Comparative in Silico Study of Lodging-Resistant Genes of Tef (Eragrostis Tef (Zucc.) Trotter) Against Wheat, Barley and Rice
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Date
2024-07
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Addis Ababa University
Abstract
Tef (Eragrostis tef), a cereal crop indigenous to Ethiopia, is essential in ensuring food and nutrition security. It is well-known for its gluten-free properties, rendering it suitable for individuals with celiac disease. However, tef is highly susceptible to lodging that negatively impacts its productivity. Efforts to develop varieties that are lodging-resistant have had limited success; particularly, because there have been a dearth of targeted genetic interventions. The aim of this study is to computationally predict and characterize six lodging-resistant genes (Rht1, BRI1, COMT1, CAD8C, CESA1 and CESA4) and the corresponding polypeptides of tef vis-à-vis three economically important cereal crops. The study began by selecting three economically important crops, namely: wheat, barley and rice and their six lodging-resistant genes. Using in silico probes, six homologous candidate lodging-resistant genes were retrieved from tef subgenomes. The candidate tef lodging-resistant nucleotide sequences were analyzed to computationally predict their gene structures and then comparatively analyzed against their homologues in the selected three crops. Putative polypeptide sequences of the six lodging-resistant genes, derived from their obtained predicted tef genes, were subjected to further amino acid level analysis to identify variations unique to tef, map the variations to specific functional or structural domains, predict the potential effects of the said variations and examine the possible impact of significant variations on the 3 dimensional structure of the proteins. Multiple sequence alignment of polypeptide sequences revealed distinct amino acid differences unique to tef in key functional and structural domains encoded by these lodging-resistant genes, with potential implications for tef's lodging susceptibility attributes. Variant effect predictions of counterfactual amino acid variations point to a subset of the unique tef variations having significant likelihood of causing damage in four of the six proteins: Rht1, BRI1, COMT1 and CESA1. Further examination of significant variation effects on the 3D structures of the four proteins revealed possible effects on the secondary structure of the polypeptides. Overall, the findings provide insights into several of tef's genetic variations related to lodging resistance features. Further experimental validation studies are needed to confirm these findings and elucidate the precise roles of these genes in tef's lodging susceptibility.
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Keywords
Comparative Analysis, Eragrostis Tef, in Silico Probe, Lodging-Resistant