Multiomic assessment of the responses of tef (Eragrostis tef) to drought and salinity stress

Tef (Eragrostis tef) is a gluten-free C4 cereal native to Ethiopia, which is rich in protein, fibre, vitamins, and minerals. Despite its significant resilience to adverse environmental conditions, tef production is limited by abiotic stresses such as drought and salinity, which threaten seedling establishment, and grain yield. This thesis investigates the metabolomic and transcriptomic responses of tef to drought and salinity stress, aiming to uncover adaptive mechanisms that could inform breeding programmes aiding in improving stress tolerance.

To investigate drought responses, multi-omics approaches were employed on tef seedlings grown under controlled drought and well-watered conditions. Four tef genotypes (Alba, Tsedy, Enatite [Ent] and Manyi) were assessed for leaf responses to drought (15% soil water content [SWC]), sampling at two time points (day 4 and 8 after reaching target SWC) and compared to normally watered controls (65% SWC). Phenotypic assessments of plant height and area suggested that each genotype showed an equivalent response to drought. Metabolomic assessments based on Flow injection electrospray mass spectrometry (FIE-MS) and multivariate statistical analyses suggested increased accumulation of osmolytes under drought, alongside significant alterations in phenylpropanoid metabolism. Transcriptomic profiling based on RNA-seq also indicated upregulation of genes associated with cell wall components and cuticle biosynthesis. Drought induced shifts in gene expression suggested diversion of phenylpropanoids towards lignin compounds and also lipid pathways towards protective cutin. These could enhance cell wall integrity and surface hydrophobicity during drought. Examination of transcriptional and metabolomic changes in phytohormones suggested the prominence of jasmonate (JA) suppression with drought. Exogenous JA application suggested that the effects of drought could be reversed, suggesting the importance of this hormone in tef stress responses.

Phenotypic assessments of Alba and Tsedy roots highlighted genotype-specific strategies. Under drought, Alba roots stopped growing compared to controls, but Tsedy roots showed lateral root growth patterns. Correspondingly, transcriptomic assessments suggested that Tsedey showed upregulated genes linked to lateral root formation (EtNEK4, EtTIR1B) as well as maintaining the root metabolome with drought compared to controls. In contrast, Alba roots showed increased expression of stress-responsive genes (EtVPE, EtATG11, EtNAC79) associated with autophagy and cell death, coupled with a decline in secondary metabolites but increases in amino acids, suggesting resource remobilisation in response to severe stress.

Additionally, the impact of salinity stress was examined by screening seeds of 19 tef varieties under 100mM NaCl treatment during germination. Varieties displayed marked differences in salt tolerance, with some maintaining high germination rates (>80%). Metabolomic analyses revealed that salt-tolerant varieties accumulated higher levels of flavonoids, sugars, and cell wall-associated metabolites, especially in roots, alongside visible pigmentation. These metabolic shifts correlated with increased antioxidant capacities, underscoring the protective role of flavonoids in mitigating salt-induced oxidative stress.

In conclusion, this work by using a multi-omics approach, provides molecular adaptations of tef under drought and salinity, highlighting key events, particularly phenylpropanoid changes, cell wall modification and genotype specific root architectural shifts. These findings offer valuable targets for breeding elite tef varieties with improved resilience to abiotic stresses.