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Genome Wide Transcriptome Analysis of tef (Eragrostis tef) 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 (Zucc.) Trotter] which accumulate high levels of Fe in the grains remained unknown. Tef is a staple crop for nearly 70 million people in East Africa, particularly Ethiopia and Eritrea. It is rich in mineral nutrients (Ca+2, Fe, Zn and Mn), vitamins and essential amino acids. In this study, tef plants were grown in 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 symptoms including leaf necrosis, leaf curling, and growth stunting. Ca2+ deficiency significantly decreased root and shoot Ca+2, potassium (K) and copper content in both root and shoots while it significantly increased root iron (Fe2+) 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 (CNGC) and glutamate receptor-like channels (GLRs), Ca2+-transporters, Ca2+-binding proteins (CBP) and Ca2+-dependent protein kinases (CDPK) were differentially regulated by Ca+2 treatment. Moreover, several Fe/metal transporters including members of vacuolar Fe transporters (VIT), yellow stripe-like (YSL), natural resistance-associated macrophage protein (NRAMP) and oligo-peptide transporters (OPT) 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.

ORGANISM(S): Eragrostis tef

PROVIDER: GSE201043 | GEO | 2022/09/23

REPOSITORIES: GEO

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Project description:Essential metals such as iron are required for healthy plant growth. Fe is an important cofactor and catalytic element in many biological processes. Fe and other metals can also be toxic when present in excess. Therefore plants have mechanisms of metal homeostasis which involve coordination of metal ion transporters for uptake, translocation and compartmentalisation. The NAS genes are supposed to play an important role in Fe homeostasis. They are coding for enzymes called nicotianaminesynthase (NAS), which synthesize nicotianamine (NA) by a one-step condensation reaction of three molecules S-adenosyl-methionine. NA acts as a chelator for Fe, Cu, Ni and Zn and might be involved in the transport and allocation of Fe throughout the plant. We generated quadruple T-DNA insertion mutant nas plants to investigate NA function as described in Klatte et al., 2009, Plant Physiol. The nas4x-1 plants show an interveinal leaf chlorosis when turning from vegetative to reproductive stage, which intensifies when growing under Fe deficiency conditions. nas4x-1 plants have strongly reduced NA contents and show an elevated Fe deficiency response in roots. By performing microarray experiments we want to reveal global changes on transcriptional level in roots and leaves of nas4x-1 mutant compared to wild type plants grown under Fe supply and Fe deficiency conditions, respectively. The loss of NAS genes has a strong impact on the regulation of other metal homeostasis genes and allows to draw conclusions about nicotianamine function in metal homeostasis of A.thaliana. For this study, four-week old nas4x-1 mutant and wild type plants were exposed for 7 days to plant medium with and without Fe supply. These conditions have been established previously and have resulted in a reproducibly strong interveinal leaf chlorosis of nas4x-1 plants compared to wild type, especially upon Fe deficiency conditions. The experiment was repeated three times in consecutive weeks to obtain three independent biological repetitions. Rosette leaves and roots of five week-old plants were harvested, RNA was isolated and microarray hybridization was performed. 24 Total samples were analyzed. We generated the following pairwise comparisons: WT + Fe vs. – Fe, nas4x-1 + Fe vs. – Fe, + Fe WT vs. + Fe nas4x-1, - Fe WT vs. - Fe nas4x-1, roots and leaves

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Genome Wide Transcriptome Analysis of tef (Eragrostis tef) Under Long-Term Low Calcium Stress

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