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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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Bekele-Alemu A, Ligaba-Osena A. Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures. BMC PLANT BIOLOGY 2023; 23:506. [PMID: 37865758 PMCID: PMC10589971 DOI: 10.1186/s12870-023-04515-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR. RESULTS We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress. CONCLUSIONS The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.
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Affiliation(s)
- Abreham Bekele-Alemu
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Ayalew Ligaba-Osena
- Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA.
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Numan M, Guo W, Choi S, Wang X, Du B, Jin W, Bhandari RK, Ligaba‐Osena A. Analysis of miRNAs responsive to long-term calcium deficiency in tef ( Eragrostis tef (Zucc.) Trotter). PLANT DIRECT 2022; 6:e400. [PMID: 35582629 PMCID: PMC9090557 DOI: 10.1002/pld3.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/23/2022] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) play an important role in growth, development, stress resilience, and epigenetic modifications of plants. However, the effect of calcium (Ca2+) deficiency on miRNA expression in the orphan crop tef (Eragrostis tef) remains unknown. In this study, we analyzed expression of miRNAs in roots and shoots of tef in response to Ca2+ treatment. miRNA-seq followed by bioinformatic analysis allowed us to identify a large number of small RNAs (sRNAs) ranging from 17 to 35 nt in length. A total of 1380 miRNAs were identified in tef experiencing long-term Ca2+ deficiency while 1495 miRNAs were detected in control plants. Among the miRNAs identified in this study, 161 miRNAs were similar with those previously characterized in other plant species and 348 miRNAs were novel, while the remaining miRNAs were uncharacterized. Putative target genes and their functions were predicted for all the known and novel miRNAs that we identified. Based on gene ontology (GO) analysis, the predicted target genes are known to have various biological and molecular functions including calcium uptake and transport. Pairwise comparison of differentially expressed miRNAs revealed that some miRNAs were specifically enriched in roots or shoots of low Ca2+-treated plants. Further characterization of the miRNAs and their targets identified in this study may help in understanding Ca2+ deficiency responses in tef and related orphan crops.
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Affiliation(s)
- Muhammad Numan
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
| | - Wanli Guo
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
- Present address:
Department of Biotechnology, College of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Sang‐Chul Choi
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
| | - Xuegeng Wang
- Laboratory of Environmental Epigenetics, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
- Institute of Modern Aquaculture Science and Engineering, College of Life SciencesSouth China Normal UniversityGuangzhouP. R. China
| | - Boxuan Du
- Present address:
Department of Biotechnology, College of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Weibo Jin
- Present address:
Department of Biotechnology, College of Life Sciences and MedicineZhejiang Sci‐Tech UniversityHangzhouChina
| | - Ramji Kumar Bhandari
- Laboratory of Environmental Epigenetics, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
| | - Ayalew Ligaba‐Osena
- Present address:
Laboratory of Plant Molecular Biology and Biotechnology, Department of BiologyUniversity of North Carolina GreensboroGreensboroNorth CarolinaUSA
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Girija A, Jifar H, Jones C, Yadav R, Doonan J, Mur LAJ. Tef: a tiny grain with enormous potential. TRENDS IN PLANT SCIENCE 2022; 27:220-223. [PMID: 34865980 DOI: 10.1016/j.tplants.2021.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Tef is a highly nutritious gluten-free Ethiopian cereal with food-feed potential. However, its productivity is affected by lodging, weed infestation, terminal drought, small seed size, and shattering. Following the recent availability of tef genome sequences, we highlight the need to harness the benefits that this underutilised crop offers to improve food security.
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Affiliation(s)
- Aiswarya Girija
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Habte Jifar
- National Tef Improvement Program, Debre Zeit Agricultural Research Center, Ethiopian Institute of Agricultural Research (EIAR), P. O. Box 2003, Adis Ababa, Ethiopia
| | - Chris Jones
- Feed and Forage Development Program, International Livestock Research Institute, Nairobi 00100, Kenya
| | - Rattan Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - John Doonan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK; The National Plant Phenomics Centre (NPPC), Aberystwyth University, Gogerddan campus, Aberystwyth, SY23 3EB, UK
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK.
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Girija A, Han J, Corke F, Brook J, Doonan J, Yadav R, Jifar H, Mur LAJ. Elucidating drought responsive networks in tef (Eragrostis tef) using phenomic and metabolomic approaches. PHYSIOLOGIA PLANTARUM 2022; 174:e13597. [PMID: 34792806 DOI: 10.1111/ppl.13597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major abiotic stress that limits crop productivity and is driving the need to introduce new tolerant crops with better economic yield. Tef (Eragrostis tef) is a neglected (orphan) Ethiopian warm-season annual gluten-free cereal with high nutritional and health benefits. Further, tef is resilient to environmental challenges such as drought, but the adaptive mechanisms remain poorly understood. In this study, metabolic changes associated with drought response in 11 tef accessions were identified using phenomic and metabolomic approaches under controlled conditions. Computerized image analysis of droughted plants indicated reductions in leaf area and green pigments compared with controls. Metabolite profiling based on flow-infusion electrospray-high-resolution mass spectroscopy (FIE-HRMS) showed drought associated changes in flavonoid, phenylpropanoid biosynthesis, sugar metabolism, valine, leucine and isoleucine biosynthesis, and pentose phosphate pathways. Flavonoid associated metabolites and TCA intermediates were lower in the drought group, whereas most of the stress-responsive amino acids and sugars were elevated. Interestingly, after drought treatment, one accession Enatite (Ent) exhibited a significantly higher plant area than the others, and greater accumulation of flavonoids, amino acids (serine and glycine), sugars (ribose, myo-inositol), and fatty acids. The increased accumulation of these metabolites could explain the increased tolerance to drought in Ent compared with other accessions. This is the first time a non-targeted metabolomics approach has been applied in tef, and our results provide a framework for a better understanding of the tef metabolome during drought stress that will help to identify traits to improve this understudied potential crop.
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Affiliation(s)
- Aiswarya Girija
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Wales, UK
| | - Jiwan Han
- Software College, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Fiona Corke
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Wales, UK
- The National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, Wales, UK
| | - Jason Brook
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Wales, UK
- The National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, Wales, UK
| | - John Doonan
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Wales, UK
- The National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, Wales, UK
| | - Rattan Yadav
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Wales, UK
- The National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, Wales, UK
| | - Habte Jifar
- National Tef Improvement Program, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Wales, UK
- Software College, Shanxi Agricultural University, Taigu, Shanxi, China
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Taheri-Dehkordi A, Naderi R, Martinelli F, Salami SA. Computational screening of miRNAs and their targets in saffron (Crocus sativus L.) by transcriptome mining. PLANTA 2021; 254:117. [PMID: 34751821 DOI: 10.1007/s00425-021-03761-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
A robust workflow for the identification of miRNAs and their targets in saffron was developed. MicroRNA-mediated gene regulation in saffron is potentially involved in several biological processes, including the biosynthesis of highly valuable apocarotenoids. Saffron (Crocus sativus L.) is the most expensive spice in the world and a major source of apocarotenoids. Even though miRNAs (20-24 nt non-coding small RNAs) are important regulators of gene expression at transcriptional and post-transcriptional levels, their role in saffron has not been thoroughly investigated. As a result, a workflow for computational identification of miRNAs and their targets can be useful to uncover the regulatory networks underlying biological processes in this valuable plant. The efficiency of several assembly tools such as Trans-ABySS, Trinity, Bridger, rnaSPAdes, and EvidentialGene was evaluated based on both reference-based and reference-free metrics using transcriptome data. A reliable workflow for computational identification of miRNAs and their targets in saffron was described. The EvidentialGene was found to be the most efficient de novo transcriptome assembler for saffron as a complex triploid model, followed by the Trinity. In total, 66 miRNAs from 19 different families that target 2880 genes, including several transcription factors involved in the flowering transition, were identified. Three of the identified targets were involved in the terpenoids backbone biosynthesis. CsCCD and CsUGT genes involved in the apocarotenoids biosynthetic pathway were targeted by csa-miR156g and csa-miR156b-3p, revealing a unique post-transcriptional regulation dynamic in saffron. The identified miRNAs and their targets add to our understanding of the many biological roles of miRNAs in saffron and shed new light on the control of the apocarotenoid biosynthetic pathway in this valuable plant.
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Affiliation(s)
- Ayat Taheri-Dehkordi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran
| | | | - Seyed Alireza Salami
- Department of Horticultural Science, Faculty of Agricultural Science and Engineering, University of Tehran, Karaj, Iran.
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Liu H, Able AJ, Able JA. Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat. Int J Mol Sci 2020; 21:ijms21176017. [PMID: 32825615 PMCID: PMC7504575 DOI: 10.3390/ijms21176017] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 11/16/2022] Open
Abstract
Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.
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Perrone A, Martinelli F. Plant stress biology in epigenomic era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110376. [PMID: 32234231 DOI: 10.1016/j.plantsci.2019.110376] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/07/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
Recent progress in "omics" methodologies allow us to gain insight into the complex molecular regulatory networks underlying plant responses to environmental stresses. Among the different genome-wide analysis, epigenomics is the most under-investigated "omic" approach requiring more critical and speculative discussion about approaches, methods and experimental designs. Epigenomics allows us to gain insight into the molecular adaptation of plants in response to environmental stresses. The identification of epigenetic marks transmitted during filial generations enables new theories to be developed on the evolution of living organisms in relation to environmental changes. The molecular mechanisms driving the capacity of plants to memorize a stress and to generate stress-resistant progenies are still unclear and scarcely investigated. The elucidation of these cryptic molecular switches will assist breeders in designing crops characterized by minimally compromised productivity in relation to stresses caused by climate change. The aim of this review is to briefly describe the most uptodate epigenomic approaches, update recent progresses in crop epigenomics in plant stress biology, and to stimulate the discussion of new epigenomic methods and approaches in the new era of "omic" sciences.
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Affiliation(s)
- Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, 90128, Italy.
| | - Federico Martinelli
- Department of Biology, University of Firenze, Sesto Fiorentino, Florence, 50019, Italy.
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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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