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

Authors: XU, XIAOSA - Cold Spring Harbor Laboratory; CROW, MAGGIE - Cold Spring Harbor Laboratory; RICE, BRIAN - University Of Illinois; LI, FORREST - Cold Spring Harbor Laboratory; HARRIS, BENJAMIN - Cold Spring Harbor Laboratory; LIU, LEI - Cold Spring Harbor Laboratory; AREVALO, EDGAR - Cold Spring Harbor Laboratory; LU, ZEFU - University Of Georgia; JACKSON, DAVID - Cold Spring Harbor Laboratory; Ware, Doreen; WANG, LIYA - Cold Spring Harbor Laboratory; FOX, NATHAN - Cold Spring Harbor Laboratory; WANG, XIAOFEI - Cold Spring Harbor Laboratory; DRENKOW, JORG - Cold Spring Harbor Laboratory; LUO, ANDING - University Of Georgia; CHAR, SI N - University Of Missouri; YANG, BING - University Of Missouri; SYLVESTER, ANNE - University Of Wyoming; GINGERAS, THOMAS - Cold Spring Harbor Laboratory; SCHMITZ, ROBERT - University Of Georgia; LIPKA, ALEXANDER - University Of Illinois; GILLIS, JESSE - Cold Spring Harbor Laboratory

Submitted to: Developmental Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/2/2021
Publication Date: 1/4/2021
Citation: Xu, X., Crow, M., Rice, B.R., Li, F., Harris, B., Liu, L., Arevalo, E.D., Lu, Z., Jackson, D., Ware, D., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S., Yang, B., Sylvester, A., Gingeras, T., Schmitz, R., Lipka, A., Gillis, J. 2021. Single-cell RNA sequencing of developing ears facilitates functional analysis and trait gene discovery in maize. Developmental Cell. 56:557-568. https://doi.org/10.1016/j.devcel.2020.12.015.
DOI: https://doi.org/10.1016/j.devcel.2020.12.015

Interpretive Summary: Crop productivity depends on activity of meristems, for example that promote development of the maize ear. A comprehensive understanding of how plants develop requires insight into the full diversity of cell types and developmental domains, and the gene networks required to specify them. However, these differences are classified mainly by morphology and single studies done via classical genetics. By performing multiple forms of next-generation sequencing of maize ear inflorescence, we were able to generate and validate the first comprehensive map of gene expression in plant shoot development. These data can further the genetic studies by predicting genetic redundancy, building transcriptional networks, and identifying candidate genes associated with crop yield traits.

Technical Abstract: Crop productivity depends on activity of meristems, for example that promote development 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. However, these are classified mainly by morphology, as well as by insights from classical genetics that are limited by genetic redundancy and pleiotropy. Here, we investigated the transcriptional profiles of 12,525 single cells from developing maize ear primordia. The resulting ear development atlas provides the first comprehensive plant shoot scRNA-seq map. We validated our results by mRNA in situ hybridization for selected cluster markers and by fluorescence activated cell sorting (FACS) RNA-seq for a specific developmental domain, and showed how these data can facilitate genetic studies by predicting genetic redundancy, building transcriptional networks, and identifying candidate genes associated with crop yield traits.