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Ramírez Gonzales LY, Cannarozzi G, Jäggi L, Assefa K, Chanyalew S, Dell'Acqua M, Tadele Z. The role of omics in improving the orphan crop tef. Trends Genet 2024; 40:449-461. [PMID: 38599921 DOI: 10.1016/j.tig.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.
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Affiliation(s)
| | - Gina Cannarozzi
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Lea Jäggi
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Kebebew Assefa
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | - Solomon Chanyalew
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, PO Box 32, Debre Zeit, Ethiopia
| | | | - Zerihun Tadele
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland.
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Tesfa D, Feyissa T, Assefa K. Genetic diversity and population structure of selected tef core germplasm lines based on microsatellite markers. Mol Biol Rep 2023; 50:8603-8613. [PMID: 37653359 DOI: 10.1007/s11033-023-08732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Tef is an indigenous and important food, feed, and cash crop for smallholder Ethiopian farmers. Knowledge of the natural genetic composition of the crop provides the option to further exploit its genetic potential through breeding. However, there are insufficient reports on the genetic variability of Ethiopian tef using a medium-throughput marker system. Hence, the current study was designed to evaluate the genetic variability of released and core germplasm that was collected earlier. METHODS AND RESULTS Eighty-one tef genotypes collected from eight Ethiopian ecological zones and released varieties were targeted using 14 SSR markers. The study yielded a total of 122 alleles across the entire locus and population. The molecular variance analysis indicated the existence of large genetic differentiation (FIS and FIT = 0.87), with 86% and 13% of the total variation accounted for among genotypes within the population and across all genotypes used for this study, respectively. However, low genetic differentiation among the populations (FST = 0.014, which accounts for 1%) was observed. Multivariate analyses such as clustering and PCoA did not cluster genotypes into distinct groups according to their geographical areas of population. This is presumably due to gene flow among populations. CONCLUSION In conclusion, our findings show that there is significant genetic diversity within populations, particularly in the Jimma, Tigray, and released varieties, as well as the presence of private alleles and heterozygosity. The study also indicates the existence of genotypic admixture in the studied materials. The identification of private alleles and their differentiation will be helpful in selecting breeding materials and creating breeding plans.
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Affiliation(s)
- Derejaw Tesfa
- Debereziet Agricultural Research Center, Ethiopian Institute of Agricultural Research, Bishoftu, Ethiopia.
- Institute of Biotechnology, Addis Abeba University, Addis Abeba, Ethiopia.
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Abeba University, Addis Abeba, Ethiopia
| | - Kebebew Assefa
- Debereziet Agricultural Research Center, Ethiopian Institute of Agricultural Research, Bishoftu, Ethiopia
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Lydia Pramitha J, Ganesan J, Francis N, Rajasekharan R, Thinakaran J. Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches. Front Genet 2023; 13:1007552. [PMID: 36699471 PMCID: PMC9870178 DOI: 10.3389/fgene.2022.1007552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.
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Affiliation(s)
- J. Lydia Pramitha
- Karunya Institute of Technology and Sciences, Coimbatore, India,*Correspondence: J. Lydia Pramitha,
| | - Jeeva Ganesan
- Tamil Nadu Agricultural University, Coimbatore, India
| | - Neethu Francis
- Karunya Institute of Technology and Sciences, Coimbatore, India
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Tadesse M, Kebede M, Girma D. Genetic Diversity of Tef [ Eragrostis tef (Zucc.)Trotter] as Revealed by Microsatellite Markers. Int J Genomics 2021; 2021:6672397. [PMID: 33977102 PMCID: PMC8087483 DOI: 10.1155/2021/6672397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/29/2022] Open
Abstract
Genetic variability is the fundamental prerequisite of any crop-breeding program to develop superior cultivars. There are about 350 Eragrostis1 species, of which, tef is the only species cultivated for human consumption. Currently, the Ethiopian Biodiversity Institute (EBI) collected over five thousand tef accessions from different geographical regions, diverse in terms of climate and elevation, which are uncharacterized yet. The objective of this study was to evaluate the genetic diversity among 64 tef accessions using 10 selected polymorphic simple sequence repeats (SSRs) markers. A total of 314 alleles were detected with an average of 14.5 alleles per locus and amplicon size ranged from 90 bp-320 bp. The mean value of polymorphic information content (PIC) was 0.87, appearing polymorphic for all loci. The lowest Fst value (0.05) was recorded among the studied tef populations. The mean value of major allele frequency and the number of effective alleles were 0.33 and 3.32, respectively. The mean value of gene flow (Nm) and Shannon's information index (I) was 4.74 and 1.65, respectively. The observed (Ho) and expected (He) heterozygosities varied from 0.34 to 0.56 and from 0.58 to 0.76, respectively. The cluster analysis has grouped the 64 tef accessions into three distinct clusters based on their similarity. The PCoA analysis showed that clustering is basing on the geographical origin of accessions. Analysis of molecular variance revealed 56%, 39% and 5% of the total variation due to variation within populations, among individuals and among populations, respectively. Structure bar-plot also inferred three gene pools, but with high level of admixtures. Thus, the present study shows that the identified tef accessions could be of great interest for the initiation of a planned breeding and conservation programs.
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Affiliation(s)
- Mahilet Tadesse
- Adama Science and Technology University, Department of Applied Biology, P. O. Box 1888, Adama, Ethiopia
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P. O. Box 32, Debre Zeit, Ethiopia
| | - Mulugeta Kebede
- Adama Science and Technology University, Department of Applied Biology, P. O. Box 1888, Adama, Ethiopia
| | - Dejene Girma
- Ethiopian Institute of Agricultural Research, National Agricultural Biotechnology Research Center, P.O. Box 249, Holetta, Ethiopia
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Genetic relationship and nuclear dna content variation in Tef [Eragrostis tef (Zucc.) Trotter] accessions. Mol Biol Rep 2020; 47:4455-4463. [DOI: 10.1007/s11033-020-05537-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/15/2020] [Indexed: 10/24/2022]
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Chanyalew S, Ferede S, Damte T, Fikre T, Genet Y, Kebede W, Tolossa K, Tadele Z, Assefa K. Significance and prospects of an orphan crop tef. PLANTA 2019; 250:753-767. [PMID: 31222492 DOI: 10.1007/s00425-019-03209-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Tef is a resilient crop from the Horn of Africa with significant importance in food and nutrition security, and currently gaining global popularity as health and performance food. Tef [Eragrostis tef (Zucc.) Trotter] is the most important cereal of Ethiopia in terms of production, consumption and cash crop value. In Ethiopia, tef is annually grown on about 3 million ha with total grain production of over 5 million tons. As such, it accounts for about 30% of the total cultivated area and one-fifth of the gross grain production of all cereals cultivated in the country. In spite of its supreme economic and agricultural significance in Ethiopia, its productivity is relatively low with national average yield of about 1.7 t/ha. This has primarily been due to the very little scientific improvement done on the crop. Tef has still been an "orphan crop" since it is globally a very much under-researched crop owing to its localized importance. Scientific research on tef in Ethiopia began in the late 1950s. The main objective of this paper is to provide an overview of the significance and major production constraints of tef, and the major achievements made to date in various tef research aspects including breeding, agronomy, crop protection, and agricultural economics and extension. Based on these reviews, the paper eventually concludes with remarks on the way forward by emphasizing on the identification of the major gaps and the improvement efforts required for realizing the ever-needed breakthrough in the productivity and production of the crop. The major focal areas of future efforts include increasing productivity of both grain and biomass, systematic conservation and mining of the genetic resources, tackling the lodging malady, mechanization of the crop's husbandry, understanding the overall physiology of the crop especially with respect to stress tolerance, unraveling the nutritional qualities, and development of recipes and value-added products.
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Affiliation(s)
- Solomon Chanyalew
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Setotaw Ferede
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Tebkew Damte
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Tsion Fikre
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Yazachew Genet
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Worku Kebede
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Kidist Tolossa
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
| | - Kebebew Assefa
- Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia.
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Khanal S, Dunne JC, Schwartz BM, Kim C, Milla-Lewis S, Raymer PL, Hanna WW, Adhikari J, Auckland SA, Rainville L, Paterson AH. Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids ( Cynodon dactylon x transvaalensis): Morphological Traits. G3 (BETHESDA, MD.) 2019; 9:2581-2596. [PMID: 31208957 PMCID: PMC6686926 DOI: 10.1534/g3.119.400061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022]
Abstract
Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11-19%), qLLS-7-1 (for LLS; R2 = 13-27%), qLEN-1-1 (for LLEN; R2 = 10-11%), and qLW-3-2 (for LW; R2 = 10-12%) were 'stable' across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.
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Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Jeffrey C Dunne
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susana Milla-Lewis
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Paul L Raymer
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA 30224
| | - Wayne W Hanna
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Lisa Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606,
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Kamies R, Farrant JM, Tadele Z, Cannarozzi G, Rafudeen MS. A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef. Proteomes 2017; 5:E32. [PMID: 29140297 PMCID: PMC5748567 DOI: 10.3390/proteomes5040032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/20/2017] [Accepted: 11/10/2017] [Indexed: 01/13/2023] Open
Abstract
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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Affiliation(s)
- Rizqah Kamies
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
| | - Jill M Farrant
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
| | - Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
| | - Gina Cannarozzi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
| | - Mohammed Suhail Rafudeen
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa.
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Zhu F. Chemical composition and food uses of teff (Eragrostis tef). Food Chem 2017; 239:402-415. [PMID: 28873585 DOI: 10.1016/j.foodchem.2017.06.101] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Teff (Eragrostis tef) is a cereal native to Ethiopia and Eritrea. It has an excellent adaptability to harsh environmental conditions and plays an important role in food security. In recent years, teff is becoming globally popular due to the attractive nutritional profile such as gluten free and high dietary fiber content. This review documents the recent advances in the genetic diversity, nutritional composition and food uses of teff grain. The attractive nutrients of teff include protein, dietary fiber, polyphenols, and certain minerals. Whole grain teff flour becomes increasingly important in healthy food market, and has been used to produce various gluten free food items such as pasta and bread. Efforts have been made to enhance the sensory quality of teff based products. There is great potential to adapt teff to the other parts of the world for healthy food and beverage production.
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Affiliation(s)
- Fan Zhu
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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Khanal S, Kim C, Auckland SA, Rainville LK, Adhikari J, Schwartz BM, Paterson AH. SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:819-839. [PMID: 28168408 DOI: 10.1007/s00122-017-2854-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/04/2017] [Indexed: 05/20/2023]
Abstract
We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F1 progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x = 9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.
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Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA, 31793, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA.
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Shah AN, Tanveer M, Rehman AU, Anjum SA, Iqbal J, Ahmad R. Lodging stress in cereal—effects and management: an overview. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:5222-5237. [PMID: 0 DOI: 10.1007/s11356-016-8237-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/09/2016] [Indexed: 05/04/2023]
Affiliation(s)
- Adnan Noor Shah
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mohsin Tanveer
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Atique Ur Rehman
- Department of Agronomy, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Javaid Iqbal
- Ghazi University, Dera Ghazi Khan, Punjab, 32200, Pakistan
| | - Riaz Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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Cheng A, Mayes S, Dalle G, Demissew S, Massawe F. Diversifying crops for food and nutrition security - a case of teff. Biol Rev Camb Philos Soc 2015; 92:188-198. [PMID: 26456883 DOI: 10.1111/brv.12225] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/01/2015] [Accepted: 09/09/2015] [Indexed: 11/28/2022]
Abstract
There are more than 50000 known edible plants in the world, yet two-thirds of global plant-derived food is provided by only three major cereals - maize (Zea mays), wheat (Triticum aestivum) and rice (Oryza sativa). The dominance of this triad, now considered truly global food commodities, has led to a decline in the number of crop species contributing to global food supplies. Our dependence on only a few crop species limits our capability to deal with challenges posed by the adverse effects of climate change and the consequences of dietary imbalance. Emerging evidence suggests that climate change will cause shifts in crop production and yield loss due to more unpredictable and hostile weather patterns. One solution to this problem is through the wider use of underutilised (also called orphan or minor) crops to diversify agricultural systems and food sources. In addition to being highly nutritious, underutilised crops are resilient in natural and agricultural conditions, making them a suitable surrogate to the major crops. One such crop is teff [Eragrostis tef (Zucc.) Trotter], a warm-season annual cereal with the tiniest grain in the world. Native to Ethiopia and often the sustenance for local small farmers, teff thrives in both moisture-stressed and waterlogged soil conditions, making it a dependable staple within and beyond its current centre of origin. Today, teff is deemed a healthy wheat alternative in the West and is sought-after by health aficionados and those with coeliac disease or gluten sensitivity. The blooming market for healthy food is breathing new life into this underutilised crop, which has received relatively limited attention from mainstream research perhaps due to its 'orphan crop' status. This review presents the past, present and future of an ancient grain with a potential beyond its size.
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Affiliation(s)
- Acga Cheng
- Biotechnology Research Centre, School of Biosciences, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Sean Mayes
- Crops For the Future, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Gemedo Dalle
- Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- The National Herbarium, Department of Plant Biology and Biodiversity Management, College of Natural Sciences, Addis Ababa University, P. O. Box 3434, Addis Ababa, Ethiopia
| | - Festo Massawe
- Biotechnology Research Centre, School of Biosciences, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.,Crops For the Future, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
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Assefa K, Cannarozzi G, Girma D, Kamies R, Chanyalew S, Plaza-Wüthrich S, Blösch R, Rindisbacher A, Rafudeen S, Tadele Z. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter]. FRONTIERS IN PLANT SCIENCE 2015; 6:177. [PMID: 25859251 PMCID: PMC4374454 DOI: 10.3389/fpls.2015.00177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/05/2015] [Indexed: 05/26/2023]
Abstract
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.
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Affiliation(s)
- Kebebew Assefa
- National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural ResearchDebre Zeit, Ethiopia
| | - Gina Cannarozzi
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Dejene Girma
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
- National Agricultural Biotechnology Laboratory, Holetta Agricultural Research Center, Ethiopian Institute of Agricultural ResearchHoletta, Ethiopia
| | - Rizqah Kamies
- Plant Stress Laboratory, Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
| | - Solomon Chanyalew
- National Tef Research Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural ResearchDebre Zeit, Ethiopia
| | - Sonia Plaza-Wüthrich
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Regula Blösch
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Abiel Rindisbacher
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
| | - Suhail Rafudeen
- Plant Stress Laboratory, Department of Molecular and Cell Biology, University of Cape TownCape Town, South Africa
| | - Zerihun Tadele
- Crop Breeding and Genomics, Institute of Plant Sciences, Department of Biology, University of BernBern, Switzerland
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Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014; 15:581. [PMID: 25007843 PMCID: PMC4119204 DOI: 10.1186/1471-2164-15-581] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023] Open
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.
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Affiliation(s)
- Gina Cannarozzi
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
| | - Sonia Plaza-Wüthrich
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Korinna Esfeld
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Stéphanie Larti
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Clinic for Parodontology, University of Bern, Freiburgstrasse 7, Bern, CH-3010 Switzerland
| | - Yi Song Wilson
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Dejene Girma
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia
| | - Edouard de Castro
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Solomon Chanyalew
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Regula Blösch
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Laurent Farinelli
- />Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates, CH-1228 Switzerland
| | - Eric Lyons
- />School of Plant Sciences, Univerisity of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036 USA
| | - Michel Schneider
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Laurent Falquet
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
- />Faculty of Science, University of Fribourg, Ch. du Musée 10, Fribourg, CH-1700 Switzerland
| | - Cris Kuhlemeier
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Kebebew Assefa
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
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Girma D, Assefa K, Chanyalew S, Cannarozzi G, Kuhlemeier C, Tadele Z. The origins and progress of genomics research on Tef (Eragrostis tef). PLANT BIOTECHNOLOGY JOURNAL 2014; 12:534-40. [PMID: 24891040 DOI: 10.1111/pbi.12199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/01/2014] [Accepted: 04/10/2014] [Indexed: 05/07/2023]
Abstract
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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Affiliation(s)
- Dejene Girma
- Institute of Plant Sciences, University of Bern, Bern, Switzerland; Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Centre, Debre Zeit, Ethiopia
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Next generation characterisation of cereal genomes for marker discovery. BIOLOGY 2013; 2:1357-77. [PMID: 24833229 PMCID: PMC4009793 DOI: 10.3390/biology2041357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/29/2013] [Accepted: 11/08/2013] [Indexed: 12/30/2022]
Abstract
Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs.
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