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

doi:10.1111/nph.14443

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

Genetics, Cell Biology and Development (CBS)

Research output: Contribution to journal › Article › peer-review

53 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 language	English (US)
Pages (from-to)	1632-1641
Number of pages	10
Journal	New Phytologist
Volume	213
Issue number	4
DOIs	https://doi.org/10.1111/nph.14443
State	Published - 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.

Publisher Copyright:
© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Publisher link

10.1111/nph.14443

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516207

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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.",

keywords = "RNA sequencing, biotechnology, cassava (Manihot esculenta), food security, friable embryogenic callus, gene expression, organized embryogenic structures",

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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. Publisher Copyright: {\textcopyright} 2017 The Authors. New Phytologist {\textcopyright} 2017 New Phytologist Trust",

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N2 - 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.

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Gene expression atlas for the food security crop cassava

Abstract

Bibliographical note

Keywords

UN SDGs

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