Kebebew Assefa

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

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.

Diversity among germplasm lines of the Ethiopian cereal tef [ Eragrostis tef (Zucc.) Trotter]

Three hundred twenty germplasm lines of the major Ethiopian cereal, tef, [ Eragrostis tef (Zucc.) Trotter], were evaluated for 20 morphological, phenological and agronomic characters in two-replicated randomized complete blocks at Debre Zeit and Melkassa Agricultural Research Centers in Ethiopia during the 1995 main season. The objectives were to assess the diversity of the lines, and to estimate the broad sense heritability (H) and genetic advance (GA) of the various characters. The mean squares of genotypes were highly significant (p ≤ 0.001) for all the traits. The phenotypic and genotypic coefficients of variation ranged in that order from about 6–40% and 3–23% for days to maturity and grain yield/plant, and days to maturity and number of spikelets/main shoot panicle, respectively. The cluster analysis grouped the genotypes into 14 major complexes consisting of one to 183 lines. Of the 19 principal components involved in explaining the entire variation among the genotypes the first five which had eigenvalues of more than one explained about 73.8%. The first principal component which accounted for about 34% of the total variance was due chiefly to plant height, culm and panicle length, diameters of the two basal culm internodes, main shoot panicle mass and grain yield, number of main shoot panicle branches and spikelets, and days to panicle emergence and maturity. Estimates of H varied from about 22% for length of the lowest main shoot stem internode to 74% for number of main shoot panicle branches. Values of GA (expected from selection of the superior 5% of the lines and expressed relative to the means) ranged from about 3% for days to maturity to 36% for number of spikelets/main shoot panicle. Overall, the study indicated the existence of trait diversity in tef germplasm and this can be exploited in the genetic improvement of the crop through hybridization and selection.

Quncho: the first popular tef variety in Ethiopia

Tef, Eragrostis tef (Zucc.) Trotter, is the main Ethiopian cereal grown on 2.5 million ha annually, and serving as a staple food grain for more than 50 million people. The major constraints in tef husbandry are low productivity (average about 1 t ha21) and lodging. Scientific research on tef began in the late 1950s and over the years a number of improved varieties and management practices have been developed. However, the research outputs have, until recently, been little adopted by farmers. This paper gives an overview of new and impactful technological, institutional and partnership innovation undertaken by Debre Zeit Agricultural Research Centre with a new tef variety called Quncho. Quncho was developed from an intra-specific hybridization between two improved pure line selection varieties (DZ-01-974 and DZ-01-196). The variety DZ-01-974 is high yielding, but because of the seed colour (pale white) its preference by farmers was limited. On the other hand, the variety DZ-01-196 has been popular for its very white seed colour, but its productivity has been relatively low (1.6–1.8t ha21). Hence, a targeted cross to bring together the high- yielding traits of DZ-01-974 with the seed quality of DZ-01-196 was made in 2000. Quncho was then developed as an F2-derived recombinant inbred line (RIL) through a single-seed descent breeding method. Officially released in 2006, the Quncho variety is presently attracting farmers and seed growers.

Quantitative trait diversity in tef [ Eragrostis tef (Zucc.) Trotter] germplasm from Central and Northern Ethiopia

One thousand and eighty tef, Eragrostis tef (Zucc.) Trotter, entries representing 36 populations collected from six central and northern regions of Ethiopia were evaluated at Debre Zeit Agricultural Research Center during the 1995 main season to assess the quantitative trait diversity in the germplasm with respect to collection regions and altitude zones. Hierarchical analysis of variance showed large (p ≤ 0.01) variations within populations, and among populations within regions and altitude zones in all the 14 traits studied. The variations among regions were significant (p ≤ 0.05) for number of main shoot culm nodes, and panicle branches and spikelets. But only days to maturity, number of culm nodes, diameters of the two basal culm internodes, and harvest index depicted discernible (p ≤ 0.05) clinal variability. The 36 populations clustered into six major (75% similarity level) groups consisting of two up to 15 populations. Five principal components (PCs) explained about 81% of the entire phenotypic diversity among the populations. Of these, the first three PCs accounted for about 65% of the gross variance. About 31% of the total variance explained by the first PC alone originated chiefly from variability in main shoot panicle grain yield and length, culm length and diameter of the two basal culm internodes. Likewise, about 23% the variance accounted for by the second PC was due mainly to variations in grain and shoot phytomass yield/plant, and harvest index. Overall, the study demonstrated that tef is a highly versatile crop species and the enormous wealth of quantitative trait diversity in the germplasm indicates immense potential for the genetic improvement of the crop through breeding.

Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers

The genomic DNA profiles of 48 chickpea cultivars released in nine countries and of historical significance to the chickpea breeding programs at ICRISAT and in Ethiopia were evaluated using 48 simple sequence repeat (SSR) markers. Across the cultivars, a total of 504 alleles representing the 48 SSR loci were detected with frequencies ranging from three to 22 (mean 10.5) alleles per locus. The polymorphism information content (PIC) for the SSR markers varied from 0.37 to 0.91 (mean 0.77). A subset of only three highly informative SSR markers (TA176, TA2, TA180) enabled complete discrimination among all 48 chickpea cultivars tested. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching dissimilarity matrix resolved the 48 cultivars into two major clusters representing desi and kabuli types. These cluster groupings of the cultivars were consistent with the pedigree information available for the cultivars as to the phenotypic classes of chickpea types. Analysis of the temporal patterns of the SSR diversity by classifying 48 chickpea cultivars into four periods of release revealed increasing tendencies in the overall genetic diversity from 0.42 for the earliest varieties developed in the 1970s to 0.62 for those released in the 1980s, and reached a maximum and equivalent level of 0.72 for the varieties developed in the 1990s and 2000s. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprint identification of cultivars.

Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

Qualitative trait variation in Tef [Eragrostis tef (Zucc.) Trotter] germplasm from Western and Southern Ethiopia

Three thousand tef [Eragrostis tef (Zucc.) Trotter] single panicle derived lines representing 60 populations from western and southern parts of Ethiopia were characterized for panicle form, pigmentation of lemma and anther, caryopsis color, number of main shoot culm internodes, and counts of florets/spikelet at the basal, middle and apical parts of the panicle at Debre Zeit Agricultural Research Center during the 1999 main season. The objectives were to assess the diversity patterns of the germplasm with respect to regions and altitude zones. Among the eight characters, high Shannon-Weaver diversity indices (H’) were noted for anther color (0.71) and number of apical spikelet florets (0.68), and the lowest occurred for panicle form (0.40). Monomorphism (H’ = 0.00) was observed for panicle form, lemma color and number of middle spikelet florets each in three different populations. The overall diversity index for all populations was 0.53. In the analysis of variance of H’ estimates, substantial (p <0.05) regional differences were obtained for lemma color, number of culm internodes, and counts of middle and basal spikelet florets. Clinal variation was significant for panicle form, lemma and seed color, and for the overall mean of traits. Over all traits, mean H’ values declined from 0.60 to 0.46 with an increase in the altitude zone of origin from below 1800 to over 2400 meters above sea level. Overall, the study showed substantial diversity in the test tef germplasm.

Semi-dwarfism and lodging tolerance in tef (Eragrostis tef) is linked to a mutation in the α-Tubulin 1 gene

Highlight The 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).

The origins and progress of genomics research on Tef (Eragrostis tef)

Tef, Eragrostis tef (Zucc.) Trotter, is the most important cereal in Ethiopia. Tef is cultivated by more than five million small-scale farmers annually and constitutes the staple food for more than half of the population of 80 million. The crop is preferred by both farmers and consumers due to its beneficial traits associated with its agronomy and utilization. The genetic and phenotypic diversity of tef in Ethiopia is a national treasure of potentially global importance. In order for this diversity to be effectively conserved and utilized, a better understanding at the genomic level is necessary. In the recent years, tef has become the subject of genomic research in Ethiopia and abroad. Genomic-assisted tef improvement holds tremendous potential for improving productivity, thereby benefiting the smallholder farmers who have cultivated and relied on the crop for thousands of years. It is hoped that such research endeavours will provide solutions to some of the age-old problems of tefs husbandry. In this review, we provide a brief description of the genesis and progress of tef genomic research to date, suggest ways to utilize the genomic tools developed so far, discuss the potential of genomics to enable sustainable conservation and use of tef genetic diversity and suggest opportunities for the future research.

Technology generation to dissemination: lessons learned from the tef improvement project

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 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.