Gene expression atlas of embryo development in Arabidopsis

  • Peng Gao
  • Daoquan Xiang
  • Teagen D. Quilichini
  • Prakash Venglat
  • Prashant K. Pandey
  • Edwin Wang
  • C. Stewart Gillmor
  • Raju DatlaEmail author
Methods Paper
Part of the following topical collections:
  1. Cellular Omics Methods in Plant Reproduction Research


Embryogenesis represents a critical phase in the life cycle of flowering plants. Here, we characterize transcriptome landscapes associated with key stages of embryogenesis by combining an optimized method for the isolation of developing Arabidopsis embryos with high-throughput RNA-seq. The resulting RNA-seq datasets identify distinct overlapping patterns of gene expression, as well as temporal shifts in gene activity across embryogenesis. Network analysis revealed stage-specific and multi-stage gene expression clusters and biological functions associated with key stages of embryo development. Methylation-related gene expression was associated with early- and middle-stage embryos, initiation of photosynthesis components with the late embryogenesis stage, and storage/energy-related protein activation with late and mature embryos. These results provide a comprehensive understanding of transcriptome programming in Arabidopsis embryogenesis and identify modules of gene expression corresponding to key stages of embryo development. This dataset and analysis are a unique resource to advance functional genetic analysis of embryo development in plants.


Embryogenesis Embryo isolation RNA-seq Transcriptome Bioinformatics Arabidopsis 



This work was funded by the Aquatic and Crop Resource Development Research Division of the National Research Council of Canada (ACRD manuscript #56424). We thank Dr. Wentao Zhang for reviewing the manuscript and providing suggestions for its improvement.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© The Author(s) 2019

Authors and Affiliations

  1. 1.Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonCanada
  2. 2.Department of Plant Sciences and Crop Development CentreUniversity of SaskatchewanSaskatoonCanada
  3. 3.Center for Health Genomics and InformaticsUniversity of Calgary Cumming School of MedicineCalgaryCanada
  4. 4.Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica AvanzadaCentro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN)IrapuatoMéxico
  5. 5.Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonCanada

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