Unraveling the gene regulators and molecular mechanisms underlying the elevated CO2 response in C3 plants

Rising atmospheric carbon dioxide ([CO2]) concentrations, a major driver of climate change, also present a unique opportunity to enhance crop productivity, particularly in C3 plants. However, the extent of this CO2 fertilization effect is modulated by complex interactions with nutrient availability, genetic regulation, and environmental conditions. While considerable progress has been made in understanding response to these interactions at the physiological level, the molecular mechanisms governing the plant responses to elevated CO2 concentration (e[CO2]) remain insufficiently understood. This dissertation addresses these gaps through a series of integrated studies aimed at uncovering the molecular and genetic basis of C3 plant responses to e[CO2]. In Chapter 2, the transcription factor AtbZIP1 was identified as a key regulator of plant responses to the interactive effects of e[CO2] and nitrogen (N) availability in Arabidopsis thaliana. Perturbations in bZIP1’s expression led to altered chlorophyll concentration, shoot biomass, shoot nitrogen mass, and soluble protein concentrations. Transcriptomic and metabolomic analyses revealed that AtbZIP1 modulates jasmonic acid (JA) signaling, raffinose accumulation, and structural carbohydrate synthesis, highlighting its role in stress management and carbon partitioning under varying [CO2] and N availability. Chapter 3 was aimed at identifying an ortholog of AtbZIP1 in soybean (Glycine max) and translating findings of Chapter 2 to soybean, an important C3 crop. While sequence homology and synteny analyses failed to identify a direct AtbZIP1 ortholog, a gene regulatory network-based approach revealed a homolog of AtbZIP53, as a potential functional analog of AtbZIP1. Promoter motif analysis corroborated the interactions predicted by gene regulatory network analysis. Further, phylogenetic analysis of the putative AtbZIP1 ortholog in soybean and its other close homologs in soybean and Arabidopsis thaliana suggested potential neofunctionalization of this gene to complement missing bZIP1 in the soybean genome. Photosynthetic efficiency can be improved by accelerating nonphotochemical quenching under fluctuating light conditions. In Chapter 4, the transcriptional response of a transgenic soybean line expressing the AtVPZ cassette—which accelerates non-photochemical quenching (NPQ) relaxation—was evaluated under ambient and elevated CO2 concentrations. Transcriptomic analysis revealed genotype-specific hormonal and stress responses, suggesting that AtVPZ expression alters growth and stress tolerance of the transgenic line under e[CO2]. Further, two genes involved in seed development were found to be differentially regulated by AtVPZ expression across all conditions and stages, highlighting potential pleiotropic effects of AtVPZ transgenes. Together, these studies provide insight into how interactions of e[CO2] and other variables (nitrogen, genotypic variants - AtbZIP1 and AtVPZ) alter the molecular scale responses. By integrating physiological, transcriptomic, and network-based approaches across model and crop species, this work advances our understanding of regulatory mechanisms that can be leveraged to develop high-yielding crops for future climate conditions.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Plant Biology

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Singh, Dilkaran

Contributors dc:contributor

• Heath, Katy
• Marshall-Colon, Amy
• Studer, Anthony Joseph
• McGrath, Justin
• Burgess, Steven James

• Elevated CO2
• transcription
• nitrogen
• functional genomics

Statement dc:rights

• Copyright 2025 Dilkaran Singh

Language dc:language

en

Handle dc:identifier

https://hdl.handle.net/2142/132737

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/132737