Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

Cannarozzi, Gina Michelle; Plaza-Wuethrich, Sonia; Esfeld, Korinna; Larti, Stephanie; Wilson, Yi Song; Kebede, Dejene Girma; de Castro, Edouard; Chanyalew, Solomon; Blösch, Regula; Farinelli, Laurent; Lyons, Eric; Schneider, Michel; Falquet, Laurent; Kuhlemeier, Cris; Assefa, Kebebew; Tadele, Zerihun (2014). Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics, 15(1), p. 581. BioMed Central 10.1186/1471-2164-15-581

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Background: Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. Results: The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. Conclusions: It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Plant Development
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)

UniBE Contributor:

Cannarozzi, Gina Michelle; Plaza, Sonia; Esfeld, Korinna; Kebede, Dejene Girma; Blösch, Regula; Kuhlemeier, Cris and Tadele, Zerihun

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

1471-2164

Publisher:

BioMed Central

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

12 Jun 2015 10:07

Last Modified:

26 Jun 2016 02:05

Publisher DOI:

10.1186/1471-2164-15-581

Uncontrolled Keywords:

Tef, Eragrostis tef, Genome, Transcriptome, Abiotic stress Prolamin

BORIS DOI:

10.7892/boris.69529

URI:

https://boris.unibe.ch/id/eprint/69529

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