RESEARCH-PGR: Role of cytokinin in regulating shoot apical meristem function in rice

Plant leaves and flowers are derived from stem cell tissues called meristems. The regulation of meristem development and activity is central to understanding plant growth and development, and impacts many agronomically important traits such as plant architecture, biomass, and grain yield. The goal of this project is to determine how the plant hormone cytokinin regulates meristem function in rice, an important crop and a model system for understanding growth and development of other cereals. For this purpose, the recently developed methodologies for single cell sequencing will be employed. Gene expression in individual cells of the shoot meristem and of the reproductive inflorescence meristem will be examined to uncover cellular mechanisms that regulate the development of leaves, flowers, and grain. In addition, the packaging of the genome will be characterized to identify DNA elements that likely play a role in controlling when, where, and to what degree the genes are expressed in specific cells. Alternations in meristem development, brought about by disrupting cytokinin function will reveal how this hormone orchestrates proper rice development at the cellular level. These studies will illuminate the mechanisms underlying the development of vegetative and inflorescence architectures, with an important emphasis on cytokinin's role in these processes. In broader context, this work has the potential to realize increased yields in rice and other agriculturally important cereal species. The proposed research will enhance the infrastructure of research and education by providing student training and the development of programs aimed at fostering science education.

The phytohormone cytokinin plays key roles in regulating the activities of the vegetative shoot apical meristem (SAM) and reproductive inflorescence meristem (IM) in rice. Here, the role of cytokinin in regulating the rice SAM and IM will be examined at the single cell and single nucleus levels using an integrative array of genetic, molecular, and single-cell '-omic' approaches. First, transcript abundance and chromatin accessibility in individual SAM/IM cells will be characterized using single-cell transcriptomics coupled with single-nucleus chromatin profiling. This will provide foundational understanding of the regulatory circuits in the SAM and IM. Marker genes and regions of open chromatin within subdomains of the SAM/IM will be correlated to polymorphisms identified in GWAS panels for panicle traits in rice, potentially identifying important genomic regulatory regions for panicle architecture. Second, cytokinin signaling will be genetically perturbed using cytokinin receptor mutants to reveal how this regulatory network influences cell types, their distribution and developmental trajectories, and the activity of genes and regulatory elements within the cell clusters. Third, because type-B Response Regulator (RR) transcription factors control the initial transcriptional output from cytokinin, the direct targets of type-B RRs will be identified by ChIP-seq. Integrating these datasets will identify key targets of cytokinin signaling in specific cells and types of the SAM/IM, a subset of which will then be examined by genetic analysis. Collectively, the proposed studies will result in complementary genome-level datasets that will identify key mediators of cytokinin in regulating meristem activity, potentially revealing emergent properties of meristem regulation.

This award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems and the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.