Proteomics in Allopolyploid Crops: Stress Resilience, Challenges and Prospects

Polyploid crops such as wheat, Brassica, and cotton are critical in the global agricultural and economic system. However, their productivity is threatened increasingly by biotic stresses such as disease, and abiotic stresses such as heat, both exacerbated by climate change. Understanding the molecular basis of stress responses in these crops is crucial but remains challenging due to their complex genetic makeup—characterized by large sizes, multiple genomes, and limited annotation resources. Proteomics is a powerful approach to elucidate molecular mechanisms, enabling the identification of stress-responsive proteins; cellular localization; physiological, biochemical, and metabolic pathways; protein–protein interaction; and post-translational modifications. It also sheds light on the evolutionary consequences of genome duplication and hybridization. Breeders can improve stress tolerance and yield traits by characterizing the proteome of polyploid crops. Functional and subcellular proteomics, and identification and introgression of stress-responsive protein biomarkers, are promising for crop improvement. Nevertheless, several challenges remain, including inefficient protein extraction methods, limited organelle-specific data, insufficient protein annotations, low proteoform coverage, reproducibility, and a lack of target-specific antibodies. This review explores the genomic complexity of three key allopolyploid crops (wheat, oilseed Brassica, and cotton), summarizes recent proteomic insights into heat stress and pathogen response, and discusses current challenges and future directions for advancing proteomics in polyploid crop improvement through proteomics.