Zach Lippman Susses Out How Gene Regulation Affects Plant Phenotypes
Zach Lippman Susses Out How Gene Regulation Affects Plant PhenotypesZach Lippman Susses Out How Gene Regulation Affects Plant Phenotypes

Zach Lippman Susses Out How Gene Regulation Affects Plant Phenotypes

The Cold Spring Harbor Laboratory researcher is fueled by curiosity about how one species’ genome can produce a wide variety of traits.

Shawna Williams
Shawna Williams
Jan 31, 2019

ABOVE: © Adam Lerner

For Zach Lippman, it all started with seeds. As a teenager with a summer job on a small farm in Connecticut that grew primarily vegetables, he marveled at how, once planted, each one “would go from this little seed to this amazing, developing plant with all these flowers and fruits,” he says. Lippman, now a plant geneticist at Cold Spring Harbor Laboratory (CSHL), was also struck by the variety in size, shape, and other traits that exists among varieties within a single cultivated species, such as the tomato plant.

That curiosity drove him to study plant breeding and genetics as an undergraduate at Cornell University, where he also worked in plant biologist Steve Tanksley’s tomato lab. He went on to earn a PhD with Rob Martienssen at CSHL, where he studied epigenetic control of mobile bits of the genome known as transposons. As a student, Lippman “was just an amazing guy,” Martienssen says. “He definitely has insight that others haven’t had, but also the sort of pragmatic ability to follow up his insights very quickly and in a very scientifically rigorous way that just generates amazing results.” In one study from Lippman’s graduate years, he, Martienssen, and colleagues found that the tightly-packed heterochromatin in Arabidopsis thaliana is made up of transposons and other repetitive elements, under the control of a chromatin-remodeling enzyme called DDM1. They also found that transposons in the model plant can regulate nearby genes, which might explain why inbred Arabidopsis lines with mutant ddm1 genes sometimes exhibit unexpected variety.1

Over the course of his PhD work, Lippman says he became “really interested in how gene regulation can impact diversity.” So, for his postdoc, he looked for a lab working on a system where tweaks in gene regulation are known to cause wide variation in traits. This led him back to the tomato plant, and to a postdoc position with Dani Zamir at The Hebrew University of Jerusalem. There, Lippman and colleagues pinpointed two genes—both of which encode regulators of other genes—that help control the branching of flower-bearing shoots in tomato plants via the timing of their expression.2

Lippman returned to CSHL in 2008 to run his own lab. There, he’s continued to study the development of tomatoes’ flower-bearing shoots, reporting in one paper that plants that are heterozygous for a mutation in a gene called SFT flower slightly later than wild-type plants, which would optimize plant architecture to produce higher yields. He and his coauthors suggested the finding helps explain hybrid vigor, a widespread plant-breeding phenomenon in which offspring of crosses of two inbred lines of a crop species are more productive than either parent line.3

Recently, Lippman and his colleagues applied lessons from tomato genetics to one of its relatives, a wild plant called groundcherry, altering three of the plant’s genes with CRISPR to bring its traits closer to what would be needed for commercial cultivation.4 (See “Opinion: GE Crops Are Seen Through a Warped Lens,” here.) Joyce Van Eck, a plant biologist at the Boyce Thompson Institute in Ithaca, New York, who has known Lippman since he was an undergraduate and worked with him on the groundcherry project and others, says that she’s found him to be creative, passionate, and open to new ideas: “He’s my ideal collaborator.”


  1. Z. Lippman et al., “Role of transposable elements in heterochromatin and epigenetic control,” Nature, 430:471–76, 2004. (Cited 1112 times)
  2. Z.B. Lippman et al., “The making of a compound inflorescence in tomato and related nightshades,” PLOS Biol, 6:e288, 2008. (Cited 118 times)
  3. K. Jiang et al., “Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture,” PLOS Genet, 9:e1004043, 2013. (Cited 51 times)
  4. Z.H. Lemmon et al., “Rapid improvement of domestication traits in an orphan crop by genome editing,” Nat Plants, 4:766–70, 2018. (Cited 1 time)