Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

Xu, X., Crow, M., Rice, B. R., Li, F., Harris, B., Liu, L., Demesa-Arevalo, E., Lu, Z., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S. N., Yang, B., Sylvester, A. W., Gingeras, T. R., Schmitz, R. J., Ware, D., Lipka, A. E., Gillis, J., Jackson, D. (December 2020) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell, S1534- (20). pp. 31021-31022. ISSN 1534-5807

Abstract

Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding of development requires insight into the full diversity of cell types and developmental domains and the gene networks required to specify them. Until now, these were identified primarily by morphology and insights from classical genetics, which are limited by genetic redundancy and pleiotropy. Here, we investigated the transcriptional profiles of 12,525 single cells from developing maize ears. The resulting developmental atlas provides a single-cell RNA sequencing (scRNA-seq) map of an inflorescence. We validated our results by mRNA in situ hybridization and by fluorescence-activated cell sorting (FACS) RNA-seq, and we show how these data may facilitate genetic studies by predicting genetic redundancy, integrating transcriptional networks, and identifying candidate genes associated with crop yield traits.

Item Type: Paper
Additional Information: 1878-1551 Xu, Xiaosa Crow, Megan Rice, Brian R Li, Forrest Harris, Benjamin Liu, Lei Demesa-Arevalo, Edgar Lu, Zefu Wang, Liya Fox, Nathan Wang, Xiaofei Drenkow, Jorg Luo, Anding Char, Si Nian Yang, Bing Sylvester, Anne W Gingeras, Thomas R Schmitz, Robert J Ware, Doreen Lipka, Alexander E Gillis, Jesse Jackson, David Journal Article United States Dev Cell. 2020 Dec 30:S1534-5807(20)31021-2. doi: 10.1016/j.devcel.2020.12.015.
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
organism description > plant > maize
Investigative techniques and equipment > assays
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
Investigative techniques and equipment > assays > Single cell sequencing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gillis Lab
CSHL labs > Gingeras lab
CSHL labs > Jackson lab
CSHL labs > Ware lab
School of Biological Sciences > Publications
CSHL Cancer Center Program
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL Cancer Center Shared Resources > Flow Cytometry Service
CSHL Cancer Center Shared Resources > Microscopy Service
CSHL Cancer Center Shared Resources > Next Generation Sequencing Service
CSHL Cancer Center Shared Resources > Single-Cell Biology Service
Depositing User: Matthew Dunn
Date: 30 December 2020
Date Deposited: 11 Jan 2021 14:35
Last Modified: 13 Feb 2024 19:33
PMCID: PMC7904613
Related URLs:
URI: https://repository.cshl.edu/id/eprint/39889

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