Plant Biology
Plant research at CSHL explores fundamental mechanisms in plant development and genetics with a goal of increasing crop productivity and biodiversity, and reducing climate change through exploring the potential of biofuels.
The plant biology group at CSHL focuses on plant development and gene expression, in an effort to uncover basic mechanisms that could lead to increased crop productivity, increased biodiversity and exploring the potential of biofuels. Researchers use Arabidopsis, maize, tomato and duckweed as model systems to uncover the principles that govern plant growth. Much of this work takes place on 12 acres of farmland at the nearby CSHL Uplands Farm, where expert staff raise crops and Arabidopsis plants for study. Research also involves bioinformatics and quantitative analysis of large data sets for functional genomics and developmental genetics, and has contributed to more than two dozen large scale collaborative genome projects funded by the National Science Foundation, the Department of Energy, and the United States Department of Agriculture.
At CSHL, plant research has a storied history, including Nobel prize-winning research done by Barbara McClintock in the 1940s and 50s. The transposable genetic elements, or “jumping genes,” that she discovered decades ago are now understood to reprogram the epigenome, and are used as research tools by current CSHL researchers studying plant genomes.
The future of food looks small, dense, and very bushy
February 18, 2020
Vertical farming could make agriculture more robust and sustainable. To unlock that potential, scientists are redesigning crops for urban life.
Lippman wins NAS Prize in Food and Agriculture Sciences
January 22, 2020
CSHL Professor and HHMI Investigator Zachary Lippman was awarded the NAS Prize for his work in the field of plant genetics.
A new tomato ideal for urban gardens and even outer space
December 23, 2019
Researchers used CRISPR gene editing to optimize tomatoes for urban agriculture, preparing them for the city rooftops and possibly space missions.
Shifting the balance of growth vs. defense boosts crop yield
December 19, 2019
Researchers found that a specific gene in maize balances both growth of the plant and its immunity.
Plant scientist David Jackson – A CSHL PI profile
November 5, 2019
CSHL Professor David Jackson studies mutated corn and flowers.
Researchers double sorghum grain number to improve food supply
October 30, 2019
A set of hormone-controlling genes may be the key to doubling grain number in sorghum plants.
The important role of an Uplands Farm cat
October 29, 2019
Cats, Uplands Farm’s smallest employees, have always played a big role in plant care and seed guarding.
Zachary Lippman named 2019 MacArthur Fellow
September 25, 2019
Cold Spring Harbor Laboratory Professor and HHMI Investigator Zachary Lippman has been named a 2019 MacArthur Fellow.
The next agricultural revolution is here
September 19, 2019
After reviewing decades of plant research, scientists suggest that with past lessons and modern tools, the next agricultural revolution is at hand.
An essay from the President: Biology for the planet
May 16, 2019
CSHL plant scientists are looking for solutions to the biggest questions in agriculture as environments are reshaped by climate change.
Profile: Doreen Ware champions the plant genome
May 8, 2019
Molecular biologist Doreen Ware uses computer science to parse out the genetic roadmaps of plants.
Cryptic mutation is cautionary tale for crop gene editing
May 6, 2019
Unexpected interactions between mutations can be a thorn in the side for plant breeders. Scientists unveil what drove one infamous “cryptic” mutation.
How do plants sense their environment?
April 30, 2019
CSHL plant scientist Ullas Pedmale details how plants sense the world we share.
Cold Spring Harbor Laboratory announces exclusive license with plant breeding start-up Inari
April 16, 2019
CSHL announced a licensing agreement with partner Inari, a company that is advancing plant breeding by tapping nature’s genetic diversity.
Rob Martienssen wins Martin Gibbs Medal for plant research
April 15, 2019
CSHL Professor Rob Martienssen wins the 2019 Martin Gibbs Medal for his contributions to plant biology.
To protect stem cells, plants have diverse genetic backup plans
April 15, 2019
Experts discover how an essential genetic circuit found in all flowering plants, regardless of species, is protected in startlingly different ways.
Crop yield in maize influenced by unexpected gene ‘moonlighting’
April 1, 2019
Yield of the maize plant is tied to activity of a gene called RAMOSA3, but new evidence suggests the gene performs other unexpected functions
The year of CRISPR
December 26, 2018
A look at the various labs across CSHL that utilize CRISPR in their research, and the groundbreaking discoveries they help uncover.
New regulators of nitrogen use in plants identified
October 24, 2018
A team of CSHL plant biologists identify gene regulators that may help plants utilize nitrogen better and prevent excess nitrogen in soil.
CRISPR could bring groundcherries to market
October 1, 2018
CSHL Professor Zachary Lippman uses CRISPR to make the groundcherry more suitable for large-scale farming
Base Pairs Episode 16.5: Fuels of the fuels
August 16, 2018
Rob Martienssen explains how genetic modification and advances in technology factor into the future of fuel as well as cinematic sci-fi fuels.
Base Pairs Episode 16: Big plans for a tiny plant
July 16, 2018
As temperatures around the globe continue to rise, scientists are working hard to develop solutions that deal with the consequences of climate change
Big plans for a tiny plant
July 15, 2018
On this episode of Base Pairs, Rob Martienssen discusses how duckweed could be the next biofuel and help combat climate change
Energy from thin air: Basic research to biofuels
June 12, 2018
A plant scientist and an industry innovator discuss how simple duckweed may help address climate change and energy needs.
Prof. Zachary Lippman named Blavatnik Award finalist
May 30, 2018
Professor Zachary Lippman was chosen as a Finalist in Life Sciences for the 2018 Blavatnik National Awards
CSHL’s Zachary Lippman named HHMI Investigator
May 23, 2018
CSHL Professor Zach Lippman is selected as an HHMI investigator, in recognition of his innovative work in the field of plant genetics
How do plants know when to flower?
May 18, 2018
Colorful flowers are a sure sign of spring. But how do flowering plants know that it is time to bloom?
One experiment: Twice the tomatoes
March 22, 2018
Zachary Lippman’s team found a way to boost tomato yield by digging into the plant’s genome and fine-tuning its branching patterns.
The secret to tripling the number of grains in sorghum and perhaps other staple crops
February 26, 2018
A simple genetic modification can triple grain production in sorghum, a drought-tolerant plant that is an important source of food and animal feed.
Counting chromosomes: Plant scientists solve a century-old mystery about reproduction
January 18, 2018
Geneticists have solved a century-old mystery by discovering a remarkable mechanism that enables plants to count their chromosomes
Light, cryptochromes, action…
November 21, 2017
Assistant Professor Ullas Pedmale has received the National Institutes of Health "Outstanding Investigator Award."
The changing relationship between humans and plants, it’s complicated
November 3, 2017
CSHL scientists Dave Jackson, Doreen Ware, and Zachary Lippman give their perspectives on the rapidly changing relationship between humans and plants.
New application of CRISPR breaks age-old yield barriers in crops
September 15, 2017
CSHL's Lippman lab has harnessed the untapped power of genome editing to improve agriculture.
Plant geneticists develop a new application of CRISPR to break yield barriers in crops
September 14, 2017
Mutating regulatory regions varies yield traits the way a dimmer switch controls a light bulb
Demystifying GMOs
July 21, 2017
We've all heard of GMOs, but what exactly ARE they? Hannes, a plant scientist from CSHL's Dave Jackson lab, explains genetic modification.
Base Pairs Episode 10.5: Tomato baby and its family
July 14, 2017
Plant scientist Zachary Lippman tells stories from the field of bizarre tomatoes, intensely hot peppers, and giant pumpkins.
Tomato baby and its family
July 14, 2017
This episode of Base Pairs talks to Associate Professor Zachary Lippman about all the weird mutations that naturally occur in plants.
CRISPR vs. climate change
June 15, 2017
This episode of Base Pairs looks at the issues climate change may bring to agriculture and how CRISPR can help overcome them.
Detailed new ‘reference’ genome for maize shows the plant has deep resources for continued adaptation
June 12, 2017
A new, much more detailed reference genome for maize, or corn, as it is called in the U.S., provides new insight into the crop.
Fine-tuning mutant genes unleashes long-trapped potential in tomato
May 19, 2017
A team of plant geneticists at CSHL publish a paper in Cell demonstrating how bringing together beneficial traits can have negative consequences.
Fine-tuning dosage of mutant genes unleashes long-trapped yield potential in tomato plants
May 18, 2017
Understanding gene interactions can enable breeders to break existing productivity barriers in agriculture.
Gene editing yields tomatoes that flower and ripen weeks earlier
December 5, 2016
Using CRISPR to expand the geographical range of important food crops.
Gene editing yields tomatoes that flower and ripen weeks earlier
December 5, 2016
Researchers use CRISPR to expand the geographical range of important food crops.
Gene network controls how many flowers and fruits plants will produce during critical growth window
November 7, 2016
Researchers use RNA sequencing to identify a network of genes that work together to determine the duration of a critical window for growth.
The people problem
September 15, 2016
This episode of Base Pairs looks at the rising population, plant biology, and the future of food.
Base Pairs Episode 4: The people problem
September 15, 2016
Josef Schmidhuber and CSHL Professor David Jackson explain how delving into the mysteries of plant genetics can help offset a bleak future.
Corn controversy
July 15, 2016
This episode of Base Pairs covers the contentious genetics and history of America’s corn production.
Base Pairs Episode 2: Corn controversy
July 15, 2016
The ongoing GMO labeling debate wasn’t the first agricultural controversy. In the early 1900s, it was a new and so-called “wicked” breeding technique
“Amazing protein diversity” is discovered in the maize plant
June 24, 2016
The genome of the corn plant “is a lot more exciting” than scientists have previously believed.
Discovery of new stem cell pathway indicates route to much higher yields in maize, staple crops
May 16, 2016
Biologists at Cold Spring Harbor Laboratory explain how plants regulate the proliferation of their stem cells.
Discovery of new stem cell pathway indicates route to much higher yields in maize, staple crops
May 16, 2016
Researchers discover a new regulatory pathway that channels signals emanating from a plant's extremities to the stem cell niche.
Ancient gene network helps plants adapt to their environments
February 9, 2016
Reseachers discovered the purpose of a tool present in both mosses and flowering plants, organisms whose common ancestor dates back 450 million years.
The iPlant Collaborative is now called CyVerse
January 15, 2016
The enhanced NSF project will now provide data management and computation across scientific disciplines
Saving our food supply with alumna Michelle Cilia
December 11, 2015
Dr. Michelle Cilia has made it her mission to understand the bacteria and viruses that strike plants—and how to stop them.
Addition of sugars plays a key developmental role in distantly related plants
November 19, 2015
Researchers found deleting the genes for enzymes in two plants widely separated in evolutionary time resulted in similar defects.
What’s behind million-dollar crop failures in oil palm? Would you believe bad karma?
September 9, 2015
A way to prevent damaged plantlets from being grown, to boost yield and reduce tropical land pressure.
Scientists pinpoint genes that make stem cells in plants, revealing origin of beefsteak tomatoes
May 25, 2015
Researchers identified a set of genes that control stem cell production in tomato, which affects its size.
NSF’s Science 360: Nature’s toolkit
December 17, 2014
A team of scientists led by CSHL's Zachary Lippman has discovered a set of gene variations that can boost fruit production in the tomato plant.
Getting more out of nature: Genetic toolkit finds new maximum for crop yields
November 2, 2014
An array of gene variants provides “breakthrough benefits” in tomato yield for breeders; other crops next
Hybrid Vigor
September 29, 2014
In 1908, Cold Spring Harbor geneticist Dr. George Shull made a discovery that helped put American science on the map.
Newly identified small-RNA pathway defends genome against the enemy within
March 16, 2014
microRNAs are found to target ‘jumping genes’ in reproductive cells, protecting against genomic damage
Genetic discovery points the way to much bigger yields in tomato, other flowering food plants
December 26, 2013
Scientists learn how tweaking a ‘hybrid vigor’ gene generates higher crop yields
Interview with CSHL Professor Rob Martienssen
November 22, 2013
Dr. Rob Martienssen leads the plant biology group at CSHL, where he focuses on epigenetic mechanisms that shape and regulate the genome.
Oil palm & the rainforest—Genome sequencing for sustainability
November 22, 2013
A multinational team of scientists, including Dr. Rob Martienssen at CSHL, has identified a single gene that regulates yield of the oil palm tree.
CSHL is part of iPlant group awarded $50 million to create US biology cyberinfrastructure
September 17, 2013
The National Science Foundation has awarded $50 million to investigators at Cold Spring Harbor Laboratory
In odd-looking mutant, clues about how maize plants control stem cell number
September 11, 2013
In plants, the growth of organs such as roots, leaves and flowers depends upon the activity of meristems.
CSHL Associate Professor Zachary Lippman at the Secret Science Club, Brooklyn, NY
August 2, 2013
Secret Science Club features CSHL Associate Professor, tomato aficionado & farmer Zachary Lippman on flower power and the DNA of feeding the world.
Full genome map of oil palm indicates a way to raise yields and protect rainforest
July 24, 2013
A single gene is identified whose regulation controls oil palm yield.
Researchers explain a key developmental mechanism for the first time in plants
March 6, 2013
When a stem cell commits to becoming a leaf cell, how does a polycomb gene-repressing protein complex know where in the genome to go, and when?
Plant scientists at CSHL demonstrate new means of boosting maize yields
February 3, 2013
Scientists successfully demonstrated what it describes as a “simple hypothesis” for making significant increases in yields for the maize plant.
One experiment: What can scientists learn from an odd-looking mutant ear of corn?
February 3, 2013
A mutated gene called COMPACT PLANT2 (CT2) renders this fruit of the maize plant flattened in shape, a phenomenon called fasciation.
Bread wheat’s large and complex genome is revealed
November 27, 2012
Analysis of the genome of one of world’s ‘big three’ food crops provides clues to better breeding, higher yield.
CSHL-led team discovers new way in which plants control flower production
November 8, 2012
Flowers don’t just catch our eyes, they catch those of pollinators like bees as well. They have to, in order to reproduce
DuPont and CSHL extend collaboration in cutting-edge plant biology research for 5 years
November 6, 2012
Continuing collaboration will facilitate development of innovative products to meet growing global food needs
Two pioneering plant genomics efforts given a funding boost by National Science Foundation
September 5, 2012
New 5-year grant awarded to the Gramene database project to apply Reactome data model supports data integration efforts.
‘Most comprehensive’ genetic analysis of maize plant will help raise yields, expand its range
June 1, 2012
An international research team involving 17 institutions has published the most comprehensive analysis to date of the maize genome.
New release of web-based resource resolves confusion over plant names
May 31, 2012
The Taxonomic Name Resolution Service ends the confusion over plant names.
Study uncovers a molecular “maturation clock” that modulates branching architecture in tomato plants
December 22, 2011
The secret to pushing tomato plants to produce more fruit might not lie in an extra dose of Miracle-Gro
New York Plant Genomics Consortium maps evolutionary relationships, gene functions for 150 species
December 16, 2011
The New York Plant Genomics Consortium have developed a genome “tree of life” that is largest yet for seed plants.
CSHL research takes center stage at the Secret Science Club
September 21, 2011
Robert Martienssen presented at the Secret Science Club in Brooklyn on super seeds, weeds, and biofuels.
Send in the clones: Superseeds, superweeds & green energy
September 20, 2011
Prof. Rob Martienssen who heads CSHL's plant biology program delivers a lecture titled, "Send in the clones: Superseeds, superweeds and green energy"
Molecular chaperones traffic signaling proteins between cells in plant stem-cell maintenance pathway
August 25, 2011
Researchers find KN1 cannot occur trafficking through plasmodesmata without the presence of chaperonins.
Plant biologists dissect genetic mechanism enabling plants to overcome environmental challenge
August 1, 2011
What can an immobile corn plant do to escape encroaching shade? Activate genes to change its shape, research reveals.
Plant scientist Rob Martienssen receives prestigious appointment as HHMI-GBMF Investigator
June 16, 2011
Rob Martienssen has been selected to join a new initiative to accelerate basic research in fundamental plant science.
CSHL is part of international team that sequences the ‘chocolate’ genome
January 14, 2011
Researchers succeeded in producing a draft genome of a cacao tree variety whose beans yield the world’s finest chocolate.
High-yield agriculture
December 14, 2010
31-year old scientist named George Shull began to grow maize, or corn, in a series of experiments that would change the face of modern agriculture.
Single gene dramatically boosts yield and sweetness in tomato hybrids, joint CSHL-Israeli study reports
March 29, 2010
Scientists find the first example of a single gene that causes hybrid vigor.
CSHL-Mexican team coaxes sexually reproducing plant to brink of asexual reproduction
March 7, 2010
Argonaute 9 inhibits asexual reproduction, apparently by silencing transposons.
Reference genome of maize, America’s most important crop, is published by team co-led by CSHL scientists
November 19, 2009
Complex sequence and "HapMap" shed light on maize's "wonderful diversity" could help future efforts to adapt the plant to a warming climate.
Scientists at CSHL discover mobile small RNAs that set up leaf patterning in plants
March 1, 2009
Small RNAs act like morphogens in helping to define the boundary between the top and bottom sides of leaves
CSHL researchers identify gene whose function explains how plant cells keep tiny communication channels open
February 17, 2009
GAT1 encodes an enzyme that maintains flow of information through transport channels
CSHL scientists discover how “companion” cells to sperm protect them from genetic damage
February 6, 2009
Small RNAs generated in companion cells enter neighboring sperm nuclei and inactivate harmful DNA
CSHL researchers map changing epigenetic modifications that enable mobile genetic elements to run amok
December 10, 2008
A shift in the pattern of small RNAs occurs in continuously dividing cells as their genomes become epigenetically reprogrammed.
Researchers find an essential gene for forming ears of corn
September 23, 2008
CSHL professor David Jackson, Ph.D., and a team of plant geneticists have identified a gene essential in controlling development of the maize plant
iPlant kickoff conference at Cold Spring Harbor Laboratory begins tackling plant biology’s grand challenges
April 4, 2008
Cold Spring Harbor Laboratory will host the inaugural conference of the iPlant Collaborative.
Cold Spring Harbor Laboratory to play central role addressing key questions in plant biology
January 30, 2008
CSHL will play a central role in an important new initiative called the iPlant Collaborative, funded by the National Science Foundation
“Gramene” database facilitates global agricultural research
October 13, 2005
CSHL researchers annouce the public release of Gramene version 19, an agricultural database.
NCGR, CSHL, and TIGR announce NSF funding for semantic web development for plant biologist
September 29, 2005
CSHL joins in collaboration of $1.7 million grant from the National Science Foundation (NSF) to develop a Virtual Plant Information Network (VPIN).
Feeding the world
August 15, 2005
Researchers finished a map-based DNA sequence of the entire rice genome.
Less is more: New technology captures gene-rich DNA segments
December 18, 2003
Plant biology researchers have found a faster way to sequence the genes of corn.
David Jackson
My lab studies genes and signals in cells that regulate the growth and shape of plants. We have discovered several genes that control plant architecture by exerting an influence on stem cells. By identifying the genes that control the number of stem cells in corn plants, for example, we’ve discovered a means of boosting the yield of that vital staple.
Zachary Lippman
My research team studies the genes that determine when and where, and thus how many, flowers are produced on plants. Flowers form on branches called inflorescences, which originate from stem cells. By studying the genes that control how stem cells become inflorescences, we are able to manipulate flower production to improve crop yields.
Rob Martienssen
Chromosomes are covered with chemical modifications that help control gene expression. I study this secondary genetic code - the epigenome - and how it is guided by small mobile RNAs in plants and fission yeast. Our discoveries impact plant breeding and human health, and we use this and other genomic information to improve aquatic plants as a source of bioenergy.
W. Richard McCombie
Over the last two decades, revolutionary improvements in DNA sequencing technology have made it faster, more accurate, and much cheaper. We are now able to sequence up to 10 trillion DNA letters in just one month. I harness these technological advancements to assemble genomes for a variety of organisms and probe the genetic basis of neurological disorders, including autism and schizophrenia, better understand cancer progression and understand the complex structures of the genomes of higher plants.
Ullas Pedmale
Unlike animals, plants neither have specific organs that see or hear various stimuli, yet, plants are sensitive to their surrounding environment and modify their development according to various external signals. My lab studies how the environment of a plant modulates its growth and development. Understanding environmental control of growth will have far-reaching implications for agriculture, energy production, and many other human activities.
Doreen Ware
When we think of evolution, we often think about physical changes, like a plant developing broader leaves to collect more solar energy. Such evolution actually occurs within the plant’s DNA. I am using computational analysis and modeling to visualize how plant genomes have evolved over time, particularly those of staple crops. We are learning from this work to improve the range and yield of modern plants.