Plant Developmental Genetics

Our research aims at understanding the genetic mechanisms that regulate flowering and flower production in plants, and how these developmental processes were shaped during crop domestication and breeding. More specifically, we study the development of inflorescences, the flower-bearing shoots, which arise when small groups of pluripotent stem cells at the growing tips cease the production of vegetative organs and transition to reproductive growth. The rate in which stem cells transition and differentiate finely balances vegetative and reproductive growth for optimized flower, fruit, and seed production.

Many genes and gene variants that affect stem cell development were selected during domestication and have potential in crop improvement. However, their effects often differ when introduced into disparate genetic backgrounds due to interactions with genetic modifiers. We use approaches in molecular genetics, genomics, and biochemistry to reveal and dissect signaling pathways and genetic interactions that regulate stem cell development in the model crop tomato, to advance our ability to fine-tune shoot and inflorescence architecture for optimized yields in tomato and other crops.

• Optimized sample selection for cost-efficient long-read population sequencing
  Ranallo-Benavidez, T. Rhyker; Lemmon, Zachary; Soyk, Sebastian; Aganezov, Sergey; Salerno, William J.; et al.
  Genome Research  10.1101/gr.264879.120. MAY 2021
• New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation
  Soyk, Sebastian; Benoit, Matthias; Lippman, Zachary B.
  Annual Review Of Genetics, Vol 54, 2020 
• Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
  Alonge, Michael; Wang, Xingang; Benoit, Matthias; Soyk, Sebastian; Pereira, Lara; et al.
  Cell  10.1016/j.cell.2020.05.021 JUL 9 2020
• RaGOO: fast and accurate reference-guided scaffolding of draft genomes
  Alonge, Michael; Soyk, Sebastian; Ramakrishnan, Srividya; Wang, Xingang; Goodwin, Sara; et al.
  Genome Biology, 10.1186/s13059-019-1829-6, OCT 28 2019
• Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato (vol 5, pg 471, 2019)
  Soyk, S; Lemmon, ZH.; Sedlazeck, FJ.; Jimenez-Gomez, JM; Alonge, M; Hutton, SF; Van Eck, J; Schatz, MC; Lippman, ZB
  NATURE PLANTS 5(8): 903-903  10.1038/s41477-019-0488-7  AUG 2019
• Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
  Soyk, S; Lemmon, ZH.; Sedlazeck, FJ.; Jimenez-Gomez, JM; Alonge, M; Hutton, SF; Van Eck, J; Schatz, MC; Lippman, ZB
  NATURE PLANTS 5(5): 471-479  10.1038/s41477-019-0422-z  MAY 2019
• Rapid improvement of domestication traits in an orphan crop by genome editing
  Lemmon, ZH; Reem, NT; Dalrymple, J; Soyk, S; Swartwood, KE; Rodriguez-Leal, D; Van Eck, J; Lippman, ZB
  NATURE PLANTS 4(10): 766-770 10.1038/s41477-018-0259-x OCT 2018
• Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene
  Soyk, S; Lemmon, ZH; Oved, M; Fisher, J; Liberatore, KL; Park, SJ; Goren, A; Jiang, K; Ramos, A; van der Knaap, E; Van Eck, J; Zamir, D; Eshed, Y; Lippman, ZB
  CELL 169(6): 1142-+  10.1016/j.cell.2017.04.032 JUN 1 2017
• Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato
  Soyk, S; Mueller, NA; Park, SJ; Schmalenbach, I; Jiang, K; Hayama, R; Zhang, L ; Van Eck, J; Jimenez-Gomez, JM; Lippman, ZB
  NATURE GENETICS  49(1):162-168  DOI: 10.1038/ng.3733  JAN 2017
• …

• Stem cell biology
• Plant architecture
• Natural variation
• Crop domestication
• Tomato

• Plant development
• Molecular Genetics
• Evolutionary Genomics
• Gene expression
• Gene editing