Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress
Abstract Calcium (Ca2+) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca2+ deficiency in orphan crops such as Tef [(Eragrostis tef) (Zucc.) Trotter], which accumulate high levels of Ca in the grains, remained unknown. Tef is a staple cr...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-23844-z |
| _version_ | 1811217646780153856 |
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| author | Ayalew Ligaba-Osena Mohammad Salehin Muhammad Numan Xuegeng Wang Sang-Chul Choi Dereje Jima Louis-Marie Bobay Wanli Guo |
| author_facet | Ayalew Ligaba-Osena Mohammad Salehin Muhammad Numan Xuegeng Wang Sang-Chul Choi Dereje Jima Louis-Marie Bobay Wanli Guo |
| author_sort | Ayalew Ligaba-Osena |
| collection | DOAJ |
| description | Abstract Calcium (Ca2+) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca2+ deficiency in orphan crops such as Tef [(Eragrostis tef) (Zucc.) Trotter], which accumulate high levels of Ca in the grains, remained unknown. Tef is a staple crop for nearly 70 million people in East Africa, particularly in Ethiopia and Eritrea. It is one of the most nutrient-dense grains, and is also more resistant to marginal soils and climatic conditions than main cereals like corn, wheat, and rice. In this study, tef plants were grown in a hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca2+, and plant growth parameters and whole-genome transcriptome were analyzed. Ca+2-deficient plants exhibited leaf necrosis, leaf curling, and growth stunting symptoms. Ca2+ deficiency significantly decreased root and shoot Ca, potassium (K), and copper content in both root and shoots. At the same time, it greatly increased root iron (Fe) content, suggesting the role of Ca2+ in the uptake and/or translocation of these minerals. Transcriptomic analysis using RNA-seq revealed that members of Ca2+ channels, including the cyclic nucleotide-gated channels and glutamate receptor-like channels, Ca2+-transporters, Ca2+-binding proteins and Ca2+-dependent protein kinases were differentially regulated by Ca+2 treatment. Moreover, several Fe/metal transporters, including members of vacuolar Fe transporters, yellow stripe-like, natural resistance-associated macrophage protein, and oligo-peptide transporters, were differentially regulated between shoot and root in response to Ca2+ treatment. Taken together, our findings suggest that Ca2+ deficiency affects plant growth and mineral accumulation by regulating the transcriptomes of several transporters and signaling genes. |
| first_indexed | 2024-04-12T06:58:16Z |
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| id | doaj.art-6d59aa3c258f49369c5be52df4645827 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-12T06:58:16Z |
| publishDate | 2022-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-6d59aa3c258f49369c5be52df46458272022-12-22T03:43:05ZengNature PortfolioScientific Reports2045-23222022-11-0112111510.1038/s41598-022-23844-zGenome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stressAyalew Ligaba-Osena0Mohammad Salehin1Muhammad Numan2Xuegeng Wang3Sang-Chul Choi4Dereje Jima5Louis-Marie Bobay6Wanli Guo7Laboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina GreensboroLaboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina GreensboroLaboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina GreensboroLaboratory of Environmental Epigenetics, Department of Biology, University of North Carolina GreensboroLaboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina GreensboroCenter of Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State UniversityLaboratory of Microbial Genomics and Evolution, Department of Biology, University of North Carolina GreensboroLaboratory of Plant Molecular Biology and Biotechnology, Department of Biology, University of North Carolina GreensboroAbstract Calcium (Ca2+) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca2+ deficiency in orphan crops such as Tef [(Eragrostis tef) (Zucc.) Trotter], which accumulate high levels of Ca in the grains, remained unknown. Tef is a staple crop for nearly 70 million people in East Africa, particularly in Ethiopia and Eritrea. It is one of the most nutrient-dense grains, and is also more resistant to marginal soils and climatic conditions than main cereals like corn, wheat, and rice. In this study, tef plants were grown in a hydroponic solution containing optimum (1 mM) or low (0.01 mM) Ca2+, and plant growth parameters and whole-genome transcriptome were analyzed. Ca+2-deficient plants exhibited leaf necrosis, leaf curling, and growth stunting symptoms. Ca2+ deficiency significantly decreased root and shoot Ca, potassium (K), and copper content in both root and shoots. At the same time, it greatly increased root iron (Fe) content, suggesting the role of Ca2+ in the uptake and/or translocation of these minerals. Transcriptomic analysis using RNA-seq revealed that members of Ca2+ channels, including the cyclic nucleotide-gated channels and glutamate receptor-like channels, Ca2+-transporters, Ca2+-binding proteins and Ca2+-dependent protein kinases were differentially regulated by Ca+2 treatment. Moreover, several Fe/metal transporters, including members of vacuolar Fe transporters, yellow stripe-like, natural resistance-associated macrophage protein, and oligo-peptide transporters, were differentially regulated between shoot and root in response to Ca2+ treatment. Taken together, our findings suggest that Ca2+ deficiency affects plant growth and mineral accumulation by regulating the transcriptomes of several transporters and signaling genes.https://doi.org/10.1038/s41598-022-23844-z |
| spellingShingle | Ayalew Ligaba-Osena Mohammad Salehin Muhammad Numan Xuegeng Wang Sang-Chul Choi Dereje Jima Louis-Marie Bobay Wanli Guo Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress Scientific Reports |
| title | Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress |
| title_full | Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress |
| title_fullStr | Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress |
| title_full_unstemmed | Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress |
| title_short | Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress |
| title_sort | genome wide transcriptome analysis of the orphan crop tef eragrostis tef zucc trotter under long term low calcium stress |
| url | https://doi.org/10.1038/s41598-022-23844-z |
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