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Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014; 15:581. [PMID: 25007843 PMCID: PMC4119204 DOI: 10.1186/1471-2164-15-581] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023] Open
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.
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Affiliation(s)
- Gina Cannarozzi
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
| | - Sonia Plaza-Wüthrich
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Korinna Esfeld
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Stéphanie Larti
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Clinic for Parodontology, University of Bern, Freiburgstrasse 7, Bern, CH-3010 Switzerland
| | - Yi Song Wilson
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Dejene Girma
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia
| | - Edouard de Castro
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Solomon Chanyalew
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Regula Blösch
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Laurent Farinelli
- />Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates, CH-1228 Switzerland
| | - Eric Lyons
- />School of Plant Sciences, Univerisity of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036 USA
| | - Michel Schneider
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Laurent Falquet
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
- />Faculty of Science, University of Fribourg, Ch. du Musée 10, Fribourg, CH-1700 Switzerland
| | - Cris Kuhlemeier
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Kebebew Assefa
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
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