Gene expression atlas for the food security crop cassava.

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

doi:10.1111/nph.14443

Mark C Wilson, Anupama Vijayaraghavan + Show 8 more

Open Access

https://doi.org/10.1111/nph.14443

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Abstract

Summary 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.

Highlights

Cassava (Manihot esculenta) is the food security crop that feeds approximately 800 million people worldwide (Liu et al, 2011; Howeler et al, 2013)
To shed light on the development and physiology of cassava plants from a gene expression perspective, eleven tissue/organ types from cassava cultivar TME 204 were sampled for transcriptome profiling (Fig. 1)
Tissue type relatedness was assessed based on Jensen-Shannon (JS) distances (Fig. 2) and principal component analysis (PCA) (Fig. 3)

Summary

Introduction

Cassava (Manihot esculenta) is the food security crop that feeds approximately 800 million people worldwide (Liu et al, 2011; Howeler et al, 2013). 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 (Gegios et al, 2010; Stephenson et al., 2010; Patil et al, 2015). Among the major food crops, cassava is unique in its ability to develop massive, underground storage roots. Despite the importance of these structures, their basic physiology remains largely unknown, especially the molecular genetic basis of storage root development. We provide molecular identities for eleven cassava tissue types through RNA-

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