Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2024 Abstracts

Using Biodiversity to Explore the Diversification of Environment-Regulated Growth


Prashanth Ramachandran* ([email protected]), Guannan Wang, Andrea Ramirez, José Dinneny


Stanford University


  1. Developing an abscisic acid responsive element binding factor (ABF) plus gene regulatory network (GRN) to define the diversification of stress-associated gene regulation and train predictive models.
  2. Utilizing evolutionary context and species phylogeny to discover novel gene
  3. Connecting phenotype to genotype using a modeling framework and advances in the rapid deployment of CRISPR/Cas9 mediated mutagenesis.


Engineering crops for sustainable growth in a rapidly changing environment requires an understanding of how growth-modulating gene regulatory networks are integrated with the environment. By analyzing 10 phylogenetically related species in the Brassicaceae family that occupy diverse ecological niches, researchers have identified species where increasing salinity causes growth reduction as well as species in which salinity promotes growth. Environment-dependent developmental decisions that are critical for an organism’s survival often rely upon the dose dependent action of signaling molecules such as hormones. Differential growth regulation by one such hormone, abscisic acid (ABA), is the primary mechanism plants use to acclimate to changes in water availability and salinity. The group identified species in which ABA predominantly functions either as a growth repressor or a growth enhancer, suggesting that the differential growth responses observed in response to salinity are partly mediated through this hormone. Comparative anatomical analysis of the Brassicaceae species revealed that reduction in meristem cell number contributes to ABA’s growth repression while growth promotion involves increases in mature cell length. Further, the team’s genetic studies reveal that the growth inhibition by ABA is dependent on components of the well-established canonical ABA signaling pathway and is accomplished through the action of ABA-responsive elements Binding Factors (ABF) transcription factors (TFs). DNA Affinity Purification sequencing (DAP-seq) analysis of the ABF TFs revealed that changes in the ABF-auxin regulatory network can explain differences in the extent of growth repression observed in the different species. To further characterize the ABF regulatory network and understand its role in different cellular and environmental contexts, researchers are now exploring the cis regulatory binding landscape of ABF interacting transcription factors across the 10 species.

Growth promotion by ABA, on the other hand, is regulated by an independent pathway which involves non-canonical ABA receptors, suggesting that the dichotomy in physiological responses to this hormone can be explained by differences at the level of perception, as well. The components of the growth promoting and growth repressing pathways identified through these comparative growth analyses in evolutionarily related species will help identify hormonal regulators of different growth patterns and provide candidates for tuning growth in agriculturally relevant species.

Funding Information

This work was funded by the U.S DOE’s BER program (Grant BER-DE-SC0020358 and BER DE-SC0022985 to J.R.D).