RNA-Seq Analysis of Herbicide-Resistant Echinochloa colona for Identification of Mutations in Target Site and Detoxification Genes
Through transcriptome profiling, this project investigates the molecular basis of herbicide resistance in Echinochloa colona (jungle rice). The main objective is identifying mutations and differential expression in genes associated with herbicide target sites (e.g., ALS, ACCase) and detoxification pathways (e.g., cytochrome P450s, GSTs, ABC transporters).Project Scope:This study involves high-throughput RNA sequencing (RNA-Seq) of resistant and susceptible E. colona populations collected from agricultural fields. Comparative transcriptome analysis will be conducted to:- Detect point mutations or SNPs in herbicide target-site genes.- Identify upregulated detoxification-related genes.- Annotate and categorize differentially expressed genes involved in resistance mechanisms.- Contribute to the development of molecular markers for resistance monitoring and management.Bioinformatics analysis using established pipelines will include read quality control, transcript assembly, annotation, and variant calling.Participants:- Principal Investigator: Prof. Dr. Hameed Abed Khashan Alfarttoosi, Field Crops Department, Agriculture College, University of Kerbala- Research Team:- Mohammed Gassid Turki Al-Kriti, MSc student, Field Crops Department, Agriculture College, University of Kerbala- Prof. Dr. Adnan A. Lahuf, Plant Protection Department, Agriculture College, University of Kerbala- Assist. Prof. Dr. Ali N. Farhood, Field Crops Department, Agriculture College, University of Kerbala