Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress

Calcium (Ca) is one of the essential mineral nutrients for plant growth and development. However, the effects of long-term Ca 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) Ca, and plant growth parameters and whole-genome transcriptome were analyzed. Ca-deficient plants exhibited leaf necrosis, leaf curling, and growth stunting symptoms. Ca 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 Ca in the uptake and/or translocation of these minerals. Transcriptomic analysis using RNA-seq revealed that members of Ca channels, including the cyclic nucleotide-gated channels and glutamate receptor-like channels, Ca-transporters, Ca-binding proteins and Ca-dependent protein kinases were differentially regulated by Ca 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 Ca treatment. Taken together, our findings suggest that Ca deficiency affects plant growth and mineral accumulation by regulating the transcriptomes of several transporters and signaling genes.