Dr. Merritt Khaipho-Burch
@MerKhaiBurch
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Ph.D. from @Cornell | 🇹🇭/Oglala Lakota | Quant gen of 🌽 | @UHHilo & @SDState Alum | Pro GM 🌽
Joined March 2018
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I'm now officially Dr. Merritt Khaipho-Burch!
I gave my seminar to the Plant Breeding and Genetics Section
@Cornell
and passed my B-exam on Tuesday! My next stop is
@corteva
, where I'll be a Research Scientist! Thanks to my committee
@EdBuckler
@CedricFeschotte
&Wojtek Pawlowski
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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 🧵
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My article is now out in
@Nature
!
It’s been ~1 year since my post about the flaws within 2 high-profile articles that claimed 33-68% increases in crop yield. Our paper describes common issues & suggests yield-testing criteria for future pubs. A thread🧵
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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 🧵
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Hot off the press is rTASSEL, an R front-end for TASSEL published in the Journal of Open Source Software!
If you’re looking for an easy R package to import & filter genotypes, run GWAS, perform genomic prediction & more - rTASSEL is the package for you. A 🧵 on the key features:
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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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My angry plant breeding student plea to future authors of “Yield increase by [insert wild number] in X crop” studies:
Please verify your yield estimates in multi-environment trials in elite backgrounds. Yield in lab-optimized, unimproved lines means very little 14/
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I beaded some teosinte earrings this weekend and they came out amazing 😍🌽
#BeadedTeosinte
#BeadingPlantBreeding
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With other scientists & the public thinking plant breeders can “solve” yield with 1 gene, more $$ goes into studying unreliable single gene effects over the incremental, stable & repeatable yield gains over 1000s of small effect loci performed by industry & uni plant breeders 11/
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We don't need your white saviorism. We don't need your settler colonialism saying what our "problem" is that you created through genocide. We don't need you to save us. There are over 574 federally recognized, sovereign nations whose land you are on. 7/
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We, I, need you all to be better mentors. Better advisors. Better allies. Deem our work as scientific enough to be presented on that stage and not just invite us here to fix your diversity problem. So I ask you all again, why did you all clap
#MGM2023
?
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There’s no Nature or Science paper for that 389-763% yield increase because it’s what plant breeders have routinely accomplished over decades of plant improvement & genetic gain 8/
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Try out rTASSEL developed by postdoc Brandon Monier in the Buckler lab! Compared to the TASSEL GUI, the R interface is highly reproducible and 1000X more intuitive than the TASSEL command-line interface.
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Why didn’t the committee on diversity, equity, and inclusion say something? As PIs, and future PIs, you need to stop tokenizing your marginalized scientists. 13/
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I need you all to take a look at yourselves and think about why you all clapped at the end of that speech. Do you think that Indigenous peoples need your help? Do you think that we need saving from being poor? From substance abuse? From living on reservations? From sickness? 6/
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Whose crops you are all working on and benefit from. And whose stories you are telling without our consent in a manner that reinforces these deficit narratives over and over again about how we are disappearing and how we are helpless. 8/
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This won’t be the last time a paper like this is published. Keep an eye out for the sample size, yield estimates against commercial lines, and if these estimates are corrected for field-design/grain-moisture/etc…. 13/
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Flashy “Yield increase by [insert wild #] in X crop” studies are frequently published in big-name journals but rarely follow the rigorous QC steps needed to verify these yield claims.
Once the news gets out - articles like these spread like wildfire (Altmetric metrics👀) 10/
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In plant breeding, we need replicated field trials in numerous backgrounds in target growing environments.
Studies that do not replicate appropriately are not going to cut it.
13/13
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had been to 5, 10, 20, up until 60 meetings. At even the 5+ year mark, I felt alone. Indigenous peoples have worked alongside maize since before colonial constructs of time began, but it is very telling that there are no Indigenous peoples here but me. 12/
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1.16-1.39 T/ha is an incredibly low yield. The average yield for Chinese rice is 6.8 T/ha; it can get up to 12 T/ha (see linked pub).
With the same vibes as their abstract, commercial varieties yield 389-763% more than lines overexpressing OsDREB1C 7/
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If you're at
#PAG30
come check out my poster PE0378 on how transposable elements contribute to gene expression in maize 🌽 on Monday from 10-11:30. I have zines with summaries of my project to pass out!!
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Not stories of our strength, power, and resilience in these historically exclusive institutions and communities. 9/
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While these genes definitely hold some promise, as a plant science community we have to stop with “click-bait” yield science. We mislead the public, other scientists, and policymakers who allocate funding towards our research 12/13
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Looking closely at their yield trials, they grew overexpressed OsDREB1C lines over 3 years in 3 environments, testing only 99-120 plants each time (Tables S1-S5). For yield trials, this is a VERY small # of plants to test for yield stability (it's usually of 1000s to millions) 4/
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There was a question earlier about how we can figure out why historically excluded scientists leave academia, and Dr. Zavala’s answer was just to ask. Well, this is one of those reasons. Why did you all clap? 10/
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Is it even my job to say something? As far as I know, I am the only (North American) Indigenous person in this community. It’s 3 AM, and I will probably regret this later, but after thinking about it for a bit, this is what I WISH I had said 5/
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I waited until the paperwork was official (and I took a breath) but I passed my A-Exam on October 5th! Stoked to be a PhD Candidate now 😎🤓 1/2
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Although large-effect single gene changes can drastically alter yield, let's not forget that evolution has had millions of opportunities (or more) to overexpress OsDREB1C over the past 10k years, have these changes become fixed, & then have it contribute to yield 12/
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I will spare the details here - but the more general comments painted Indigenous communities as impoverished groups who needed to be saved from substance abuse, poverty, death, and the reservation. Very much viewing Indigenous communities through a deficit narrative 3/
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This is my 8th maize meeting. During the yearly maize meeting tradition, those who have attended this meeting for the most years stay standing, and those who haven’t sit down. I watched the majority of the historically excluded participants sit down as they called out who 11/
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The authors claimed that overexpressing this gene improved rice yields by 41-68%. Looking into their genotypes, they used a non-commercial rice variety (Nipponbare), a genetic background not intended for yield trials but great for studying genetics and transformation 3/
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What made this worse was that people clapped after this comment/speech. Hundreds of people listened, and no one said anything. They clapped. I felt too uncomfortable and shocked to get up, collect my thoughts, and say something 4/
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My first first-author pub is out!
We looked at pleiotropy across 120,597 traits in 2 maize pops & found:
1) 1.56-32.3% of intervals show pleiotropy
2) Most pleiotropy is explained by noise variables imparted by GWAS
3) No relationship with RNA/open chromatin/GERP
More below!🧵
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We taught a workshop called “Cabbages and their cousins: the dogs of the plant world” (a play on Chris Pires’s catchphrase) to NY State teachers as part of the Research and Education Activities for Community Teachers (REACT) program
#scicomm
#STEMoutreach
A 🧵on the activity 1/7
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Zooming in on their yield, they report the 41-68% yield gain on a per-plot basis from 1 year in 1 environment where they yielded 910-1084s vs 644g.
Yield is typically measured in tons per hectare, so going from g to T/ha given their plot spacing, they get 1.16-1.39 T/ha. 5/
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For context, one individual (a white guy) who has been in the maize community for a very long time got up and gave a 4-5 minute comment on the VERY intimate life details of an Indigenous maize geneticist who worked in their lab 2/
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The variety they used, Nipponbare, isn’t meant to be a high-yielding variety. This is probably why the authors overexpressed OsDREB1C in the elite cultivar Xiushui134. Their grain yield was ~7-8 T/ha. In other studies, Xiushui134 yields ~10T/ha (9/)
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Thanks everyone for reading through.
For those interested in a plant breeder's take on another
@ScienceMagazine
article about the "41-86% yield increase" in rice, check out my last thread:
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 🧵
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While this paper was cool, the yield trials lack sufficient replication to make any claims. The experiment was grown over 2 years (‘20, ‘21) in just 1 environment in Illinois. Solid yield trials are tested in 15-20 target location-year combos in numerous genetic backgrounds 4/13
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If you're at
#PEQG22
come stop by poster 351T tonight at 9:15! I'll be talking about the patterns of pleiotropy in maize🌽 with key project takeaways made into zines to give away.
If you need to find/recognize me, I'm wearing beaded teosinte earrings 🌽
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My first day of the 22nd grade is today 🎉. S/O to my partner for photoshopping together the emotions that best explain starting out the 4th year of my Ph.D.: happiness, anger, sadness, and acceptance.
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For context, this paper overexpressed the rice gene Dehydration-Responsive Element-Binding Protein 1C (OsDREB1C). OsDREB1C is a member of the APETALA2/ethylene-responsive element binding factor (AP2/ERF) family that modulates photosynthesis and nitrogen utilization 2/
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My article is highlighted on
@Nature
's official X account and main website today! Give it a read! The link to my thread explaining the paper is below.
With a changing climate and a growing population, the world increasingly needs more-productive and resilient crops. But improving them requires a knowledge of what actually works in the field
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I received the David L. Call Achievement Award last night from the American Indian and Indigenous Studies Program here at Cornell! My name is on a plaque Ma!
Pilamaya and ขอบคุณ to AIISP & the Indigenous Graduate Student Association for the award and nomination❤️💛🧡
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Some
#IndigenousFoodSovereignty
for your timeline, pictures from the Iroquois White Corn Project Husking Bee at the Seneca Art & Culture Center at Ganondagan. We husked a mountain of ears before they were braided into long strands and hung to dry. The ears were HUGE 🌽🌽
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Math for the yield numbers:
20 rows*10 plants per row*.233 interspace rows *.167 interspace plants=7.78 meters^2/plot
1 hectare=(100 meters)^2=10000 meters^2
# of their plots that could fit in a ha: (10,000m^2)/(7.78 m^2/plot)=1284 plots/ha
1284 plots/ha*1084g=1.39 T/ha
6/
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I found out this morning that my mentor & friend at
@SDState
, Dr. Don Auger, passed away last night. Don was a fantastic teacher and mentor and shared his love of maize genetics with everyone. I’m going to miss him.
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This Friday, I'm giving a talk about maize quantitative genetics at the Indigenous Computing Symposium 🌽. If you're around, come stop by or join us through Zoom!
Wanted to share an awesome event coming up this Friday (April 28th) titled "Indigenous Computing." We have a rad line-up of talks! If you are interested- registration link can be found here:
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I can't think of two more appropriate books to prop up my laptop as I record my 5-minute poster presentation for .
@ICQG6_Brisbane
#ICGQ6
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I'm presenting my poster at the virtual maize meeting today at 12:30-1 PM PDT/3:30-4PM EDT. It's poster 16 in the Quantitative Genetics and Breeding section, come hear about my project, chat, or just hear some terrible corn puns 🌽🌽🌽
#VMM2020
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Before vs after my student seminar, the panic and anxiety buildup was intense and I'm glad it's over now 😅
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That's me!
Merritt Khaipho-Burch
@MerKhaiBurch
is a 3rd year Ph.D. student in the
@EdBuckler
lab studying pleiotropy across maize mapping populations & the role of transposable elements in the regulation of gene expression. Merritt is a graduate of both
@UHHilo
and
@SDState
🌽🌽🌽🌽
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This is my first
@sacnas
conference & I'm stoked for the first full day of talks!
#SACNAS2020
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I spent this past week on Dakota homelands at
@IndigiData
to learn how Indigenous data sovereignty, kin and relationality, and ethics will interact with new machine learning/AI techniques and gene editing.
It was an absolute blast filled with laughter, poetry, and community 🧵
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@jrossibarra
I took your labs meme one step further and printed it on a cake to thank all the summer undergrads for their work! It brought some good Ken-ergy and laughs group 🩷🌽
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Thanks
@SJB_SynBio
for a thoughtful reply to your soy yield paper! You made good points on the theory & evolution behind this. Small yield trials are okay, BUT we need to be cautious to highlight the limitations of our experimental design & results w/in our papers & the media 1/3
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And like my last set of tweets, this is my plant breeding student plea to future authors of “Yield increase by [insert wild number] in X crop” studies: Please verify your yield estimates & think about some of our other yield testing criteria before making such claims 15/15
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If you’d like to learn more about what to look for in studies claiming massive increases in yield, check out our website, where we list these common issues and offer a free downloadable flier to decorate your lab! 13/15
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I got to ride in a combine for the first time on Tuesday in the heart of Iowa's corn country and it was AWESOME.
THERE. WAS. SO. MUCH. CORN. 🌽😍🌽
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This time all their high-yielding lines yielded LESS than their WT. Weather happens & they do mention this. However, the emphasis in their discussion & in the news don’t hype SFig 12.
Replication is key in science & unreplicated results make effects hard to believe 10/
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Attending my first Cold Spring Harbor meeting
@cshlmeetings
virtually on Transposable Elements. Super stoked to hear all the talks!
#cshlTE2020
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Check out our pre-print on using haplotype associated RNA expression to predict a bunch of complex traits in maize with
@AnjuAnjugiri1
and
@GuillRamstein
!
Haplotype Associated RNA Expression (HARE) Improves Prediction of Complex Traits in Maize
#bioRxiv
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Fun fact: Doudna also grew up in Hilo Hawaii! I emailed her back in 2014 when I was still an undergrad at
@UHHilo
after hearing an NPR segment on CRISPR and was 1) blown away that she responded and 2) amazed at how kind and supportive she was towards rouge undergrads emails 😅
BREAKING NEWS:
The 2020
#NobelPrize
in Chemistry has been awarded to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing.”
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I received my first dose of the Pfizer-BioNTech COVID-19 vaccine today! I feel great & incredibly lucky 🎉💉🎊
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The Plant Breeding Symposium at Cornell is seeking grad-student speakers for our April 17 2020 symposium "Bringing Back Biodiversity". We're offering 2 travel scholarships. All are welcome to apply!
Applications due Feb 7
More info
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The virtual Maize Genetics Meeting just started and I'm so excited for all the amazing talks and posters happening over the next two days!
#VMM2020
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In this paper, the authors introduced three photosynthesis genes related to non-photochemical quenching - an essential process of protecting plants from high light intensity☀️ by avoiding the damaging effects of reactive oxygen species on the photosynthetic apparatus🌱 2/13
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This article has already taken off in the media (Altmetrics📈👀), with even the New York Times
@nytimes
writing a column on it in today’s print edition paper: 11/13
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More beaded teosinte earrings (and a somewhat matching necklace), this time with actual Zea mays parviglumis seeds as cabs!
#BeadingPlantBreeding
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Their yield estimates are ~5 t/ha for the WT and ~7 t/ha in their best line. This is where the 33% yield increase comes from, 1 environment in 1 year with 1 line.
The average increase was 24.5% (Fig 1B). Also, these results were only marginally significant (** = p < 0.05) 7/13
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This is so cool! 🌽🌽🌽
@EdBuckler
shares at
#TAGC20
how his lab applies machine learning to improve selection/breeding in plants and to match genotype to phenotype across many species! 🌾🌽🍚
#scicomm
#sketchnotes
#livesketching
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Almost everything you dreamed of doing in TASSEL is available in rTASSEL. Multithreaded association analysis (GLM, MLM, fast association), BLUP calculation, linkage analysis, genomic prediction, kinship analysis, and more!
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Genotypes: they used an elite, transformable soybean line (Maverick) to test their constructs which is great. However, testing in more lines, especially elite ones backcrossed into un-transformed lines with blank constructs would be ideal, but this is a preliminary study 5/13
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“Breaking inequalities requires intentionality” in health outcomes and data stewardship for Indigenous communities -- thanks
@ajcalac
for a great talk at this year's
@IndigiData
workshop!
2023
@IndigiData
in Prior Lake, MN! I shared my perspective on responsible stewardship of digital data and how to contextualize and report on Indigenous health disparities data in medicine and public health. Such a great group of students,
@kstsosie
!
@KeoluFox
@tkmackey
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Pictures from around the Cornell campus last August compared to today.
#Smoke
from the fires in Canada is making the air around Ithaca and NY State hazardous (according to AirNow).
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Made some fancy beaded and ribbon facemasks this weekend. I tried to bead a wheat spike but it turned out looking like a bromegrass inflorescence. It's all in the Poaceae family I guess 🌾😅🌾
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The 9th Annual Synapsis Symposium is happening on April 17 completely virtually. Tune in to hear an awesome series of talks centered around the theme "Bringing Back Biodiversity".
Register here:
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My beaded mask is done! The maize ears are not to scale with teosinte but beading a full ear was too much! From what I've read mahiz is the Taino origin for the spanish word maiz and wagmiza is the Lakota word for maize.
Fun fact: this mask is 20X heavier than a normal mask!
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For those on or around the Cornell campus, consider buying seeds from Synapsis, the graduate student group in Plant Breeding and Genetics! All varieties were made by Cornell plant breeders! 🍅🍈🍉🥒
The Synapsis Seed Sale Fundraiser has returned! We are conducting sales online and will be available for local pick up on April 26th on the 3rd floor of the Plant Science Building
For more information visit:
To place an order visit:
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Took a break from beading plants and made Alf (Alien Life Form) from the planet Melmac.
Alf was a character from an 80's sitcom who crash-lands into a family's garage in California and tries to eat the family's cat (a delicacy on his home planet). This guy took 4 days to bead!
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This is a cool paper on the physiology of photosynthesis& shading. In modern AG we control the amount of light that reaches the canopy, unlike in natural ecosystems that have to deal with layers of shading constantly. So there’s potential here for building on knowledge gaps 3/13
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The average yield of soy in Illinois is ~4 t/ha so what they’re seeing is on the same level as state-wide trends (given their field design and ag management practices) 8/13
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Amazing defense seminar from Vivek Shrestha (
@KviveManiStha
) in the
@angelovicir
Lab from
@MizzouBiology
! Best wishes for graduation & your post-doc!
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In 2020, all 9 lines were grown (WT untransformed, 8 versions of the constructs). Plants were grown in 20 blocks, with 1 line/block & 17 plants/line (n = 340). A quarter of a million soybean plants are typically grown, so 340 plants is REALLY small 6/13
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A pair of custom beaded 🥕🥕carrot 🥕🥕 earrings I finished yesterday that came out AMAZING (with only a dozen small mistakes 😅).
#sciart
#beadedplants
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@facundoromani
@ScienceMagazine
Yes, they did test this in an elite cultivar, but their yields were ~7-8 T/ha. That same cultivar yields ~10T/ha when expressed at normal levels
It's absolutely ok that bio studies & verifies the effects of single genes. It's just not going to be a single gene that solves yield.
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Apply as a grad/undergrad student speaker to the Cornell-Corteva plant breeding symposium this April! It's a great way to network, meet new folks, and get feedback on your research!
We are looking for graduate students to present their work at the 2024 Cornell Corteva Plant Breeding Symposium "Breeding for novel systems and complex problems" on April 12th, 2024. Come share your work and network!
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There's no substitute for large yield trials to verify genes &make these yield claims. Field trials should be budgeted for in grants with the same importance as molecular or publication costs. I'd even bet there are plant breeders that would collaborate on something like this 3/3
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In 2021 they only grew 4 lines (WT+3 highest yielding lines from '20). Plants were grown in 16 blocks, 1 line/block, 17 plants/line (n = 272). Again not enough reps BUT a storm hit their field during grain-fill and caused many plants to lodge (fall over & not right themselves) 9/
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My little Asian heart is bursting with joy and freaking out, this is so amazing! ♥️🎉
Kamala Harris makes history as the first Black woman and first person of South Asian descent elected as vice president of the U.S. Harris served as San Francisco's district attorney and California's attorney general before becoming a U.S. senator.
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We discuss how genetic engineering tech, such as CRISPR, can play a major role in adapting plants to climate change. However, this rapid need for solutions may lead to the overselling of early-stage results that have little experimental replication in high-profile pubs 3/15
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I'm proud to be attending my 6th maize meeting this year even though I'm nowhere close to the year count of some long-time attendees!
#MGM2021
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Our first in-person Expanding Your Horizons (
@CornellEYH
) event was a success! Aimee (
@aimeejschulz
) and I ran three workshops named Plant Domestication and Adaptation: A seed dispersal game for local 7-8th girls interested in science. A thread🧵on how the game is played👇
Thanks to fellow Synapsis members Merritt and Aimee for organizing the Explore Your Horizon’s workshop on plant domestication and seed dispersal! Synapsis volunteers helped young women scientists design crafty “seeds” that were optimal for dispersal and domestication settings.
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To hammer the idea home, we then create “super cabbages” and glue the selected modern cabbages onto a wild Brassica. It looks absolutely ridiculous, but it’s fun 🥦🥬 6/7
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During my undergrad evolution course I wrote a paper on maize domestication & took a deep dive into the 5-6 major domestication loci and the ‘drama’ behind maize evolution theories. It was awesome to hear about the stories, experiences & discoveries from Doebley himself!
#MGM2021
Congratulations to Dr. John Doebley, 2021 recipient of the MGC Barbara McClintock Prize for Plant Genetics and Genome Studies. He is recognized for his significant contributions to our understanding of genome evolution and maize as a model system for crop domestication.
#MGM2021
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Yep! This Science paper could have been a strong, standalone physiology + molecular biology study without any clickbait-like yield claims.
@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 met my first ever Thai professor (อาจารย์) this morning during
@seapcornell
's Thai language table. As a little Thai kid trying to make it in academia it's nice to see other Thai folks striving at high levels (even if they don't study plants!) 🇹🇭🌱
The Language Table for Thai will be held on Fri. April 23 at 9-10am EDT on Zoom.
Learn about studying Thai at Cornell, with an opportunity to ask the instructor and current students questions!
Southeast Asia Language Month Event
@EinaudiCenter
@CornellLRC
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There's now a chromosomal level assembly and sequencing data on tons of ʻōhiʻa lehua/Metrosideros taxa. What an amazing resource for a culturally significant and gorgeous plant!
Prob better to share preprint now then couple of hours later today. I want to share a study on the evolutionary genomics of incipient adaptive radiation of the Hawaiian Metrosideros complex. People interested in plants speciation genomics check it out! 1/
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This was one of the posts I made last year critiquing a paper published in
@ScienceMagazine
claiming a 41-68% increase in rice yield that had very limited plot and environmental replication (among other issues). 2/15
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 🧵
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I just want to do a shoutout to our awesome participants at the Cornell Synapsis Symposium for cultivating a great discussion during the breaks and after talks
#SynSymp2020
@Kezipar
@goel_peshal
@AgSystemScience
@WStafstrom
@san_dweeney
@etaagen
@EstefaniaTav
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