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Tadele Zerihun - One of the best experts on this subject based on the ideXlab platform.
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Application of mutation breeding to the improvement of the under-studied crop Tef (Eragrostis Tef (Zucc.) Trotter).
'CABI Publishing', 2021Co-Authors: Tadele Zerihun, Weichert Annett, Chanyalew Solomon, Assefa Kebebew, Röckel Nora, Bekele Abate, Schnell Mirjam, Hussein Negussu, Cannarozzi GinaAbstract:Induced mutation has been playing a significant role in the improvement of diverse crop types. This led to the release of over 3200 crop varieties in over 70 countries. We implemented induced mutation on Tef (Eragrostis Tef (Zucc.) Trotter), one of the most important cereal crops in the Horn of Africa, especially in Ethiopia, where it is annually cultivated on over 3 million hectares of land, equivalent to 30% of the total area allocated to cereals. Although Tef is extensively cultivated in Ethiopia due to its resilience to diverse environmental stresses, the productivity of the crop is very low. The Tef Improvement Project based at the University of Bern in Switzerland employs mutation breeding to tackle major constraints in Tef in order to enhance crop productivity. About 12,000 EMS (ethyl methanesulfonate) mutagenized M2 families were generated from four improved Tef varieties, namely ‘Tsedey’, ‘Dukem’, ‘Kora’ and ‘Dagim’. Screening for major traits of importance helped us to obtain several candidate lines, including semi-dwarf and lodging-tolerant, drought-tolerant and acid-soil-tolerant lines. Among these, the most promising ones were introgressed to locally adapted improved varieties followed by several years of testing at representative locations for traits of interest. As a result, a new variety called ‘Tesfa’ with a novel and desirable combination of traits was approved for release to the farming community. This shows that the project has been actively involved in all three phases of induced mutation: mutation induction, mutation detection and mutation breeding
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From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef Eragrostis Tef (Zucc.) Trotter
'MDPI AG', 2021Co-Authors: Numan Muhammad, Tadele Zerihun, Khan, Abdul Latif, Asaf Sajjad, Salehin Mohammad, Beyene Getu, Ligaba-osena AyalewAbstract:Tef (Eragrostis Tef (Zucc.) Trotter) is a staple food crop for 70 of the Ethiopian population and is currently cultivated in several countries for grain and forage production. It is one of the most nutritious grains, and is also more resilient to marginal soil and climate conditions than major cereals such as maize, wheat and rice. However, Tef is an extremely low-yielding crop, mainly due to lodging, which is when stalks fall on the ground irreversibly, and prolonged drought during the growing season. Climate change is triggering several biotic and abiotic stresses which are expected to cause severe food shortages in the foreseeable future. This has necessitated an alternative and robust approach in order to improve resilience to diverse types of stresses and increase crop yields. Traditional breeding has been extensively implemented to develop crop varieties with traits of interest, although the technique has several limitations. Currently, genome editing technologies are receiving increased interest among plant biologists as a means of improving key agronomic traits. In this review, the potential application of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) technology in improving stress resilience in Tef is discussed. Several putative abiotic stress-resilient genes of the related monocot plant species have been discussed and proposed as target genes for editing in Tef through the CRISPR-Cas system. This is expected to improve stress resilience and boost productivity, thereby ensuring food and nutrition security in the region where it is needed the most
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Restriction Site Associated DNA Sequencing based Single Nucleotide Polymorphism Discovery in Selected Tef (Eragrostis Tef) and Wild Eragrostis Species
'African Journals Online (AJOL)', 2020Co-Authors: Girma Dejene, Cannarozzi Gina, Weichert Annett, Tadele ZerihunAbstract:Genome-wide knowledge about the nature and extent of genetic diversity present in Tef (Eragrostis Tef), the most consumed food grain in Ethiopia is limited. Adopting next generation sequencing (NGS) protocols to enhance its genomics and breeding is essential. Here, we applied the Restriction Site Associated DNA (RAD) sequencing protocol and surveyed the genomes of 43 Tef landraces, one mutant line and two wild Eragrostis species. After mapping sequencing reads to the de novo assembled unitag and the Tef reference genome, a total of 9,024 and 58,735 high quality single nucleotide polymorphisms (SNPs) were identified, respectively. We identified greater number of SNPs and greater nucleotide diversity in the two wild Eragrostis species than in the Tef landraces. The Tef landrace populations in this study were poorly differentiated with FST values of 0.015. In the phylogenetic analysis, grouping of the landraces was not consistent with the area of collection, but few localized grouping of the landraces was evident, probably showing the communality of Tef seed use across geographical boundaries. The improved Tef varieties show reduced genetic diversity compared to the landraces and were all grouped into one cluster reflecting the nature of Tef breeding which largely targets common genomic regions. We suggest that future work needs to aim beyond common genomic regions. The work presented here is a valuable addition to the growing molecular resources developed for Tef genetic improvement.ጤፍ በኢትዮጵያ የተገኘ እና በኢትዮጵያዊያን አርሶአደሮች ለብዙ አመታት ሲመረት የኖረ ዘርፈ ብዙ ጥቅሞች ያሉት የሰብል አይነት ነዉ፡፡ ጤፍ የሚመረተውና ጥቅም ላይ የሚውለው በአብዛኛው በኢትዮጵያ በመሆኑ በአለም አቀፍ ደረጃ ጤፍ ላይ የሚደረጉ ምርምሮች ውሱን ናቸው፡፡ በተለይ የጤፍን ምርምር ለማሳለጥ የተዘጋጁ የሞለኪውላር ሳይንስ ግብአቶች ውሱን በመሆናቸው በሌሎች ሰብሎች ላይ ጥቅም ላይ የዋሉ የዲ ኤን ኤ ሲኩዌንሲንግ ቴክኖሎጂን መሰረት ያደረጉ የምርምር አቅጣጫዎችን መከተል ወሳኝ ነው፡፡ እዚህ በቀረበው የምርምር ስራ የዲ ኤን ኤ ሲኩዌንሲንግ ቴክኖሎጂን መሰረት ያደረገን የምርምር ስልት በመከተል ከአገሪቱ የተለያዩ አካባቢዎች የተሰበሰቡ አርባ ሁለት የጤፍ ዝርያዎች፡ አንድ ሚውታንት ላይን እና ሁለት ለጤፍ ቅርብ የሆኑ ዋይልድ ሬላቲቭስ ላይ ጥናት ተደርጎ የጤፍን ምርምር በዘመናዊ መልኩ የሚያግዙ ግብአቶች ተገኝተዋል፡
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Tef (Eragrostis Tef (Zucc.) Trotter) Variety ‘Felagot’
'African Journals Online (AJOL)', 2020Co-Authors: Fikre Tsion, Chanyalew Solomon, Assefa Kebebew, Genet Yazachew, Kebede Worku, Tolossa Kidist, Hussein Nigussu, Fentahun Atinkut, Belay Nigussie, Tadele ZerihunAbstract:Tef [Eragrostis Tef (Zucc.) Trotter] is the major cultivated cereal crop in Ethiopia and serves as staple food grain for over 65% of the population. The area under Tef cultivation is over three million hectares of land each year. Depending on the type of seed color, Tef grains are categorized into white and brown, while some admixtures and intermediate seed colors also exist. However, the productivity of Tef is very low as compared to other cereals due, among others, to lack of high yielding varieties. The objective of this study was to evaluate the performance of released brown seeded Tef variety called Felagot and to provide unique morphological and agronomic descriptions of this new variety. Twelve genotypes resulting from two independent crossesnd breed for at least seven generations plus local and standard check varieties were tested over two years (2014 and 2015 main season) at six Tef growing locations namely: Debre Zeit light soil, Debre Zeit Black soil, Minjar, Adet, Bichena and Holetta using randomized complete block design with four replications. The study found that Felagot (DZ-Cr-442/ RIL-77C) which was obtained from a cross between Quncho (the popular variety) and Gea Lammie (local cultivar) exceled the other genotypes and it was approved for release by the Ethiopian National Variety Release Committee in March 2017. The main advantages of Felagot over the other tested lines were its higher grain yield together with high straw yield and brown seed color. In addition, it was released under the brown seed category after one and half decades. Furthermore, it is anticipated that because of the brown seed color Felagot will command high external market preferences and prices, and thereby contribute for future Tef export market.ጤፍ በኢትዮጵያ ከሚመረቱ የብርዕና አገዳ ሰብሎች ዋነኛው ሲሆን ከ65 በመቶ ለማያንስ ህዝብ ዋና የምግብ ሰብል በመሆን ያገለግላል፡፡ የጤፍ የዘር ቀለም ተለያይነት ያለው ሲሆን በአብዛኛው ነጭና ቡናማ/ቀይ አንዳንዴም ድብልቅ እና መካከለኛ የዘር ቀለም በየዓመቱ ከሶሰት ሚሊዮን ማሳ በላይ በመሸፈን ይመረታል፡፡ ይሁን እንጂ ከሌሎች ሰብሎች ጋር ሲወዳደር ምርትና ምርታማነቱ ዝቅተኛ ነው፡፡ ለዚህም ዋና ዋና ምክንያት በመሆን የሚጠቀሰው የተሻሻሉ ዝርያዎች በበቂ ሁኔታ አለመኖር ነው፡፡ የዚህ ጥናት ዋና ዓላማ እየጨመረ የመጣውን የቡናማ/ቀይ ጤፍ ፍላጎት ለማሟላት በተለያየ የምርምር አሰራርና ሂደት የተገኘ የጤፍ ዝርያን በመፈተሽ የተሻለ ምርት የሚሰጥና በአርሶ አደሩና በተጠቃሚው ተመራጭ የሆነ ዝርያ ማፍለቅ ነበር፡፡ በጥናቱም አስራ ሁለት የተለያዩ የጤፍ ዓይነቶችን ጨምሮ አንድ በቅርቡ የተለቀቀ እና አንድ የአካባቢ ዝርያን በማካተት በስድስት ወካይ ጤፍ አብቃይ ቦታዎች ላይ ተፈትሸው ፍላጎት (ደዘ-ክሮስ-442) የተባለው ቡናማ/ቀይ ዘር ቀለም ያለው ዝርያ ከሌሎች ማወዳደሪያ ዝርያዎች የተሻለ ውጤት በማስመዝገቡ በብሄራዊ የዝርያ አፅዳቂ ኮሚቴ ተገምግሞ ለምርት እንዲውል ተወስኗል፡፡ በተጨማሪም ይህ ዝርያ ቡናማ/ቀይ ዘር ቀለም ያለው ዝርያ ከተለቀቀ ከአስራ አምስት አመታት በኃላ የተገኘና የወደፊት የውጭ ገበያ ፍላጎትን ለሟሟላት ከፍተኛ አስተዋፅኦ ሊያበረክት የሚችል ነው፡
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Tef [Eragrostis Tef (Zucc.) Trotter] Breeding
'Springer Science and Business Media LLC', 2019Co-Authors: Chanyalew Solomon, Assefa Kebebew, Tadele ZerihunAbstract:Tef or Teff Eragrostis Tef (Zucc.) Trotter, a cereal crop which adapts to extreme climatic and soil conditions, is extensively cultivated in the Horn of Africa. It is also considered as nutritious and a life-style crop due to its richness in essential nutrients and health-related benefits. However, the productivity of the crop is extremely low due to little scientific improvement made globally. It is, therefore, in the category of orphan crops. Together with all cereal crops, Tef belongs to the Grass or Poaceae family. The improvement of Tef focuses on selection and hybridization techniques. However, recently, molecular and high-throughput techniques have also been implemented to a limited scale. Forty-two Tef varieties were approved for release by the Ethiopian National Variety Release Committee in the past four decades. Due to the adoption of improved varieties and technologies, the national average yield of Tef has more than doubled over the last 20Â years. This review describes the progress in Tef breeding and variety development as well as dissemination of the improved varieties to the farming community
Kebebew Assefa - One of the best experts on this subject based on the ideXlab platform.
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waterlogging affects plant morphology and the expression of key genes in Tef Eragrostis Tef
Plant direct, 2018Co-Authors: Gina Cannarozzi, Solomon Chanyalew, Sonia Plazawuthrich, Regula Blosch, Annett Weichert, Mirjam Schnell, Celia Ruiz, Svenja Bossard, Kebebew AssefaAbstract:Tef [Eragrostis Tef (Zucc.) Trotter], an allotetraploid cereal that is a staple food to over 60 million people in the Horn of Africa, has a high nutritional content and is resistant to many biotic and abiotic stresses such as waterlogging and drought. Three Tef genotypes, Alba, Tsedey, and Quncho, were subjected to waterlogging conditions and their growth, physiology, and change in transcript expression were measured with the goal of identifying targets for breeding cultivars with improved waterlogging tolerance. Root and shoot growth and dry weight were observed over 22 days. Stomatal conductance and chlorophyll and carotenoid contents were quantified. Microscopy was used to monitor changes in the stem cross sections. Illumina RNA sequencing was used to obtain the expression profiles of Tef under flooding and control conditions and was verified using qPCR. Results indicated differences in growth between the three genotypes. Waterlogged Tsedey plants grew higher and had more root biomass than normally watered Tsedey plants. Quncho and Alba genotypes were more susceptible to the excess moisture stress. The effects of these changes were observed on the plant physiology. Among the three tested Tef genotypes, Tsedey formed more aerenchyma than Alba and had accelerated growth under waterlogging. Tsedey and Quncho had constitutive aerenchyma. Genes affecting carbohydrate metabolism, cell growth, response to reactive oxygen species, transport, signaling, and stress responses were found to change under excess moisture stress. In general, these results show the presence of substantial anatomical and physiological differences among Tef genotypes when waterlogged during the early growth stage.
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grain yield variation and association of major traits in brown seeded genotypes of Tef Eragrostis Tef zucc trotter
Agricultural and Food Science, 2015Co-Authors: Habte Jifar, Kebebew Assefa, Zerihun TadeleAbstract:Tef [Eragrostis Tef (Zucc.) Trotter] is the major cereal crop of Ethiopia where it is annually cultivated on more than three million hectares of land by over six million small-scale farmers. It is broadly grouped into white and brown-seeded type depending on grain color, although some intermediate color grains also exist. Earlier breeding experiments focused on white-seeded Tef, and a number of improved varieties were released to the farming community. Thirty-six brown-seeded Tef genotypes were evaluated using a 6 × 6 simple lattice design at three locations in the central highlands of Ethiopia to assess the productivity, heritability, and association among major pheno-morphic traits. The mean square due to genotypes, locations, and genotype by locations were significant (P < 0.01) for all traits studied. Genotypic and phenotypic coefficients of variations ranged from 2.5 to 20.3 % and from 4.3 to 21.7 %, respectively. Grain yield showed significant (P < 0.01) genotypic correlation with shoot biomass and harvest index, while it had highly significant (P < 0.01) phenotypic correlation with all the traits evaluated. Besides, association of lodging index with biomass and grain yield was negative and significant at phenotypic level while it was not significant at genotypic level. Cluster analysis grouped the 36 test genotypes into seven distinct classes. Furthermore, the first three principal components with eigenvalues greater than unity extracted 78.3 % of the total variation. The current study, generally, revealed the identification of genotypes with superior grain yield and other desirable traits for further evaluation and eventual release to the farming community.
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genetic diversity in Tef Eragrostis Tef zucc trotter
Frontiers in Plant Science, 2015Co-Authors: Kebebew Assefa, Dejene Girma, Gina Cannarozzi, Rizqah Kamies, Solomon Chanyalew, Sonia Plazawuthrich, Regula Blosch, Abiel Rindisbacher, Suhail Rafudeen, Zerihun TadeleAbstract: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 Gaertn), to the Subfamily Chloridoideae. It was believed to have originated 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.
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the origins and progress of genomics research on Tef Eragrostis Tef
Plant Biotechnology Journal, 2014Co-Authors: Dejene Girma, Gina Cannarozzi, Kebebew Assefa, Solomon Chanyalew, Cris Kuhlemeier, Zerihun TadeleAbstract: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 Tef's 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.
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breeding Tef Eragrostis Tef zucc trotter conventional and molecular approaches
Plant Breeding, 2011Co-Authors: Kebebew Assefa, Hailu Tefera, Getachew Belay, M Zeid, Jukyung Yu, Mark E SorrellsAbstract:With 2 figures and 5 tables Abstract Tef [Eragrostis Tef (Zucc.) Trotter] is an important food staple cereal crop in Ethiopia. Despite its importance in the Ethiopian agriculture, there are constraints that need to be addressed through scientific research. The major constraints are low yield of landrace cultivars under widespread cultivation, susceptibility to lodging and a lack of knowledge concerning the genetic control of agronomic traits. Conventional Tef breeding efforts started in the late 1950s, and since then a total of 24 varieties have been developed and released. Yield gain from Tef breeding has been linear with an average annual increase of 0.8%. Tef genomics has provided much molecular genetic information on important agronomic traits. More than 1500 PCR-based molecular markers have been developed and several genetic linkage maps based on intra- and inter-specific crosses have been constructed. Results from quantitative trait loci studies have provided information necessary for marker-assisted selection. Lodging is the number one cause of yield loss in Tef. Recently, molecular breeding techniques and biotechnologies are being employed to understand the genetic control of lodging.
Gina Cannarozzi - One of the best experts on this subject based on the ideXlab platform.
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identification of mirnas linked with the drought response of Tef Eragrostis Tef zucc trotter
Journal of Plant Physiology, 2018Co-Authors: Federico Martinelli, Gina Cannarozzi, Zerihun Tadele, Regula Blosch, Bipin Balan, Fredy Siegrist, Annett WeichertAbstract:Tef [Eragrostis Tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of Tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two Tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the Tef response to drought could be included in next-generation breeding programs.
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waterlogging affects plant morphology and the expression of key genes in Tef Eragrostis Tef
Plant direct, 2018Co-Authors: Gina Cannarozzi, Solomon Chanyalew, Sonia Plazawuthrich, Regula Blosch, Annett Weichert, Mirjam Schnell, Celia Ruiz, Svenja Bossard, Kebebew AssefaAbstract:Tef [Eragrostis Tef (Zucc.) Trotter], an allotetraploid cereal that is a staple food to over 60 million people in the Horn of Africa, has a high nutritional content and is resistant to many biotic and abiotic stresses such as waterlogging and drought. Three Tef genotypes, Alba, Tsedey, and Quncho, were subjected to waterlogging conditions and their growth, physiology, and change in transcript expression were measured with the goal of identifying targets for breeding cultivars with improved waterlogging tolerance. Root and shoot growth and dry weight were observed over 22 days. Stomatal conductance and chlorophyll and carotenoid contents were quantified. Microscopy was used to monitor changes in the stem cross sections. Illumina RNA sequencing was used to obtain the expression profiles of Tef under flooding and control conditions and was verified using qPCR. Results indicated differences in growth between the three genotypes. Waterlogged Tsedey plants grew higher and had more root biomass than normally watered Tsedey plants. Quncho and Alba genotypes were more susceptible to the excess moisture stress. The effects of these changes were observed on the plant physiology. Among the three tested Tef genotypes, Tsedey formed more aerenchyma than Alba and had accelerated growth under waterlogging. Tsedey and Quncho had constitutive aerenchyma. Genes affecting carbohydrate metabolism, cell growth, response to reactive oxygen species, transport, signaling, and stress responses were found to change under excess moisture stress. In general, these results show the presence of substantial anatomical and physiological differences among Tef genotypes when waterlogged during the early growth stage.
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a proteomic approach to investigate the drought response in the orphan crop Eragrostis Tef
Proteome, 2017Co-Authors: Rizqah Kamies, Gina Cannarozzi, Zerihun Tadele, Jill M Farrant, M S RafudeenAbstract:The orphan crop, Eragrostis Tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed Tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in Tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in Tef downregulated proteins.
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genetic diversity in Tef Eragrostis Tef zucc trotter
Frontiers in Plant Science, 2015Co-Authors: Kebebew Assefa, Dejene Girma, Gina Cannarozzi, Rizqah Kamies, Solomon Chanyalew, Sonia Plazawuthrich, Regula Blosch, Abiel Rindisbacher, Suhail Rafudeen, Zerihun TadeleAbstract: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 Gaertn), to the Subfamily Chloridoideae. It was believed to have originated 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.
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genome and transcriptome sequencing identifies breeding targets in the orphan crop Tef Eragrostis Tef
BMC Genomics, 2014Co-Authors: Dejene Girma, Gina Cannarozzi, Sonia Plazawuthrich, Korinna Esfeld, Stephanie Larti, Yi Song Wilson, Edouard De Castro, Solomon ChanyalewAbstract: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. 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. 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.
Dejene Girma - One of the best experts on this subject based on the ideXlab platform.
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genetic diversity in Tef Eragrostis Tef zucc trotter
Frontiers in Plant Science, 2015Co-Authors: Kebebew Assefa, Dejene Girma, Gina Cannarozzi, Rizqah Kamies, Solomon Chanyalew, Sonia Plazawuthrich, Regula Blosch, Abiel Rindisbacher, Suhail Rafudeen, Zerihun TadeleAbstract: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 Gaertn), to the Subfamily Chloridoideae. It was believed to have originated 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.
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genome and transcriptome sequencing identifies breeding targets in the orphan crop Tef Eragrostis Tef
BMC Genomics, 2014Co-Authors: Dejene Girma, Gina Cannarozzi, Sonia Plazawuthrich, Korinna Esfeld, Stephanie Larti, Yi Song Wilson, Edouard De Castro, Solomon ChanyalewAbstract: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. 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. 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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Genome and transcriptome sequencing identifies breeding targets in the orphan crop Tef (Eragrostis Tef)
BMC Genomics, 2014Co-Authors: Gina Cannarozzi, Dejene Girma, Solomon Chanyalew, Regula Blosch, Korinna Esfeld, Stephanie Larti, Yi Song Wilson, Edouard De Castro, Sonia Plaza-wüthrich, Laurent FarinelliAbstract: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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the origins and progress of genomics research on Tef Eragrostis Tef
Plant Biotechnology Journal, 2014Co-Authors: Dejene Girma, Gina Cannarozzi, Kebebew Assefa, Solomon Chanyalew, Cris Kuhlemeier, Zerihun TadeleAbstract: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 Tef's 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.
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breeding Tef Eragrostis Tef zucc trotter conventional and molecular approaches
Plant Breeding, 2011Co-Authors: Kebebew Assefa, Hailu Tefera, Getachew Belay, M Zeid, Jukyung Yu, Mark E SorrellsAbstract:With 2 figures and 5 tables Abstract Tef [Eragrostis Tef (Zucc.) Trotter] is an important food staple cereal crop in Ethiopia. Despite its importance in the Ethiopian agriculture, there are constraints that need to be addressed through scientific research. The major constraints are low yield of landrace cultivars under widespread cultivation, susceptibility to lodging and a lack of knowledge concerning the genetic control of agronomic traits. Conventional Tef breeding efforts started in the late 1950s, and since then a total of 24 varieties have been developed and released. Yield gain from Tef breeding has been linear with an average annual increase of 0.8%. Tef genomics has provided much molecular genetic information on important agronomic traits. More than 1500 PCR-based molecular markers have been developed and several genetic linkage maps based on intra- and inter-specific crosses have been constructed. Results from quantitative trait loci studies have provided information necessary for marker-assisted selection. Lodging is the number one cause of yield loss in Tef. Recently, molecular breeding techniques and biotechnologies are being employed to understand the genetic control of lodging.
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highly client oriented breeding with farmer participation in the ethiopian cereal Tef Eragrostis Tef zucc trotter
African Journal of Agricultural Research, 2008Co-Authors: Getachew Belay, Hailu Tefera, Kebebew Assefa, Anteneh Getachew, Gizaw MetaferiaAbstract:This paper describes a highly client-oriented breeding applied to enhance the development and release of a Tef (Eragrostis Tef) variety with farmer participation in Ethiopia. The main features include; clear objective, target cross, early-stage researcher selection, multi-location yield trial, farmer on-station selection, judicious selection of few candidate varieties based on farmers' and researchers' selections, farmer managed on-farm trials, and release through the existing formal procedure. In the application of this strategy, Tef exemplifies a crop with local importance, a clear market-driven selection criterion (cash crop) and farmers have better judgment of the criterion than researchers. Using farmers' consistent selection of genotypes, in conjunction with the required quantifiable data, breeders were able to release a new Tef variety named "Quncho". The new variety was not the highest yielder, but it was higher in grain yield and better in seed-color quality (very white seed-color) than the long-time cultivated variety DZ-01-196 (Magna), which was used as quality check. Given the appropriate degree of client-orientation, the results also show how farmer participation and formal breeding programs complement each other so as to overcome the rather prohibitive variety release procedures based on data from participatory breeding alone. Key words: Highly client-oriented breeding, Eragrostis Tef, Ethiopia, participatory breeding, Tef variety.
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qtl mapping of agronomic traits in Tef Eragrostis Tef zucc trotter
BMC Plant Biology, 2007Co-Authors: Elizabeth Graznak, Hailu Tefera, F Breseghello, Mark E SorrellsAbstract:Tef [Eragrostis Tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. Tef and E. pilosa (30-5). Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. The extensive QTL data generated for Tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.
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a genetic linkage map for Tef Eragrostis Tef zucc trotter
Theoretical and Applied Genetics, 2006Co-Authors: Hailu Tefera, Elizabeth Graznak, Ramesh V Kantety, David Benscher, Mark E SorrellsAbstract:Tef [Eragrostis Tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. Ninety-four F9 recombinant inbred lines (RIL) derived from the interspecific cross, Eragrostis Tef cv. Kaye Murri × Eragrostis pilosa (accession 30-5), were mapped using restriction fragment length polymorphisms (RFLP), simple sequence repeats derived from expressed sequence tags (EST–SSR), single nucleotide polymorphism/insertion and deletion (SNP/INDEL), intron fragment length polymorphism (IFLP) and inter-simple sequence repeat amplification (ISSR). A total of 156 loci from 121 markers was grouped into 21 linkage groups at LOD 4, and the map covered 2,081.5 cM with a mean density of 12.3 cM per locus. Three putative homoeologous groups were identified based on multi-locus markers. Sixteen percent of the loci deviated from normal segregation with a predominance of E. Tef alleles, and a majority of the distorted loci were clustered on three linkage groups. This map will be useful for further genetic studies in Tef including mapping of loci controlling quantitative traits (QTL), and comparative analysis with other cereal crops.
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expressed sequence tag analysis in Tef Eragrostis Tef zucc trotter
Genome, 2006Co-Authors: Qi Sun, Mauricio La Rota, Hugh Edwards, Hailu Tefera, Mark E SorrellsAbstract:Tef (Eragrostis Tef (Zucc.) Trotter) is the most important cereal crop in Ethiopia; however, there is very little DNA sequence information available for this species. Expressed sequence tags (ESTs) were generated from 4 cDNA li- braries: seedling leaf, seedling root, and inflorescence of E. Tef and seedling leaf of Eragrostis pilosa, a wild relative of E. Tef. Clustering of 3603 sequences produced 530 clusters and 1890 singletons, resulting in 2420 Tef unigenes. Ap- proximately 3/4 of Tef unigenes matched protein or nucleotide sequences in public databases. Annotation of unigenes associated 68% of the putative Tef genes with gene ontology categories. Identification of the translated unigenes for con- served protein domains revealed 389 protein family domains (Pfam), the most frequent of which was protein kinase. A total of 170 ESTs containing simple sequence repeats (EST-SSRs) were identified and 80 EST-SSR markers were developed. In addition, 19 single-nucleotide polymorphism (SNP) and (or) insertion-deletion (indel) and 34 intron frag- ment length polymorphism (IFLP) markers were developed. The EST database and molecular markers generated in this study will be valuable resources for further Tef genetic research. Resume : Le Tef (Eragrostis Tef (Zucc.) Trotter) est la plus importante culture cerealiere en Ethiopie. Cependant, il existe tres peu de sequences nucleotidiques qui soient connues pour cette espece. Des etiquettes de sequences expri- mees (EST) ont ete produites a partir de quatre banques d'ADNc : feuilles de plantule, racines de plantule et inflores- cences de l'E. Tef ainsi que des feuilles de plantules de l'Eragrostis pilosa, une espece sauvage apparentee. Une analyse de groupement des 3 603 sequences a permis de produire 530 contigs et 1 890 singlons pour un total de 2 420 unige- nes pour le Tef. Environ trois quarts des unigenes du Tef etaient homologues a des sequences proteiques ou nucleotidi- ques connues. L'annotation de ces unigenes a permis de classifier 68 % de ceux-ci parmi l'une ou l'autre des categories ontologiques. L'identification de domaines proteiques conserves a revele la presence de 389 domaines de fa- milles proteiques (Pfam) au sein des unigenes traduits dont le plus repandu etait celui des proteines kinases. Au total, 170 EST contenaient des microsatellites (EST-SSR) et 80 marqueurs en ont ete tires. De plus, 19 polymorphismes mo- nonucleotidiques (SNP) ou insertion-deletion (indel) ainsi que 34 polymorphismes de longueur des introns (IFLP) ont ete developpes. La banque de donnees pour les EST et les marqueurs moleculaires generes au cours de ce travail se- ront des outils utiles pour de futures etudes genetiques sur le Tef. Mots cles : Tef, culture cerealiere ethiopienne, EST, marqueurs moleculaires. (Traduit par la Redaction) Yu et al. 372