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Open Access Highly Accessed Research article

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

Gina Cannarozzi12, Sonia Plaza-Wüthrich1, Korinna Esfeld1, Stéphanie Larti18, Yi Song Wilson1, Dejene Girma13, Edouard de Castro4, Solomon Chanyalew5, Regula Blösch1, Laurent Farinelli6, Eric Lyons7, Michel Schneider4, Laurent Falquet29, Cris Kuhlemeier1, Kebebew Assefa5 and Zerihun Tadele1*

Author Affiliations

1 University of Bern, Institute of Plant Sciences, Altenbergrain 21, Bern CH-3013, Switzerland

2 Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne 1015, Switzerland

3 Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia

4 Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland

5 Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia

6 Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates CH-1228, Switzerland

7 Univerisity of Arizona, School of Plant Sciences, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036, USA

8 Current address: University of Bern, Clinic for Parodontology, Freiburgstrasse 7, Bern CH-3010, Switzerland

9 Current address: University of Fribourg, Faculty of Science, Ch. du Musée 10, Fribourg CH-1700, Switzerland

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BMC Genomics 2014, 15:581  doi:10.1186/1471-2164-15-581

Published: 9 July 2014

Abstract

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.

Keywords:
Tef; Eragrostis tef; Genome; Transcriptome; Abiotic stress; Prolamin