Zachary Lippman
Professor & HHMI Investigator
Jacob Goldfield Professor of Genetics
Director of Graduate Studies
Ph.D., Watson School of Biological Sciences at Cold Spring Harbor Laboratory, 2004
lippman@cshl.edu | 516-367-8897
My research team studies when and where, and how many branches, flowers, and fruits are produced on plants. All of plant development depends on small groups of stem cells at the tips of shoots known as meristems. By studying the genes that control stem cell production and maturation over space and time, within and between different developmental contexts, we are able to manipulate plant architecture and reproduction to improve crop yields.
Zachary Lippman’s research program integrates development, genetics, genomics, and genome editing to uncover, explore, and exploit the mechanisms that determine how plant stem cells become shoots and flowers. The lab takes advantage of extensive natural and engineered genetic variation that influence vegetative and inflorescence production and architecture in tomato and related nightshade (Solanaceae) species (e.g. potato, pepper, groundcherry) to explore how differences in these processes explain the remarkable diversity in the architectures of these shoot systems found in nature and agriculture. Recent discoveries on the genes and networks underlying this diversity have led to broader questions on the significance of genomic structural variation, genetic redundancy, gene dosage, and epistasis in development, evolution, domestication, and breeding. By linking these fundamental and applied discoveries, Lippman is developing and applying innovative concepts and tools to accelerate crop improvement.
Inside Jones Laboratory
March 28, 2024
Jones is CSHL’s oldest building. Since 1893, its exterior has remained virtually unchanged. Inside is a different story.
An evolutionary mystery 125 million years in the making
March 4, 2024
CSHL plant biologists have stumbled on a peculiar case involving a gene that’s key for controlling growth in tomatoes and other crops.
You say genome editing, I say natural mutation
October 19, 2023
CSHL scientists have discovered that evolution and genome editing in crops are less predictable than previously thought.
CSHL celebrates 20th graduating class
May 9, 2023
Friends, family, and faculty applauded 11 Ph.D. recipients at the CSHL School of Biological Sciences’ 2023 commencement.
The CSHL School of Biological Sciences’ class of 2023
May 7, 2023
The School of Biological Sciences awarded 11 Ph.D. degrees this year. Here, the graduates reflect on their time and experiences at CSHL.
How evolved is your knowledge?
January 26, 2023
Test your knowledge of evolution with this quiz, inspired by the March 2023 performances of Isabella Rossellini’s play, Darwin’s Smile, at CSHL.
Tomato cousin’s coolest quirk
January 25, 2023
Take an up-close look at what CSHL Professor Zachary Lippman describes as “one of the coolest evolutionary novelties to emerge in plants.”
Reinvigorating CSHL’s Ph.D. program
December 13, 2022
Graduate student turned director of graduate studies, Zachary Lippman shares his vision for the CSHL School of Biological Sciences.
CSHL groundcherry research bears new fruits
October 31, 2022
New genetic blueprints for two types of groundcherry may help strengthen food supplies and reveal how plants evolve.
Lippman named Director of CSHL School of Biological Sciences
October 27, 2022
A former student and faculty member at the School of Biological Sciences, Lippman takes on the new role effective December 1, 2022.
Selected Publications
Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
21 Oct 2022 | The Plant Cell | 35(1):351-368
He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan, Hendelman, Anat, Van Eck, Joyce, Schatz, Michael, Lippman, Zachary
Rapid customization of Solanaceae fruit crops for urban agriculture
23 Dec 2019 | Nature Biotechnology | 38:182-188
Kwon, C, Heo, J, Lemmon, Z, Capua, Y, Hutton, S, Van Eck, J, Park, S, Lippman, Z
Revolutions in agriculture chart a course for targeted breeding of old and new crops
5 Sep 2019 | Science | 366(6466)
Eshed, Y, Lippman, Z
Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
6 May 2019 | Nature Plants | 5(5):471-497
Soyk, S, Lemmon, Z, Sedlazeck, F, Jimenez-Gomez, J, Alonge, M, Hutton, S, Van Eck, J, Schatz, M, Lippman, Z
All Publications
Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator
4 Mar 2024 | PLoS Genetics | 20(3):e1011174
Ciren, Danielle, Zebell, Sophia, Lippman, Zachary, Hake, Sarah
Convergent evolution of plant prickles is driven by repeated gene co-option over deep time
22 Feb 2024 | bioRxiv
Satterlee, James, Alonso, David, Gramazio, Pietro, Jenike, Katharine, He, Jia, Arrones, Andrea, Villanueva, Gloria, Plazas, Mariola, Ramakrishnan, Srividya, Benoit, Matthias, Gentile, Iacopo, Hendelman, Anat, Shohat, Hagai, Fitzgerald, Blaine, Robitaille, Gina, Green, Yumi, Swartwood, Kerry, Passalacqua, Michael, Gagnon, Edeline, Hilgenhof, Rebecca, Huggins, Trevis, Eizenga, Georgia, Gur, Amit, Rutten, Twan, Stein, Nils, Yao, Shengrui, Bellot, Clement, Bendahmane, Mohammed, Frary, Amy, Knapp, Sandra, Särkinen, Tiina, Gillis, Jesse, Van Eck, Joyce, Schatz, Michael, Eshed, Yuval, Prohens, Jaime, Vilanova, Santiago, Lippman, Zachary
Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator
20 Dec 2023 | bioRxiv
Ciren, Danielle, Zebell, Sophia, Lippman, Zachary
Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size
20 Oct 2023 | Science | 382(6668):315-320
Aguirre, Lyndsey, Hendelman, Anat, Hutton, Samuel, McCandlish, David, Lippman, Zachary
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing
15 Dec 2022 | Genome Biology | 23(1):258
Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary, Schatz, Michael, Soyk, Sebastian
Establishing Physalisas a new Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome
30 Jul 2022 | bioRxiv
He, Jia, Alonge, Michael, Ramakrishnan, Srividya, Benoit, Matthias, Soyk, Sebastian, Reem, Nathan, Hendelman, Anat, Eck, Joyce, Schatz, Michael, Lippman, Zachary