Gene expression atlas for the food security crop cassava

Mark C. Wilson, Andrew M. Mutka, Aaron W. Hummel, Jeffrey Berry, Raj Deepika Chauhan, Anupama Vijayaraghavan, Nigel J. Taylor, Daniel F Voytas, Daniel H. Chitwood, Rebecca S. Bart

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

Abstract

Cassava (Manihot esculenta) feeds c. 800 million people world-wide. Although this crop displays high productivity under drought and poor soil conditions, it is susceptible to disease, postharvest deterioration and the roots contain low nutritional content. Here, we provide molecular identities for 11 cassava tissue/organ types through RNA-sequencing and develop an open access, web-based interface for further interrogation of the data. Through this dataset, we consider the physiology of cassava. Specifically, we focus on identification of the transcriptional signatures that define the massive, underground storage roots used as a food source and the favored target tissue for transgene integration and genome editing, friable embryogenic callus (FEC). Further, we identify promoters able to drive strong expression in multiple tissue/organs. The information gained from this study is of value for both conventional and biotechnological improvement programs.

Original languageEnglish (US)
Pages (from-to)1632-1641
Number of pages10
JournalNew Phytologist
Volume213
Issue number4
DOIs
StatePublished - Mar 1 2017

Bibliographical note

Funding Information:
This research was supported by the Bill and Melinda Gates Foundation. Sequencing was performed at the Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine. The Center is partially supported by NCI Cancer Center Support Grant #P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA Grant #UL1 TR000448 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official view of NCRR or NIH.

Keywords

  • RNA sequencing
  • biotechnology
  • cassava (Manihot esculenta)
  • food security
  • friable embryogenic callus
  • gene expression
  • organized embryogenic structures

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