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

Xiaosa Xu, Megan Crow, Brian R Rice, Forrest Li, Benjamin Harris, Lei Liu, Edgar Demesa-Arevalo, Zefu Lu, Liya Wang, Nathan Fox, Xiaofei Wang, Jorg Drenkow, Anding Luo, Si Nian Char, Bing Yang, Anne W Sylvester, Thomas R Gingeras, Robert J Schmitz, Doreen Ware, Alexander E LipkaJesse Gillis, David Jackson

Research output: Contribution to journalArticlepeer-review


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. Xu et al. construct and validate a single-cell transcriptomic atlas of developing maize ears. Their single-cell gene co-expression networks will facilitate developmental genetics studies by predicting genetic redundancy and revealing transcriptional regulatory networks. Their results also inform maize breeding by identifying candidate trait-associated genes.

Original languageEnglish (US)
Pages (from-to)557-568.e6
JournalDevelopmental cell
Issue number4
StatePublished - Feb 22 2021


  • developmental networks
  • GWAS
  • maize ear
  • meristem
  • scRNA-seq
  • trait genes

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology
  • Molecular Biology
  • Cell Biology
  • Developmental Biology


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