive better in local conditions, in real time. Which is really cool. But I’m still wondering how much of these epigenetic mutations could happen with sterilized seed. Wish I had a lab and Phd students, but I’ll certainly be trying to test this this year.
The Nature study they reference is about epigenetic forces influencing how genes are recombined in future generations… at least I think it is… but this is an interesting read on this topic.
I’m working my way through the Nature study they’re summarizing, I’ll try to summarize it after that.