Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection

Anat Hendelman, Sophia Zebell, Daniel Rodriguez-Leal, Noah Dukler, Gina Robitaille, Xuelin Wu, Jamie Kostyun, Lior Tal, Peipei Wang, Madelaine E Bartlett, Yuval Eshed, Idan Efroni, Zachary B Lippman

Research output: Contribution to journalArticlepeer-review


Divergence of gene function is a hallmark of evolution, but assessing functional divergence over deep time is not trivial. The few alleles available for cross-species studies often fail to expose the entire functional spectrum of genes, potentially obscuring deeply conserved pleiotropic roles. Here, we explore the functional divergence of WUSCHEL HOMEOBOX9 (WOX9), suggested to have species-specific roles in embryo and inflorescence development. Using a cis-regulatory editing drive system, we generate a comprehensive allelic series in tomato, which revealed hidden pleiotropic roles for WOX9. Analysis of accessible chromatin and conserved cis-regulatory sequences identifies the regions responsible for this pleiotropic activity, the functions of which are conserved in groundcherry, a tomato relative. Mimicking these alleles in Arabidopsis, distantly related to tomato and groundcherry, reveals new inflorescence phenotypes, exposing a deeply conserved pleiotropy. We suggest that targeted cis-regulatory mutations can uncover conserved gene functions and reduce undesirable effects in crop improvement.
Original languageEnglish
Pages (from-to)1724-1739
Number of pages17
Issue number7
Early online date4 Mar 2021
StatePublished - 1 Apr 2021


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