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Saw this really amazing video[0] the other day about American Chestnut Foundation's breeding program in Virginia to revive the American chestnut Basically they

by culi 4y ago

Saw this really amazing video[0] the other day about American Chestnut Foundation's breeding program in Virginia to revive the American chestnut Basically they hybridized it with Chinese/Japanese chestnuts (which are blight resistant). Then they take the offspring, test for blight resistance and rebreed those back with purebred American chestnuts. Then they repeat the process. Take those offspring, select for blight resistance, rebreed with American species, etc After a few generations they created an American chestnut tree that looks almost exactly like the purebred versions but retains the blight resistance of the Japanese and Chinese species Really amazing work [0] https://www.youtube.com/watch?v=DbrY-J0bpto https://www.youtube.com/watch?v=DbrY-J0bpto

echelon 4y ago
Why don't they use agrobacterium transfection, gene guns, or molecular techniques to directly transfer the resistance genes over? Do we not know what the genes themselves are? I'm not criticizing their technique! Nor do I think I know better. This is amazing and valuable work, and I'd love to know more.
- ch4s3 4y ago
  IIRC the breeding program predates those tools.
- systems_glitch 4y ago
  Low-tech, non flash solution that delivers.
- culi 4y ago
  Good question. I'd imagine something like blight resistance would probably not be a simple case of a few specific genes we can just switch over. It could also just be technology. This breeding program has been around for 50 years or so and CRISPR only really took off around 2011. In addition, the original CRISPR-Ca9 caused a lot of unintended changes in DNA and it's really critical that the new trees are morphologically equivalent to the original trees in order for the birds, insects, and animals that depended on them to resume their interactions. Newer technologies like CRISPR-Nickase are much more precise but also very recently developed
  - JshWright 4y ago
    It actually is pretty "simple" in this case (the tree needs to produce a single chemical, oxalate oxidase). There is a program that has done this very successfully, and it just working through the regulatory process before wider distribution can happen. They have thousands of trees in (controlled) forest plots, including three generations of offspring.
    - culi 4y ago
      That's very interesting. The video I linked showed that blight resistant trees had a very specific response to grow extra tissue around the infection site to stop it from spreading further so I assumed it was more of a multi-pronged defense
      - empyrrhicist 4y ago
        Yes - the Asian ones that evolved with the fungus have a more complex strategy, making a purely breeding-based program challenging. Separately, some clever genetic engineering allows the trees to break down oxalic acid, which prevents the fungus from being able to efficiently attack the plant cells. Two separate things.
        pfdietz 4y ago
        These two approaches could be combined, and probably will be naturally if both varieties are introduced to the wild.
        JshWright 4y ago
        Indeed, part of the work being done by the team working on the genetic engineering approach is breeding Darling 58 with the Chinese backcrossed version.
    - empyrrhicist 4y ago
      That's the genetic engineering approach, but the Chinese ones have a different, more complex, less well understood, and potentially complementary resistance mechanism.
- at_a_remove 4y ago
  If I recall, someone has jammed a wheat gene into a few of them in just that manner. It's a tricky business, because chestnut had very particular properties, as wood, that made it quite valuable, and any gene interference, well ... who knows how it will change the resultant wood?
- mistrial9 4y ago
  Do we not know ....
- notsapiensatall 4y ago
  I've been wondering the same things for the past decade. It seems like it's very hard to get your gene into the right place so that it will be expressed at the right time, with enough consistency to make a stable cell line. Also, it seems rare to find just one gene that encodes a property or compound. Usually you need several genes to form a pathway from a common precursor chemical to your target result. That pathway will be leaky, and it may take resources away from other important chemicals that the plant's lifecycle relies on. It sounds expensive and time consuming - plants take a long time to compile, and you can forget about reproducible builds. Plus, once you have your GMO, you'll be expected to take care not to release it into the wild, and in today's world, a decent chunk of people will oppose your product because of their personal beliefs.
- space_fountain 4y ago
  There is actually a parallel technique nearing the finish line that does sort of this. The gene they moved though is from wheat not another tree species, but still seems to give great blight resistance. Currently the barrier to it is entirely regularity. I believe it would be one of the first plants approved to just be released into the wild without something to prevent it reproducing naturally. The normal anti genetic engineering types are very opposed, but it seems likely it will get approved in the next few years. https://www.nytimes.com/2020/04/30/magazine/american-chestnut.html?unlocked_article_code=E9SWUJi2vbxvUl6Arfwr6vkHQtiRNsxy-9d5Ya4tu0Ii1iNYCGwAuCpQqH20PzgZBJbuzDm2q9RIJra4euNfFpKWXwFsBHSSNcYOrjCrag31Pt9ZtWk4o_pet_9r45Ln_9XXJwG4SFmZ_hFdNIDaY6ctN95fWPiICDDvydKAuzhYnnSX6nBOh4Mc3NhA9Kw2L4n3EcxIxmBuM0-aSYKlq-RWMj1Ehbt-SPcCTsTxkoSSKUKtfcvWTHPXxOVpk-I2OfJzfMwCFqKYDPp56fmnQ0931jPGFvDNgR2IqS8Cmep656jR8mIYOmnEb8upf2i3hWRMjchHs1ESKVDn&smid=share-url https://www.nytimes.com/2020/04/30/magazine/american-chestnu...
  - JshWright 4y ago
    A buddy of mine has been involved in this project for years at SUNY ESF, and it's very exciting how successful it has been. There are dozens of test sites around central New York that have healthy (albeit very young) populations of American Chestnuts.
  - canjobear 4y ago
    What authority can enforce approval or disapproval to release something into the wild? Suppose I own land next to a national park. Then can’t I plant whatever I want on that land, trusting that it will spread into the park?
    - robwwilliams 4y ago
      These are not GMO plants—just selectively bred plants. This is similar to almost all domestic animals and most plants.
      - julienchastang 4y ago
        There are two parallel efforts going on at present for restoring the American chestnut, a backcross effort and a GMO-based approach. This sub-thread is concerned with the GMO strategy.
- tsol 4y ago
  Honestly there's probably a benefit to just avoiding more controversial tech like GMOs. There will be that much less resistance to re-introducing them back into the wild
- exmadscientist 4y ago
  The things the gene gun can do turn out to be not the most useful things one could hope for from it. (It's a surprisingly brute-force device, though I guess that was all in the name if you actually took it at face value!) I don't see a ton of future for it as a generalist technology, though what things it does well it does very well. CRISPR is... awful in different ways. (It seems to have a lot of trouble controlling how much material it transfers.) It's a laboratory curio or one-off stunt now, but I fully expect it will improve.
- robwwilliams 4y ago
  They probably have no firm idea about the key genes involved in resistance. There could be half a dozen.
  - adenner 4y ago
    There are methods like GWAS that could help nail that down.
greenonions 4y ago
Saw that video recently as well. What's remarkable about this find is the size of the specimen, and that it's confirmed to be 100% American Chestnut. Hopefully with the hybrid approach, this find, and further breeding/propagation work, we can see a large scale return of this incredible species.
dfc 4y ago
The chestnut project is from the Commonwealth of Virginia, not West Virginia.
- culi 4y ago
  Woops, thanks for the correction
nebul 4y ago
For anyone wanting to learn more about this breeding technique, it's called backcrossing[1]. It's also used for agricultural crops, but requires many generations. [1] https://en.wikipedia.org/wiki/Backcrossing https://en.wikipedia.org/wiki/Backcrossing
- tsol 4y ago
  Simple, yet effective. I've heard it said modern fruits are relatively tasteless compared to their older counterparts because they are bred for size and hardiness. I wonder if these can be backcrossed as well to produce more flavorful fruits with similar sizes
  - nebul 4y ago
    The hard thing with taste is that it's usually the sum of many quantitative traits, each one being governed by several genes which can be located on different chromosomes, as seen in tomato[1]. Transferring enough of them into the modern genome through backcross would probably require a crazy amount of generations... or a crazy amount of luck :) [1] https://doi.org/10.1093/jxb/erf058 https://doi.org/10.1093/jxb/erf058
    - DuskStar 4y ago
      Or, you know, CRISPR.
      - robbiep 4y ago
        CRISPR as currently used is not functionally capable of cutting and pasting large swaths of the genome, it is for small specific edits
    - robwwilliams 4y ago
      You would need to map the relevant loci and then use a speed congenic selection strategy. Done in mice easily. Mapping the loci modulating traits like disease resistance or taste is the hard part.
lettergram 4y ago
Unfortunately, I can’t buy them yet. Driving me nuts
- cpfohl 4y ago
  You can buy the backcrosses, as far as I know...it's the modified ones from SUNY ESF that you can't buy yet.
  - lettergram 4y ago
    You can actually buy them for 2023 - https://support.acf.org/membership/new-seed-level https://support.acf.org/membership/new-seed-level But they still have to pass the FDA, EPA, USDA - https://www.federalregister.gov/documents/2021/08/06/2021-16771/state-university-of-new-york-college-of-environmental-science-and-forestry-notice-of-intent-to https://www.federalregister.gov/documents/2021/08/06/2021-16...
- DeanStevenson 4y ago
  > Driving me nuts I see what you did there.
bergenty 4y ago
I sent them an email asking them for seeds a few months ago, unfortunately they stopped giving them out.
- culi 4y ago
  Do you know if they'll resume giving them out at some point? Maybe someone else who got access to seeds can help you out
subpixel 4y ago
The genetic modification the ACF is doing is actually very controversial among the community of people commuted to restoring fruit and nut biodiversity. I just saw Eliza Greenman speak on this subject, never expected that to circle back to HN.
- jonstewart 4y ago
  Backcrossing/“breeding” is relatively uncontroversial and not considered GMO — though it may be controversial whether the eventual derived breed is a true American Chestnut. There is a GMO effort which adds a gene to the American Chestnut so that it produces an enzyme called oxalate oxidase; the gene comes from wheat plants. The enzyme breaks down the oxalate acid produced by the blight fungus. The first GMO tree was planted in 2006 and has held up, as have others in the test plot. IIRC, USDA permission is being sought so it can be planted freely. Assuming it wins approval, I’m really hoping I can get some seedlings in a few years to plant in my forest. https://www.esf.edu/chestnut/genes.htm https://www.esf.edu/chestnut/genes.htm
  - subpixel 4y ago
    "To save the American chestnut tree, researchers want to release genetically engineered trees into the wild to reproduce. It would be a first — a possible breakthrough and an irreversible experiment." https://acf.org/ny/news-events/how-gmos-might-save-the-american-chestnut-tree/ https://acf.org/ny/news-events/how-gmos-might-save-the-ameri...
audiodude 4y ago
I hate these awful GMO trees! Why can't we have certified USDA Organic trees anymore!
- robwwilliams 4y ago
  Assume this is a joke, right? Have to add the ;-) even for nominally bright people.
  - collegeburner 4y ago
    nah, the whole ";)" "/s" "/j" nonsense can go yeet itself off a cliff. i absolutely hate that stuff.
    - mrelectric 4y ago
      Yoink that back.
  - audiodude 4y ago
    It's a joke, but I do have questions in general about "Certified Non-GMO" versus "Modern day bananas, corn and tomatoes look nothing like they did 400 years ago". There are some types of genetic modifications that are considered "natural" and "OK" and somehow there are others that are "artificial" and "scary", but damned if I know which are which.
    - audiodude 4y ago
      To play devil's advocate to myself and possibly answer my own question: I imagine there are ecological effects of GMO (some of your corn SHOULD get killed by insects). Not to mention the fact that GMO seeds are probably mostly sold by god-awful Monsanto.
      - AlbertCory 4y ago
        Maybe someone with an agricultural background would have an easier time researching this, but: "mostly" Monsanto? Or is that just an older, famous example? Lots of companies sell seeds in mass quantities -- are you saying none of them sell GMO seeds?
lettergram 4y ago
You can actually buy some of those seeds now - https://support.acf.org/membership/new-seed-level https://support.acf.org/membership/new-seed-level Though, they are still going through the FDA, EPA, and USDA process... https://www.federalregister.gov/documents/2021/08/06/2021-16771/state-university-of-new-york-college-of-environmental-science-and-forestry-notice-of-intent-to https://www.federalregister.gov/documents/2021/08/06/2021-16...

by culi 4y ago

echelon 4y ago

Why don't they use agrobacterium transfection, gene guns, or molecular techniques to directly transfer the resistance genes over? Do we not know what the genes themselves are? I'm not criticizing their technique! Nor do I think I know better. This is amazing and valuable work, and I'd love to know more.

ch4s3 4y ago
IIRC the breeding program predates those tools.
systems_glitch 4y ago
Low-tech, non flash solution that delivers.
culi 4y ago
Good question. I'd imagine something like blight resistance would probably not be a simple case of a few specific genes we can just switch over. It could also just be technology. This breeding program has been around for 50 years or so and CRISPR only really took off around 2011. In addition, the original CRISPR-Ca9 caused a lot of unintended changes in DNA and it's really critical that the new trees are morphologically equivalent to the original trees in order for the birds, insects, and animals that depended on them to resume their interactions. Newer technologies like CRISPR-Nickase are much more precise but also very recently developed
- JshWright 4y ago
  It actually is pretty "simple" in this case (the tree needs to produce a single chemical, oxalate oxidase). There is a program that has done this very successfully, and it just working through the regulatory process before wider distribution can happen. They have thousands of trees in (controlled) forest plots, including three generations of offspring.
  - culi 4y ago
    That's very interesting. The video I linked showed that blight resistant trees had a very specific response to grow extra tissue around the infection site to stop it from spreading further so I assumed it was more of a multi-pronged defense
    - empyrrhicist 4y ago
      Yes - the Asian ones that evolved with the fungus have a more complex strategy, making a purely breeding-based program challenging. Separately, some clever genetic engineering allows the trees to break down oxalic acid, which prevents the fungus from being able to efficiently attack the plant cells. Two separate things.
      - pfdietz 4y ago
        These two approaches could be combined, and probably will be naturally if both varieties are introduced to the wild.
        JshWright 4y ago
        Indeed, part of the work being done by the team working on the genetic engineering approach is breeding Darling 58 with the Chinese backcrossed version.
  - empyrrhicist 4y ago
    That's the genetic engineering approach, but the Chinese ones have a different, more complex, less well understood, and potentially complementary resistance mechanism.
at_a_remove 4y ago
If I recall, someone has jammed a wheat gene into a few of them in just that manner. It's a tricky business, because chestnut had very particular properties, as wood, that made it quite valuable, and any gene interference, well ... who knows how it will change the resultant wood?
mistrial9 4y ago
Do we not know ....
notsapiensatall 4y ago
I've been wondering the same things for the past decade. It seems like it's very hard to get your gene into the right place so that it will be expressed at the right time, with enough consistency to make a stable cell line. Also, it seems rare to find just one gene that encodes a property or compound. Usually you need several genes to form a pathway from a common precursor chemical to your target result. That pathway will be leaky, and it may take resources away from other important chemicals that the plant's lifecycle relies on. It sounds expensive and time consuming - plants take a long time to compile, and you can forget about reproducible builds. Plus, once you have your GMO, you'll be expected to take care not to release it into the wild, and in today's world, a decent chunk of people will oppose your product because of their personal beliefs.
space_fountain 4y ago
There is actually a parallel technique nearing the finish line that does sort of this. The gene they moved though is from wheat not another tree species, but still seems to give great blight resistance. Currently the barrier to it is entirely regularity. I believe it would be one of the first plants approved to just be released into the wild without something to prevent it reproducing naturally. The normal anti genetic engineering types are very opposed, but it seems likely it will get approved in the next few years. https://www.nytimes.com/2020/04/30/magazine/american-chestnut.html?unlocked_article_code=E9SWUJi2vbxvUl6Arfwr6vkHQtiRNsxy-9d5Ya4tu0Ii1iNYCGwAuCpQqH20PzgZBJbuzDm2q9RIJra4euNfFpKWXwFsBHSSNcYOrjCrag31Pt9ZtWk4o_pet_9r45Ln_9XXJwG4SFmZ_hFdNIDaY6ctN95fWPiICDDvydKAuzhYnnSX6nBOh4Mc3NhA9Kw2L4n3EcxIxmBuM0-aSYKlq-RWMj1Ehbt-SPcCTsTxkoSSKUKtfcvWTHPXxOVpk-I2OfJzfMwCFqKYDPp56fmnQ0931jPGFvDNgR2IqS8Cmep656jR8mIYOmnEb8upf2i3hWRMjchHs1ESKVDn&smid=share-url https://www.nytimes.com/2020/04/30/magazine/american-chestnu...
- JshWright 4y ago
  A buddy of mine has been involved in this project for years at SUNY ESF, and it's very exciting how successful it has been. There are dozens of test sites around central New York that have healthy (albeit very young) populations of American Chestnuts.
- canjobear 4y ago
  What authority can enforce approval or disapproval to release something into the wild? Suppose I own land next to a national park. Then can’t I plant whatever I want on that land, trusting that it will spread into the park?
  - robwwilliams 4y ago
    These are not GMO plants—just selectively bred plants. This is similar to almost all domestic animals and most plants.
    - julienchastang 4y ago
      There are two parallel efforts going on at present for restoring the American chestnut, a backcross effort and a GMO-based approach. This sub-thread is concerned with the GMO strategy.
tsol 4y ago
Honestly there's probably a benefit to just avoiding more controversial tech like GMOs. There will be that much less resistance to re-introducing them back into the wild
exmadscientist 4y ago
The things the gene gun can do turn out to be not the most useful things one could hope for from it. (It's a surprisingly brute-force device, though I guess that was all in the name if you actually took it at face value!) I don't see a ton of future for it as a generalist technology, though what things it does well it does very well. CRISPR is... awful in different ways. (It seems to have a lot of trouble controlling how much material it transfers.) It's a laboratory curio or one-off stunt now, but I fully expect it will improve.
robwwilliams 4y ago
They probably have no firm idea about the key genes involved in resistance. There could be half a dozen.
- adenner 4y ago
  There are methods like GWAS that could help nail that down.

greenonions 4y ago

Saw that video recently as well. What's remarkable about this find is the size of the specimen, and that it's confirmed to be 100% American Chestnut. Hopefully with the hybrid approach, this find, and further breeding/propagation work, we can see a large scale return of this incredible species.

dfc 4y ago

The chestnut project is from the Commonwealth of Virginia, not West Virginia.

culi 4y ago
Woops, thanks for the correction

nebul 4y ago

For anyone wanting to learn more about this breeding technique, it's called backcrossing[1]. It's also used for agricultural crops, but requires many generations. [1] https://en.wikipedia.org/wiki/Backcrossing https://en.wikipedia.org/wiki/Backcrossing

tsol 4y ago
Simple, yet effective. I've heard it said modern fruits are relatively tasteless compared to their older counterparts because they are bred for size and hardiness. I wonder if these can be backcrossed as well to produce more flavorful fruits with similar sizes
- nebul 4y ago
  The hard thing with taste is that it's usually the sum of many quantitative traits, each one being governed by several genes which can be located on different chromosomes, as seen in tomato[1]. Transferring enough of them into the modern genome through backcross would probably require a crazy amount of generations... or a crazy amount of luck :) [1] https://doi.org/10.1093/jxb/erf058 https://doi.org/10.1093/jxb/erf058
  - DuskStar 4y ago
    Or, you know, CRISPR.
    - robbiep 4y ago
      CRISPR as currently used is not functionally capable of cutting and pasting large swaths of the genome, it is for small specific edits
  - robwwilliams 4y ago
    You would need to map the relevant loci and then use a speed congenic selection strategy. Done in mice easily. Mapping the loci modulating traits like disease resistance or taste is the hard part.

lettergram 4y ago

Unfortunately, I can’t buy them yet. Driving me nuts

cpfohl 4y ago
You can buy the backcrosses, as far as I know...it's the modified ones from SUNY ESF that you can't buy yet.
- lettergram 4y ago
  You can actually buy them for 2023 - https://support.acf.org/membership/new-seed-level https://support.acf.org/membership/new-seed-level But they still have to pass the FDA, EPA, USDA - https://www.federalregister.gov/documents/2021/08/06/2021-16771/state-university-of-new-york-college-of-environmental-science-and-forestry-notice-of-intent-to https://www.federalregister.gov/documents/2021/08/06/2021-16...
DeanStevenson 4y ago
> Driving me nuts I see what you did there.

bergenty 4y ago

I sent them an email asking them for seeds a few months ago, unfortunately they stopped giving them out.

culi 4y ago
Do you know if they'll resume giving them out at some point? Maybe someone else who got access to seeds can help you out

subpixel 4y ago

The genetic modification the ACF is doing is actually very controversial among the community of people commuted to restoring fruit and nut biodiversity. I just saw Eliza Greenman speak on this subject, never expected that to circle back to HN.

jonstewart 4y ago
Backcrossing/“breeding” is relatively uncontroversial and not considered GMO — though it may be controversial whether the eventual derived breed is a true American Chestnut. There is a GMO effort which adds a gene to the American Chestnut so that it produces an enzyme called oxalate oxidase; the gene comes from wheat plants. The enzyme breaks down the oxalate acid produced by the blight fungus. The first GMO tree was planted in 2006 and has held up, as have others in the test plot. IIRC, USDA permission is being sought so it can be planted freely. Assuming it wins approval, I’m really hoping I can get some seedlings in a few years to plant in my forest. https://www.esf.edu/chestnut/genes.htm https://www.esf.edu/chestnut/genes.htm
- subpixel 4y ago
  "To save the American chestnut tree, researchers want to release genetically engineered trees into the wild to reproduce. It would be a first — a possible breakthrough and an irreversible experiment." https://acf.org/ny/news-events/how-gmos-might-save-the-american-chestnut-tree/ https://acf.org/ny/news-events/how-gmos-might-save-the-ameri...

audiodude 4y ago

I hate these awful GMO trees! Why can't we have certified USDA Organic trees anymore!

robwwilliams 4y ago
Assume this is a joke, right? Have to add the ;-) even for nominally bright people.
- collegeburner 4y ago
  nah, the whole ";)" "/s" "/j" nonsense can go yeet itself off a cliff. i absolutely hate that stuff.
  - mrelectric 4y ago
    Yoink that back.
- audiodude 4y ago
  It's a joke, but I do have questions in general about "Certified Non-GMO" versus "Modern day bananas, corn and tomatoes look nothing like they did 400 years ago". There are some types of genetic modifications that are considered "natural" and "OK" and somehow there are others that are "artificial" and "scary", but damned if I know which are which.
  - audiodude 4y ago
    To play devil's advocate to myself and possibly answer my own question: I imagine there are ecological effects of GMO (some of your corn SHOULD get killed by insects). Not to mention the fact that GMO seeds are probably mostly sold by god-awful Monsanto.
    - AlbertCory 4y ago
      Maybe someone with an agricultural background would have an easier time researching this, but: "mostly" Monsanto? Or is that just an older, famous example? Lots of companies sell seeds in mass quantities -- are you saying none of them sell GMO seeds?

lettergram 4y ago

You can actually buy some of those seeds now - https://support.acf.org/membership/new-seed-level https://support.acf.org/membership/new-seed-level Though, they are still going through the FDA, EPA, and USDA process... https://www.federalregister.gov/documents/2021/08/06/2021-16771/state-university-of-new-york-college-of-environmental-science-and-forestry-notice-of-intent-to https://www.federalregister.gov/documents/2021/08/06/2021-16...