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

Persistent Link:
http://hdl.handle.net/10150/610025
Title:
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)
Author:
Cannarozzi, Gina; Plaza-Wuthrich, Sonia; Esfeld, Korinna; Larti, Stephanie; Wilson, Yi; Girma, Dejene; de Castro, Edouard; Chanyalew, Solomon; Blosch, Regula; Farinelli, Laurent; Lyons, Eric; Schneider, Michel; Falquet, Laurent; Kuhlemeier, Cris; Assefa, Kebebew; Tadele, Zerihun
Affiliation:
University of Bern, Institute of Plant Sciences, Altenbergrain 21, Bern CH-3013, Switzerland; Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne 1015, Switzerland; Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia; Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland; Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia; Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates CH-1228, Switzerland; Univerisity of Arizona, School of Plant Sciences, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036, USA; Current address: University of Bern, Clinic for Parodontology, Freiburgstrasse 7, Bern CH-3010, Switzerland; Current address: University of Fribourg, Faculty of Science, Ch. du Musée 10, Fribourg CH-1700, Switzerland
Issue Date:
2014
Publisher:
BioMed Central
Citation:
Cannarozzi et al. BMC Genomics 2014, 15:581 http://www.biomedcentral.com/1471-2164/15/581
Journal:
BMC Genomics
Rights:
© 2014 Cannarozzi et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-15-581
Keywords:
Tef; Eragrostis tef; Genome; Transcriptome; Abiotic stress; Prolamin
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/15/581

Full metadata record

DC FieldValue Language
dc.contributor.authorCannarozzi, Ginaen
dc.contributor.authorPlaza-Wuthrich, Soniaen
dc.contributor.authorEsfeld, Korinnaen
dc.contributor.authorLarti, Stephanieen
dc.contributor.authorWilson, Yien
dc.contributor.authorGirma, Dejeneen
dc.contributor.authorde Castro, Edouarden
dc.contributor.authorChanyalew, Solomonen
dc.contributor.authorBlosch, Regulaen
dc.contributor.authorFarinelli, Laurenten
dc.contributor.authorLyons, Ericen
dc.contributor.authorSchneider, Michelen
dc.contributor.authorFalquet, Laurenten
dc.contributor.authorKuhlemeier, Crisen
dc.contributor.authorAssefa, Kebebewen
dc.contributor.authorTadele, Zerihunen
dc.date.accessioned2016-05-20T08:56:47Z-
dc.date.available2016-05-20T08:56:47Z-
dc.date.issued2014en
dc.identifier.citationCannarozzi et al. BMC Genomics 2014, 15:581 http://www.biomedcentral.com/1471-2164/15/581en
dc.identifier.doi10.1186/1471-2164-15-581en
dc.identifier.urihttp://hdl.handle.net/10150/610025-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/15/581en
dc.rights© 2014 Cannarozzi et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)en
dc.subjectTefen
dc.subjectEragrostis tefen
dc.subjectGenomeen
dc.subjectTranscriptomeen
dc.subjectAbiotic stressen
dc.subjectProlaminen
dc.titleGenome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)en
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentUniversity of Bern, Institute of Plant Sciences, Altenbergrain 21, Bern CH-3013, Switzerlanden
dc.contributor.departmentSwiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne 1015, Switzerlanden
dc.contributor.departmentEthiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopiaen
dc.contributor.departmentSwiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211, Geneva 4, Switzerlanden
dc.contributor.departmentEthiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopiaen
dc.contributor.departmentFasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates CH-1228, Switzerlanden
dc.contributor.departmentUniverisity of Arizona, School of Plant Sciences, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036, USAen
dc.contributor.departmentCurrent address: University of Bern, Clinic for Parodontology, Freiburgstrasse 7, Bern CH-3010, Switzerlanden
dc.contributor.departmentCurrent address: University of Fribourg, Faculty of Science, Ch. du Musée 10, Fribourg CH-1700, Switzerlanden
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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