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BackgroundTef (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.ResultsThe 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.ConclusionsIt 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-581) contains supplementary material, which is available to authorized users.

Highlights d The R2R3-MYB transcription factor AN2 is a hotspot for evolutionary change d Resurrection of AN2 by a 2-bp deletion during reversal to bee pollination d Complex trait modified by two regulatory mutations of large effect d Trait reversal is possible in recent radiations

Red flower color has arisen multiple times and is generally associated with hummingbird pollination. The majority of evolutionary transitions to red color proceeded from purple lineages and tend to be genetically simple, almost always involving a few loss-of-function mutations of major phenotypic effect. Here we report on the complex evolution of a novel red floral color in the hummingbird-pollinated Petunia exserta (Solanaceae) from a colorless ancestor. The presence of a red color is remarkable because the genus cannot synthesize red anthocyanins and P. exserta retains a nonfunctional copy of the key MYB transcription factor AN2. We show that moderate up-regulation and a shift in tissue specificity of an AN2 paralog, DEEP PURPLE (DPL), restores anthocyanin biosynthesis in P. exserta. An essential shift in anthocyanin hydroxylation occurred through re-balancing the expression of three hydroxylating genes. Furthermore, the down-regulation of an acyltransferase promotes reddish hues in typically purple pigments by preventing acyl group decoration of anthocyanins. This study presents a rare case of a genetically complex evolutionary transition towards the gain of a novel red color.

Former lignite mining areas in Eastern Germany are valuable secondary habitats for many plant and animal species endangered in the natural landscape. Here, we present a study on genetic structure and diversity of 16 populations of the threatened orchid Epipactis palustris (Orchidaceae) from five mining pits and 11 natural habitats, which we carried out in order to ascertain how many times this species immigrated into former lignite mining areas, and where the source populations are located. We used two different anonymous genetic marker methods, random amplified polymorphic DNA (RAPD) and microRNA-primed genomic fingerprinting (miRPF) to analyze patterns of genetic variation. Results of a multivariate analysis based on asymmetric Soerensen similarity, principal coordinate analysis and a neighbor-joining cluster analysis indicate high within populationvariability and a moderate genetic differentiation among E. palustris populations. We found no differences between genetic diversity values of populations from former mining areas and those of natural habitats. Thus, we could not find evidences for genetic bottlenecks in the mining populations due to founder events. Source populations are predominantly close surrounding populations as geographic distance and genetic dissimilarity were correlated. However, exchanges may reach beyond 125 km and repeated independent colonization events are highly likely.

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HighlightThe semi-dwarf and lodging-tolerant kegne mutant linked to defects in microtubule orientation has the potential to enhance the productivity of an African orphan crop tef (Eragrostis tef).

Indigenous crops also known as orphan crops are key contributors to food security, which is becoming increasingly vulnerable with the current trend of population growth and climate change. They have the major advantage that they fit well into the general socio-economic and ecological context of developing world agriculture. However, most indigenous crops did not benefit from the Green Revolution, which dramatically increased the yield of major crops such as wheat and rice. Here, we describe the Tef Improvement Project, which employs both conventional-and molecular-breeding techniques to improve tef-an orphan crop important to the food security in the Horn of Africa, a region of the world with recurring devastating famines. We have established an efficient pipeline to bring improved tef lines from the laboratory to the farmers of Ethiopia. Of critical importance to the long-term success of this project is -018-2115-5 the cooperation among participants in Ethiopia and Switzerland, including donors, policy makers, research institutions, and farmers. Together, European and African scientists have developed a pipeline using breeding and genomic tools to improve the orphan crop tef and bring new cultivars to the farmers in Ethiopia. We highlight a new variety, Tesfa, developed in this pipeline and possessing a novel and desirable combination of traits. Tesfa's recent approval for release illustrates the success of the project and marks a milestone as it is the first variety (of many in the pipeline) to be released.