Proteomics in Allopolyploid Crops: Challenges and Prospects

Polyploid crops such as wheat, Brassica and cotton are critical in 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 meta-bolic pathways, protein-protein interactions, and post-translational modifications. It also sheds light on the evolutionary consequences of genome duplication and hybridi-zation. Breeders can improve stress tolerance and yield traits by characterizing the proteome of polyploid crops. Functional and subcellular proteomics, and the identifi-cation and introgression of stress-responsive protein biomarkers, are promising for crop improvement. Nonetheless, several challenges remain, including inefficient pro-tein extraction method, limited organelle-specific data, insufficient protein annota-tions, low proteoform coverage, reproducibility and 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 ad-vancing proteomics in polyploid crop improvement through proteomics.