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Ed Buckler
47 posts
Over two decades ago, we mapped the variant making sweet corn sweet—after tremendous effort. PlantCaduceus easily identifies this single base pair causal variant. 🌽
Give it a try—this model paves the way for treating all plants as a single molecular system!
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What’s remarkable about PlantCaduceus is its ability to be fine-tuned in Arabidopsis and still retain accuracy in distant species like major grass crops, such as corn. 🌱→ 🌽🌾
This class of models are a game changer for plant genomics! biorxiv.org/content/10.110…
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PlantCaduceus - Cross-species modeling of plant genomes
Led by Jingjing Zhai and Aaron Gokaslan, with the Kuleshov lab, we’re having our “ChatGPT moment” with DNA Large Models. PlantCaduceus predicts functional DNA sequences with single base resolution across flowering plants.
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Ed Buckler retweetledi
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@jrossibarra receives the @theNASciences prize in Food and Agriculture for his amaizing use of evolution to understand where we came from and where we can go!
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New whole-genome alignment tools are needed for tapping into plant div... sciencedirect.com/science/articl…
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Ed Buckler retweetledi
Comments were made last night at #MGM2023 that were hurtful to members of our community. Discrimination and harassment, even in the absence of malicious intent, is a violation of our code of conduct, and the damage to members of our community is no less real. 1/3
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Ed Buckler retweetledi
Dr.MariaElena Zavala's talk at #MGM2023 was amazing. Dr. Zavala talked about research, mentors & work to increase the number of historically excluded folks in the academy. The Q&A session however had VERY disparaging comments about Indigenous peoples and I want to tell you why 🧵
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@facundoromani @SJB_SynBio @JohnathanNapie1 @facundoromani @SJB_SynBio @JohnathanNapie1 - perhaps this is not clear from Europe, but most every US public Ag school (~50) is growing GM trials every year. We have the land and procedures to do this responsibly. Soybean is particularly easy given its selfing nature.
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@EdBuckler @SJB_SynBio @JohnathanNapie1 Not an expert, but I am not talking about paperwork but a lot of guidelines that need to be followed in GMO trials. That affects the use of the adjacent land, barriers to prevent cross-pollination, incineration of the plants, future use of the land, etc..
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@BioNetworksbyAB @BioNetworksbyAB - there are thousands of public sector plant breeders globally able to run trials at multiple locations with their colleagues. Thousands of articles a year report those results. Yield is about interactions with the environment and needs to be measured there.
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If we need plot replication in multiple locations for publication, we can never again publish on yield gains (only companies have the money and facilities for this kind of replication). This demand kills public sector research if it became the standard, I am afraid.
Dr. Merritt Khaipho-Burch@MerKhaiBurch
ANOTHER paper in @ScienceMagazine came out claiming a 33% increase in soy yield. Since my last “yield” tweet took off - lets do it again! From a (wanna be) plant breeder 5 years into my PhD, let me explain how this 33% increase in yield is misleading 🧵science.org/doi/10.1126/sc…
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Ed Buckler retweetledi
.#JaneSilverthorne dedicated her career to helping #scientists succeed and to raising public awareness of the importance of #plant #biology @NSF @ASPB @ASPB_WiPB Her support and mentorship lifted me up when I needed it most during my career ❤️
Global Plant Council@GlobalPlantGPC
#plantbio20 Jane Silverthorne just shared the lessons learned during her time working at the National Science Foundation @NSF
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My great colleague @LongLab published a neat paper on how plants deal with light, but @MerKhaiBurch is right; yield increases that don’t replicate should not be claimed in abstracts or press releases.
Dr. Merritt Khaipho-Burch@MerKhaiBurch
ANOTHER paper in @ScienceMagazine came out claiming a 33% increase in soy yield. Since my last “yield” tweet took off - lets do it again! From a (wanna be) plant breeder 5 years into my PhD, let me explain how this 33% increase in yield is misleading 🧵science.org/doi/10.1126/sc…
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Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks acsess.onlinelibrary.wiley.com/doi/10.1002/tp… Congrats Travis Wrightsman and team on the really nice paper!
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Wonderful to see @edanquah240 again! Agree so much we can do together and for the next generation to design better food systems.
Eric Danquah@EY_Danquah
Erasing inequities in capacity to innovate in the Ag. Development space will save our world. Inescapable conclusion in meetings with Ed Buckler and Vern Gracen today at Cornell University. @gatesfoundation @RockefellerFdn @Agnes_Kalibata @AGRAAlliance @UnivofGh @CornellGlobal
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@Yan_Geneticist @Yan_Geneticist - the big advantage of these genes lies in their ability to stop lodging ONCE you have applied lots of fertilizer. The Green Revolution was driven by fertilizer, and then genetics plays an important stabilizing role.
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@Liana_Ace @MerKhaiBurch @ScienceMagazine @Liana_Ace - I think we all agree that this is a really neat physiology paper - but the abstract directly claims 41-68% yield increases. And that is what the press releases focused on.
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@MerKhaiBurch @ScienceMagazine I understand where you’re coming from – these are conversations we have w breeders when talking about how physiology can guide breeding. But, I think your assessment is somewhat unfair. The objective of this study is not that of a breeding program but rather a proof of concept.
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Ed Buckler retweetledi
A misleading paper in @ScienceMagazine just came out talking about how a single gene can increase rice yield by 41-68%. As a (wanna-be) plant breeder, I’m here to tell you why this study is misleading, and we can’t “solve” yield through single genes 🧵
science.org/doi/10.1126/sc…
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@MerKhaiBurch @ScienceMagazine @MerKhaiBurch is exactly right. This study has lots of neat biology, but we need to measure genetic impacts on yield in elite varieties across numerous target environments.
The study could easily have just focused on impressive physiology and molecular biology.
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I’ve been a professor for 12 years and a dad for nine. In my experience inbox zero is way more attainable than dirty dishes zero.
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