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

Dev Cell. 2021 Feb 22;56(4):557-568.e6. doi: 10.1016/j.devcel.2020.12.015. Epub 2021 Jan 4.


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.

Keywords: GWAS; developmental networks; maize ear; meristem; scRNA-seq; trait genes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks
  • Genetic Association Studies*
  • Protoplasts / metabolism
  • Quantitative Trait Loci / genetics*
  • Reproducibility of Results
  • Sequence Analysis, RNA*
  • Single-Cell Analysis*
  • Transcriptome / genetics
  • Zea mays / genetics*
  • Zea mays / growth & development*