Maize shoot and inflorescence architecture are controlled by tightly coordinated genetic networks, molecular mechanisms, and hormonal pathways. Understanding how these factors integrate to produce consistent, yet flexible developmental outcomes is essential for elucidating the source of major morphological traits and for enabling precise architectural manipulation. This dissertation examines four regulatory aspects that govern maize development: the modulation of maize reproductive architecture by phytohormones (reviewed in Chapter 1); the discovery of the ascorbate-dependent ferrireductase, EARY (Chapter 2); the function of the duplicated SBP-box transcription factors TEOSINTE GLUME ARCHITECTURE1 (TGA1) and NEIGHBOR OF TGA1 (NOT1) (Chapter 3); and the functional characterization of cis-regulatory modules (CRMs) controlling the TGA1 and TASSEL SHEATH1 (TSH1) genes (Chapters 4 and 5). Collectively, these studies demonstrate how architectural genes, transcription factor diversification, and cis-regulatory variation converge to shape inflorescence and shoot architecture.Firstly, I reviewed the role of plant hormones in maize inflorescence development and reproduction (Chapter 1). Next, I positionally cloned a previously uncharacterized regulator of maize shoot development, the EARY gene. Through an EMS mutagenesis screen, I identified eary, a dwarf and highly prolific mutant exhibiting severe internode compression, elongated shanks, elevated tillering, and multiple ears. Bulked segregant analysis, variant filtering, and the use of molecular markers identified a single missense lesion (E180K) in the coding region of Zm00001eb042480, encoding a predicted CYB561-family ascorbate-dependent ferrireductase. Marker-based mapping and non-complementation with a Mutator transposon insertion line confirmed that this gene corresponds to EARY. Genetic analysis revealed synergistic interaction between eary and grassy tillers1 (gt1). These results indicate that EARY and GT1 regulate complementary processes—internode elongation and axillary meristem fate—that together define overall shoot architecture. These findings establish EARY as a key regulator of maize architecture (Chapter 2).In Chapter 3, functional dissection of the duplicated SBP-box transcription factors TGA1 and NOT1 revealed their distinct and cooperative contributions to reproductive development. Using CRISPR-Cas9 editing, a set of tga1, not1, and tga1;not1 mutant alleles was generated that allowed direct resolution of their overlapping and divergent functions. Loss of NOT1 increased proliferative capacity in both tassels and ears, producing slightly elongated ears and excessive tassel branching. In contrast, tga1 mutants displayed pronounced shank elongation, consistent with a role in suppressing lateral outgrowth. Kernel morphology was also affected by these mutations and suggests functional divergence to some extent. Expression analyses revealed asymmetric dosage compensation, where NOT1 was strongly upregulated in tga1 mutants, while TGA1 levels remained unchanged in the not1 background. This work resolves discrepancies arising from earlier RNAi studies and demonstrates that these paralogs act as distinct yet coordinated regulators of inflorescence architecture, branching, and kernel morphology.Lastly, in Chapters 4 and 5, I investigated cis-regulatory regions of the TGA1 and TSH1 genes, and demonstrated how non-coding regulatory regions exert modular control of developmental traits. Editing TGA1 CRMs consistently reduced TGA1 expression while increasing NOT1 expression. Despite substantial transcriptional changes, no obvious phenotypes were observed, reflecting the buffering capacity of NOT1. In contrast, CRM edits upstream of TSH1 produced a wide spectrum of phenotypes, including mild to severe bract outgrowth and variable changes in tassel branching. In a Nature Plants publication of which I am a co-author (Chapter 4), I examined a few strong alleles of TSH1. In Chapter 5, I expanded this analysis to other CRM edits and determined that specific combinations of CRM lesions can uncouple bract suppression and branching in tassels, which were previously thought to be coupled, through perturbation of distinct regulatory modules. Together, these CRM studies show that cis-regulatory variation enables fine-scale modulation of developmental programs and reveal how specific regulatory elements contribute to specific traits. This work provides a mechanistic foundation for targeted manipulation of maize architecture using CRM engineering.Across the two published and three unpublished chapters, this dissertation presents examples of how architectural genes, transcription factor divergence, and cis-regulatory organization influence maize architecture. These findings provide new mechanistic insight into the evolution, regulation, and potential manipulation of key agronomic traits in maize.
Amina Chaudhry (Thu,) studied this question.