Plant development is driven by pools of undifferentiated stem cells called meristems. Meristems have two functions, to divide producing cells that will replenish the stem-cell niche, and cells that will differentiate into new organs. Together, the fine regulation of these divisions is referred to as meristem maintenance. Over a plant's lifetime, meristems undergo a specific developmental progression that continues to create organs throughout vegetative and reproductive development. Defects in the pathways that regulate meristem maintenance result in altered meristem size or number of organs typically produced by a specific meristem type, resulting in altered mature plant morphology. While many meristem maintenance pathways are shared between species, and thus information learned from one developmental time can be used to form another, specificity of these pathways between species can also be seen. Thus, by first chapter focuses on the similarities and differences in meristem maintenance pathways between the model species Arabidopsis and maize and touches on lessons researchers can glean from studying general patterns of development. The semi-dominant Suppressor of sessile spikelets2 (Sos2) gene in maize displays developmental defects in meristem maintenance throughout maize development. The Sos2 heterozygous mutants display a large variation of phenotypes while the Sos2 homozygous mutants and seedling lethal. The goal of Chapter 2 was to summarize the role of the Sos2 gene in known meristem maintenance pathways, as well as understand the genetic and environmental factors that influence the penetrance and expressivity of the Sos2 phenotype. In addition, an RNA-seq anlaysis uncovered additional pathways in which the Sos2 gene may directly or indirectly function, as well as identified a candidate gene for the Sos2 mutation, one that that has not yet been published to function in maize meristem maintenance pathways. Links within the literature of genes orthologous to the Sos2 candidate gene, taken alongside RNA-seq results, indicated Sos2 might act on phytohormone pathways. To further explore this link, Chapter 3 analysis results from hormone level assays and confocal analysis, which found significant differences in the cytokinin and auxin pathways. Sos2 is a member of the Sos class of mutants, along with Sos1 and Sos3. All three Sos mutants have similar mutant phenotypes, in that the structures on the ends of short branches that contain the flowers called spikelets, which are usually produced in pairs, develop singly in the heterozygote. In order to compare the meristem maintenance pathways effected by each Sos mutants, as well as determine their individual effects on phytohormone pathways during development, RNA-seq analysis was performed. This study found that Sos2 and Sos3 are more likely to share similar functions in meristem maintenance pathways than either when compared to Sos1. Chapter 4 sought to further unravel how phytohormone pathways regulate meristems, specifically at the point of axillary meristem initiation from the inflorescence meristem during reproductive development. To the end, transcriptomes of three auxin mutants barren stalk 1, barren inflroescnece2, and barren stalk 2 were performed and compared using a Weighted Gene Co- Expression Analysis (WGCNA). This study found less shared elements between these three auxin mutants, as was hypothesized, and highlighted the individual and unique targets of ba1, bif2, and ba2. These targets provide additional avenues of research that will lead to a better understanding of axillary meristem initiation during reproductive development. In summary, this study identified a possible gene involved in meristem maintenance not previously described in maize or any other monocot species, and provide insight into how that gene functions in known meristem maintenance and phytohormone pathways. In addition, research in understanding how axillary meristems develop within the context of auxin regulation uncovered unique targets of known auxin development mutants. Taken together, the results outlined in this thesis provide a more comprehensive understanding of meristem maintenance throughout maize development.Includes bibliographical references
