An Overview of Advances in Genomic Tools for Durable Rust Resistance in Wheat Breeding

Wheat rusts, caused by Puccinia graminis, P. triticina, and P. striiformis, are among the most destructive fungal diseases threatening global wheat production, leading to significant yield losses and economic disruption. Conventional breeding approaches, though historically effective, face substantial limitations due to the rapid evolution of rust pathotypes, genotype-by-environment interactions, and narrow genetic diversity in elite germplasm. Wheat (Triticum aestivum L.) is one of the most critical cereal crops grown worldwide, occupying approximately 220 million hectares annually and contributing to over 20% of global calorie intake. The study aims to advent of genomic tools has revolutionised rust resistance breeding by enabling precise, efficient, and accelerated development of resistant cultivars. This review highlights the current progress, challenges, and strategic directions in leveraging genomics for sustainable rust resistance breeding in wheat. Marker-assisted selection (MAS) has facilitated the introgression and pyramiding of key resistance genes such as Sr2, Lr34, and Yr18. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) have identified numerous loci contributing to adult plant resistance across diverse environments. Genomic selection (GS) and high-throughput genotyping platforms, including SNP arrays and genotyping-by-sequencing (GBS), have significantly improved prediction accuracy and selection efficiency in breeding programs. Genome editing tools like CRISPR/Cas9 offer opportunities to modify susceptibility genes and develop resistant lines without foreign DNA introduction. Functional genomics and transcriptomic profiling are unravelling the complex molecular basis of host-pathogen interactions and enabling the identification of novel defence regulators. Integration of these tools into breeding pipelines—through marker-assisted backcrossing, speed breeding, and doubled haploid technologies—has reduced breeding cycle time and enhanced resistance durability. Despite these advances, challenges remain, including limited resistance diversity in cultivated lines, infrastructural and computational constraints, and unresolved regulatory issues for gene-edited crops. Mining resistance genes from wild relatives, expanding pangenome resources, and deploying artificial intelligence for predictive breeding are future priorities. Strengthening national breeding capacities and promoting participatory approaches are essential for translating genomic gains into field-level impact. Sustained investment in genomic breeding and global collaborations is essential for safeguarding wheat productivity and food security under dynamic agro-climatic and pathogen scenarios.