Genome-Wide Candidate Gene And Expression Analysis For Stress Tolerance In Brassica

Abstract

Brassica crops include oilseed rape, mustard, cabbage, broccoli, turnip, and Chinese cabbage, and their productivity is increasingly constrained by drought, salinity, heat, and low-temperature stress.  In Brassica genomes, the stress tolerance is rarely controlled by a single locus due to whole-genome triplication and recent allopolyploid formation. This manuscript integrates genome-wide resources and published expression evidence to develop a practical candidate-gene framework for improving stress tolerance in Brassica. We reviewed reference genomes, pangenomes, resequencing panels and public transcriptome studies to identify recurrently responsive gene families. Special attention was paid to transcription factors, abscisic acid signalling, osmoprotectant biosynthesis, ion transport, reactive oxygen species detoxification, heat-shock proteins, dehydrins and genes involved in photosynthesis. The most common candidate groups in drought, salt, heat and cold studies were DREB/CBF, NAC, WRKY, bZIP/ABF, HSF/HSP, LEA/dehydrin, P5CS, SOS/NHX/HKT and antioxidant enzyme families. Candidates were ranked based on their biological function, repeated differential expression, stress specificity, behaviour of duplicated copies and feasibility for marker development or functional validation. The proposed pipeline combines orthology, synteny, promoter analysis, expression profiling, qRT-PCR validation, and genome editing or association mapping.  The analysis shows that breeding for stress tolerance in Brassica should target conserved regulatory hubs, but retain subgenome-specific gene copies that may confer adaptive plasticity. The candidate list thus generated provides a structured starting point for molecular breeding, functional genomics and stress resilient Brassica improvement.