title: Gene expression atlas for the food security crop cassava.
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.
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Mark C
authors.initials: MC
authors.lastname: Wilson
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Mutka
authors.affiliation: Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
authors.forename: Aaron W
authors.initials: AW
authors.lastname: Hummel
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Berry
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Raj Deepika
authors.initials: RD
authors.lastname: Chauhan
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Anupama
authors.initials: A
authors.lastname: Vijayaraghavan
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: Taylor
authors.affiliation: Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Voytas
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Chitwood
authors.affiliation: Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.
authors.forename: Rebecca S
authors.initials: RS
authors.lastname: Bart
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics*; D005523:Food Supply; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D002365:Manihot / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger
keywords: RNA sequencing; biotechnology; cassava (Manihot esculenta); food security; friable embryogenic callus; gene expression; organized embryogenic structures