Genomic dissection of productivity, lodging, and morpho‐physiological traits in Eragrostis tef under contrasting water availabilities

Abstract

Societal Impact StatementUnderutilized species (also known as orphan crops) present opportunities to increase crop diversity and food security. Such crops lack modern genetic tools and knowledge to facilitate efficient modern breeding approaches. A wide collection of tef (Eragrostis tef (Zucc.) Trotter) genotypes was used to identify genomic regions associated with productivity, lodging, and morpho‐physiological traits under contrasting water availabilities. The obtained results are expected to enhance modern breeding and improve tef productivity under traditional and modern cropping systems, thus improving farmers' livelihood and food security.Summary Tef (E. tef (Zucc.) Trotter) is an allotetraploid (2n = 4x = 40) C4 cereal crop, endemic to Ethiopia and mainly cultivated in the Horn of Africa. Tef is characterized by high grain and feed nutritional qualities and resilience to abiotic and biotic stresses; thus, it holds great potential to sustain food and nutrition security in Africa and other parts of the world. The objective of this study was to identify genomic regions associated with responses to contrasting water regimes, as a basis for future improvement. A tef diversity panel was genotyped with 28,837 single nucleotide polymorphisms (SNPs) and phenotyped for productivity, lodging, and morpho‐physiological traits along two seasons (2020 and 2021) under well‐watered and water‐limited treatments. A genome‐wide association study was performed to identify genomic regions associated with key traits for tef breeding. A total of 107 SNPs were associated with one or more of the studied traits, resulting in 138 marker–trait associations (MTAs) detected under both water treatments. Of these, 22 SNPs were associated with more than one trait, showing either multiple trait (pleiotropic) or multiple environment associations or both. A particularly strong association was found between grain yield, lodging, and time to heading. These findings open new avenues to further research on the genetic basis and physiological mechanisms underlying major traits in tef, as well as to marker‐assisted breeding of drought‐resilient tef cultivars.

Dynamic physiological response of tef to contrasting water availabilities

“…Osmotic adjustment (i.e., reducing OP) is a common plant response to drought stress, enabling the maintenance of water absorption, turgor pressure and structural integrity ( Turner, 2017 ; Condorelli et al., 2022 ). Similar to our previous study ( Alemu et al., 2024 ), tef plants exhibited a significant reduction of OP in response to drought ( Table 1 ). It is worth noting that leaves were water-saturated prior to the OP measurement and therefore, the reduction in OP under drought represents active solute accumulation per se, rather than passive water loss.…”

“…Drought is one of the most severe environmental stresses affecting pivotal physiological, developmental and metabolic processes in plants, ultimately reducing growth and productivity ( Brodersen et al., 2019 ; Kerchev and Van Breusegem, 2022 ). Tef is a self-pollinated, annual C 4 cereal crop that is resilient to various environmental and biotic stresses ( Assefa et al., 2011 ; Kamies et al., 2017 ; Girija et al., 2022 ; Alemu et al., 2024 ), but its stress-adaptive mechanisms have not been sufficiently studied. In response to drought stress, tef exhibits changes in transpiration, Chl, photosynthesis, electrolyte leakage, ultrastructure, protein content and metabolites ( Ginbot and Farrant, 2011 ; Kamies et al., 2017 ; Girija et al., 2022 ).…”

“…Tef genotypes were selected from our tef diversity panel (TDP-300) based on a previous study ( Alemu et al., 2024 ). Genotypes with similar, medium phenology (heading time), but diverse productivity were selected based on their performances in a replicated field experiment conducted in 2021 ( Supplementary Table S1 ).…”

“…Days from planting to heading were recorded based on visual observations. Leaf osmotic potential (OP), measured as previously described by Alemu et al. (2024) , and chlorophyll content (Chl), measured using a SPAD 502Plus chlorophyll meter (Konica Minolta, Japan), were recorded twice: at the end of the differential irrigation treatment and at the end of the recovery/experimental period.…”

“…In our previous study, we documented phenological, morpho-physiological, lodging, and productivity traits of a wide tef germplasm collection under contrasting water regimes, and identified their underlying genomic loci ( Alemu et al., 2024 ). Here, we focus on six selected tef genotypes and characterize their dynamic physiological responses to contrasting water regimes.…”