Developmental Cell
Volume 56, Issue 4, 22 February 2021, Pages 557-568.e6
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Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

https://doi.org/10.1016/j.devcel.2020.12.015Get rights and content
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Highlights

  • scRNA-seq of developing maize ears reveals major cell types and developmental markers

  • scRNA-seq co-expression networks predict genetic redundancy

  • Integration of scRNA-seq and ChIP-seq/ATAC-seq helps build transcriptional networks

  • Integration of scRNA-seq and GWAS identifies candidate maize yield-associated genes

Summary

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

maize ear
meristem
scRNA-seq
developmental networks
GWAS
trait genes

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