A genome-wide atlas of rust resistance loci in wheat was compiled to summarize the genetic basis of resistance to leaf, stripe, and stem rust diseases. The atlas integrates 920 quantitative trait loci (QTL) and characterized resistance genes from 170 publications over the past two decades, mapped onto the 21 wheat chromosomes using the latest wheat reference genome (IWGSC RefSeq v2.1). The study identified 26 genomic regions containing multiple rust loci, suggesting potential pleiotropic effects on two or more rust diseases. The atlas provides a comprehensive overview of rust resistance loci, including QTL-rich clusters (QRCs) and cloned resistance genes, which can be used to guide future research and breeding efforts. The review discusses strategies for utilizing this genetic information to develop wheat cultivars with enhanced resistance to rust diseases. It highlights the importance of genomic information for stacking desirable QTL and developing durable resistance. The study also identifies key genes and loci responsible for rust resistance, including pleiotropic genes such as Lr34/Yr18/Sr57 and Lr67/Yr46/Sr55, which confer partial and race-nonspecific resistance to multiple rust pathogens. These genes are valuable for wheat breeding due to their ability to provide long-lasting resistance. The review also explores the potential of genomic regions harboring loci with pleiotropic effects on multiple rust resistance. It identifies 22 potential multi-rust resistance loci based on shared markers from different studies, with one locus (MDQ7B.1) affecting all three rust diseases. These findings highlight the importance of further research into pleiotropic rust resistance loci to support resistance breeding efforts. The study emphasizes the role of marker-assisted selection (MAS) and genomic selection (GS) in wheat breeding. MAS uses molecular markers to track and select for resistance genes, while GS predicts genomic estimated breeding values (GEBVs) based on training populations and prediction models. GS has the potential to significantly improve the rate of genetic gain for rust resistance and is particularly useful for stacking multiple loci with minor effects. The review also discusses gene cloning and genetic engineering approaches for rust resistance, including the use of CRISPR/Cas9 systems to create new resistance alleles. These methods offer the potential to develop wheat cultivars with enhanced resistance to rust diseases. Additionally, the integration of computational simulation and speed breeding techniques can accelerate the stacking of resistance loci into elite wheat varieties. Overall, the study provides a comprehensive overview of the genetic basis of rust resistance in wheat, highlighting the importance of genomic resources, marker-assisted selection, and gene cloning in developing wheat cultivars with enhanced resistance to rust diseases. The atlas serves as a valuable resource for wheat breeders and pathologists to identify and utilize resistance loci for future breeding programs.A genome-wide atlas of rust resistance loci in wheat was compiled to summarize the genetic basis of resistance to leaf, stripe, and stem rust diseases. The atlas integrates 920 quantitative trait loci (QTL) and characterized resistance genes from 170 publications over the past two decades, mapped onto the 21 wheat chromosomes using the latest wheat reference genome (IWGSC RefSeq v2.1). The study identified 26 genomic regions containing multiple rust loci, suggesting potential pleiotropic effects on two or more rust diseases. The atlas provides a comprehensive overview of rust resistance loci, including QTL-rich clusters (QRCs) and cloned resistance genes, which can be used to guide future research and breeding efforts. The review discusses strategies for utilizing this genetic information to develop wheat cultivars with enhanced resistance to rust diseases. It highlights the importance of genomic information for stacking desirable QTL and developing durable resistance. The study also identifies key genes and loci responsible for rust resistance, including pleiotropic genes such as Lr34/Yr18/Sr57 and Lr67/Yr46/Sr55, which confer partial and race-nonspecific resistance to multiple rust pathogens. These genes are valuable for wheat breeding due to their ability to provide long-lasting resistance. The review also explores the potential of genomic regions harboring loci with pleiotropic effects on multiple rust resistance. It identifies 22 potential multi-rust resistance loci based on shared markers from different studies, with one locus (MDQ7B.1) affecting all three rust diseases. These findings highlight the importance of further research into pleiotropic rust resistance loci to support resistance breeding efforts. The study emphasizes the role of marker-assisted selection (MAS) and genomic selection (GS) in wheat breeding. MAS uses molecular markers to track and select for resistance genes, while GS predicts genomic estimated breeding values (GEBVs) based on training populations and prediction models. GS has the potential to significantly improve the rate of genetic gain for rust resistance and is particularly useful for stacking multiple loci with minor effects. The review also discusses gene cloning and genetic engineering approaches for rust resistance, including the use of CRISPR/Cas9 systems to create new resistance alleles. These methods offer the potential to develop wheat cultivars with enhanced resistance to rust diseases. Additionally, the integration of computational simulation and speed breeding techniques can accelerate the stacking of resistance loci into elite wheat varieties. Overall, the study provides a comprehensive overview of the genetic basis of rust resistance in wheat, highlighting the importance of genomic resources, marker-assisted selection, and gene cloning in developing wheat cultivars with enhanced resistance to rust diseases. The atlas serves as a valuable resource for wheat breeders and pathologists to identify and utilize resistance loci for future breeding programs.