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.

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniv., 2003. / Härtill 7 uppsatser.

Master of Science / Department of Agronomy / Robert M. Aiken / Doohong Min / Finding a high-value forage crop with limited water requirements to produce livestock feed is becoming increasingly important as producers adapt to restricted water supply conditions. Our objectives were to determine the forage yield, nutritive values, and crop water productivity (CWP) of teff grass (Eragrostis tef [Zucc.] Trotter) under field conditions when compared to sorghum sudangrass (SS, S. x drummondii[(Nees ex. Steud.) Millsp. & Chase]) and pearl millet (PM, P. glaucum [L.]R.Br.). Crop water productivity was determined by dividing above-ground biomass by crop water use. Crop water use was determined by the summation of soil water depletion, precipitation, and irrigation. Yield was determined by quadrat area clippings of above-ground biomass. Nutritive value was determined using wet chemical analysis. Cultivars showed significant differences in biomass production and CWP in both years. Excalibur teff grass variety had the greatest CWP (418 kg ha-1 cm-1) 40 days after planting (DAP) in 2016, and was similar to SS and PM for the rest of the season until 58 DAP. Pearl millet had the greatest overall CWP (443 kg ha-1 cm-1) at 44 DAP. In 2017, sorghum sudangrass had significantly greater CWP than teff grass and pearl millet throughout most of the season. Among the teff varieties, Haymore had the greatest CWP (239 kg ha-1 cm-1) when harvested 10 days after boot stage (DAB). Crude protein values of teff grass varieties ranged from 9.3% to 21.3%, depending on the harvest date and year. Teff grass showed equivalent or greater nitrogen use efficiency (27.8 – 88.8 kg biomass kg-1 N applied) in our study than previously reported. Teff grass demonstrated potential to provide producers with a fast-growing and competitive forage crop with less overall water use due to a shortened growing season.

Lodging is a key agronomic problem in E. tef. due to morpho-physiological features, such tall and slender phenotype of the plant. Gibberellins metabolic genes are key targets in the control of plant height. Plant growth regulators (PGRs) that inhibit GA biosynthesis are used to shorten stem length thereby increasing lodging resistance. E. tef responded to treatment with PGRs such as GA, chlormequat chloride (CCC) and paclobutrazol (PBZ). Both PGRs reduced E. tef plant height but CCC treatment did not affect grain yield. Stem diameter was not affected by PGR treatment and also not the poor tapering (acropitally increasing diameter). Putatively transformed E. tef plants carrying a bean GA 2-oxidase (PcGA2ox) coding sequence were further produced via embryogenic callus after Agrobacterium-mediated transformation and plants were successfully grown into mature fertile plants. Eight putative transformed plants were finally generated carrying the insert (PcGA20 ox or nptII gene sequence) at the T0 generation. Constitutive expression of the GA 2-oxidase (PcGA2ox) coding sequence in E. tef resulted in phenotypic changes such as reduction in culm height, change in biomass, reduction in amount of GA in putative transformant semi-dwarf plants. The challenges found in the transgene detection in the T1 generation has been highlighted. Pheno-morphic changes occurred with little or no effect on yield. Genes involved in height control (orthologs to the rice sd-1 gene) and signaling (Rht) in E. tef were also identified and characterized. Activity of the protein for the putative rice sd-1 orthologs was further confirmed by heterologous expression. The three putative sequences in E. tef were named EtGA20ox1a, EtGA20ox1b and EtGA20ox2. Expression analysis showed that EtGA20ox2 were much less transcribed compared to the others and EtGA20ox1b could be the functional equivalent to the rice sd-1 (OsGA20ox2) gene in E. tef. Further, E. tef mutants with a semi-dwarf phenotype could be developed through mutagenesis and TILLING. However, regardless of height, grain yield was severely reduced in all mutants except in the semi-dwarf mutant GA-10. This line also had significantly higher diameter in most internodes which might contribute to the stiffness of stem. G-10 is therefore a promising line for further investigations. / Thesis (PhD)--University of Pretoria, 2012. / Plant Science / unrestricted