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 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.

Relative Availability of Nitrogen and Calcium Regulates the Growth of Poplar Seedlings Due to Transcriptome Changes

“…As a nutrient element essential for plant growth and development, calcium is involved in a variety of cellular metabolic processes [92]. Ligaba-Osena et al [93] showed that under low calcium concentrations, GO analysis highlighted the significant enrichment of several Ca 2+ transporters, signaling genes, genes with transport activities, ATPase activity, catalytic activities, etc. Wang et al [84] found that the application of exogenous calcium increased the proline and soluble sugar content in tea (Camellia sinensis) and improved heat resistance by enhancing heat stress signal transduction to mitogen-activated protein kinase terms.…”

“…In studies on perennial ryegrass, KEGG enrichment analysis indicated that "photosynthesis-antenna protein" may have a positive response to appropriate nitrogen conditions, while "steroid biosynthesis", "carotenoid biosynthesis", and "c5 bis metabolism" are the most significantly enriched pathways in response to excess nitrogen [99]. Meanwhile, Ca 2+ deficiency affects plant growth and mineral accumulation by regulating the transcription of Ca 2+ transporter, Ca 2+ -binding protein, and Ca 2+ -dependent protein kinase and signaling genes [93]. Photosynthetic metabolism is one of the most enriched KEGG pathways in plants under high calcium stress.…”

Metabolomics targets tissue-specific responses in alleviating the negative effects of salinity in tef (Eragrostis tef) during germination

“…Compared to other major cereals such as wheat, rice, barley, oats, maize, tef grains are high in amino acid, protein, fiber, vitamin, and mineral content (Zhu 2018 ; Girija et al 2022b ). Tef grains are also gluten free with low glycemic index which makes it an alternative cereal for people suffering from gluten intolerance and Type 2 diabetes (Ligaba-Osena et al 2020 , 2022 ). As a result, apart from Ethiopia, tef is cultivated as a food and forage crop in USA, Netherlands, South Africa, Australia, Indian, Kenya and Israel (Tadele and Hibistu 2021 ).…”