Biology subjects

Torabi, S.

Publications and source records attributed to Torabi, S..

3 recordsLinked to original sources

bioRxiv2021

Machine Learning based Genome-Wide Association Studies for Uncovering QTL Underlying Soybean Yield and its Components

Genome-wide association study (GWAS) is currently one of the important approaches for discovering quantitative trait loci (QTL) associated with traits of interest. However, insufficient statistical power is the limiting factor in current conventional GWAS methods for characterizing quantitative traits, especially in narrow genetic bases plants such as soybean. In this study, we evaluated the potential use of machine learning (ML) algorithms such as support vector machine (SVR) and random forest (RF) in GWAS, compared with two conventional methods of mixed linear models (MLM) and fixed and random model circulating probability unification (FarmCPU), for identifying QTL associated with soybean yield components. In this study, important soybean yield component traits, including the number of reproductive nodes (RNP), non-reproductive nodes (NRNP), total nodes (NP), and total pods (PP) per plant along with yield and maturity were assessed using 227 soybean genotypes evaluated across four environments. Our results indicated SVR-mediated GWAS outperformed RF, MLM and FarmCPU in discovering the most relevant QTL associated with the traits, supported by the functional annotation of candidate gene analyses. This study for the first time demonstrated the potential benefit of using sophisticated mathematical approaches such as ML algorithms in GWAS for identifying QTL suitable for genomic-based breeding programs.

plant biology↗

bioRxiv2021

Influence of Fara-darmani Consciousness Field on Bacterial Population Growth

The treatment of bacterial infections and the rising challenges of antibiotics resistance are global concerns and the primary topics in basic science and clinical microbiology. In the present study, the effectiveness of treatment of selected populations of bacteria using an immaterial and non-energetic method called Fara-darmani Consciousness Field treatment is investigated. Population growth was assessed by turbidimetry, colony counting and tetrazolium chloride reduction assays in non-treated control and Fara-darmani-treated groups. Our results suggest effectiveness of the Fara-darmani Consciousness Field on reducing various types of bacterial strain growth rates (up to 46%). In addition, along with a decrease in bacterial population, evidence of increased survival can be seen in the larger healthy population (up to about 60%). Thus, in this study, we confirm the effects of the Consciousness Field on bacterial population survival. This study also warrants additional research.

microbiology↗

bioRxiv2019

Duplicated KAI2 receptors with divergent ligand-binding specificities control distinct developmental traits in Lotus japonicus

Karrikins (KARs), smoke-derived butenolides, are perceived by the /{beta}-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and are thought to mimic endogenous, yet elusive plant hormones tentatively called KAI2-ligands (KLs). The sensitivity to different karrikin types as well as the number of KAI2 paralogs varies among plant species, suggesting diversification and co-evolution of ligand-receptor relationships. In legumes, which comprise a number of important crops with protein-rich, nutritious seed, KAI2 has duplicated. We report sub-functionalization of KAI2a and KAI2b in the model legume Lotus japonicus and demonstrate that their ability to bind the synthetic ligand GR24ent-5DS differs in vitro as well as in genetic assays in Lotus japonicus and in the heterologous Arabidopsis thaliana background. These differences can be explained by the exchange of a widely conserved phenylalanine in the binding pocket of KAI2a with a tryptophan in KAI2b, which occured independently in KAI2 proteins of several unrelated angiosperms. Furthermore, two polymorphic residues in the binding pocket are conserved across a number of legumes and may contribute to ligand binding preferences. Unexpectedly, L. japonicus responds to diverse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl development responds to KAR1, KAR2 and rac-GR24, while root system development responds only to KAR1. This organ-specificity cannot be explained by receptor-ligand preferences alone, because LjKAI2a is sufficient for karrikin responses in the hypocotyl, while LjKAI2a and LjKAI2b operate redundantly in roots. Our findings open novel research avenues into the evolution and diversity of butenolide ligand-receptor relationships, their ecological significance and the mechanisms controlling diverse developmental responses to different KAI2 ligands.

plant biology↗