A Comprehensive Study of the Maize Shoot Apex - Deciphering Genes Underlying Shoot Apical Meristem Allometry
Developmental Biology
Final Report Abstract
The shoot apical meristem (SAM), a specialized stem cell niche at the growing shoot tip, integrates developmental and environmental signals to direct the initiation and patterning of new organs such as leaves. Its activity throughout the plant’s lifetime is tightly controlled. To gain insight into gene regulatory networks behind stem cell maintenance and organogenesis, a high-resolution gene expression atlas of 10 distinct domains and cell types within the vegetative maize shoot apex was generated using laser microdissection and RNA deep sequencing. Approximately 10% of all transcribed genes are differentially expressed across these tissue types, including a valuable collection of cell type specific genes. Interestingly, very few functional categories are enriched among the differentially expressed genes, which reflects prominent sub-functionalization within gene families involved in a vast number of biological processes, including cell fate determinants like hormones, redox regulation and cell wall remodeling. A mutant survey confirmed reduced redundancy among key developmental factors, providing highly-specific targets via which to manipulate these critical pathways. Strong enrichments, however, were seen for transcription factor (TF) families, and principle component analysis identified unique TF signatures predictive of meristematic, vascular, and internode fate, respectively. Natural variation present at meristem correlated TFs is associated with key plant architectural traits in GWAS, providing functional support for these findings. Moreover, cluster analysis identified genes whose expression specifically marks the functional zones of the maize SAM, the stem cell harboring central zone, the organogenic peripheral zone, and the organizing center. Genes defining these zones are in part conserved between maize and Arabidopsis, but also reveal remarkable differences and novel gene functions associated with these domains in maize. Mutational analysis and correlations with meristem related traits validated the biological importance of genes expressed in these zones. The resources generated in this project will be of tremendous interest for the plant research community as well as breeders, which are provided with genes/SNPs to specifically select for beneficial traits. These data, and especially the genes displaying mutant phenotypes, will also allow me to independently conduct follow-up studies. Furthermore, during this project I acquired new expertise in crop genetics and data analyses, and I became part of collaborative team with experts in a variety of disciplines, which will be very beneficial to address specific question in the future.
Publications
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57th Annual Maize Genetics Conference, March 12-15, 2015, St. Charles, Illinois, USA: ‘An expression atlas of the maize shoot apex’
Knauer, Steffen; Javelle, Marie; Li, Lin; Li, Xianran; Wimalanathan, Kokulapalan; Kumari, Sunita; Samuel, Leiboff; Ware, Doreen; Lawrence, Carolyn; Schnable, Patrick; Yu, Jianming; Muehlbauer, Gary; Scanlon, Michael; Timmermans, Marja
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59th Annual Maize Genetics Conference, March 9-12, 2017, St. Louis, Missouri, USA: ‘An expression atlas of the maize shoot apex reveals signatures TFs as important drivers for cell identity and sub-functionalization of key downstream factors’
Knauer, Steffen; Javelle, Marie; Li, Lin; Li, Xianran; Wimalanathan, Kokulapalan; Kumari, Sunita; Leiboff, Samuel; Johnston, Robyn; Ware, Doreen; Lawrence, Carolyn J; Schnable, Patrick S; Yu, Jianming; Muehlbauer, Gary J; Scanlon, Michael J; Timmermans, Marja
