Molecular Plant Breeding 2024, Vol.15, No.6, 403-416 http://genbreedpublisher.com/index.php/mpb 404 stacking of multiple resistance genes, potentially providing more durable and long-lasting resistance against a range of pathogens (Sucher et al., 2016; Dracatos et al., 2023). This study highlights the challenges posed by diseases to global wheat production and emphasizes the importance of disease resistance in current wheat breeding programs. It also discusses the advantages and prospects of genomic-based breeding methods and provides a comprehensive overview of the latest research developments in developing disease-resistant wheat varieties. By synthesizing recent research findings, this study offers insights into the future directions of wheat breeding and explores the potential of genomic tools in enhancing disease resistance and ensuring global food security. 2 Genomic Basis of Wheat Diseases 2.1 Mapping and function of known disease resistance genes The mapping and functional characterization of disease resistance genes in wheat have been significantly advanced through various genomic approaches. For instance, the identification of multiple disease resistance meta-QTLs (MDR-MQTLs) has been a crucial step in understanding the genetic basis of resistance to diseases such as leaf rust, stem rust, and yellow rust. A study identified 86 MQTLs, including 71 MDR-MQTLs, which were validated using marker-trait associations from genome-wide association studies (GWAS). These MQTLs were found to co-localize with known resistance (R) genes, providing a robust framework for breeding disease-resistant wheat varieties (Pal et al., 2022). Additionally, the candidate-gene approach has been employed to map QTLs for resistance to various diseases, revealing that many minor resistance QTLs may be attributed to defense response (DR) genes. This approach has identified several candidate genes, such as oxalate oxidase and chitinase, which are associated with significant resistance effects. Moreover, the creation of a wheat resistance gene atlas has been proposed to facilitate the rapid deployment of R genes in breeding programs. This atlas would serve as an online directory, enabling breeders to identify and utilize sources of resistance against major wheat pathogens. The atlas aims to capture the interacting molecular components governing disease resistance through various genomic techniques, including biparental mapping and whole-genome association genetics (Hafeez et al., 2021). This initiative underscores the importance of a coordinated effort to enhance the functional characterization and application of R genes in wheat breeding. 2.2 Genomic regions and QTLs associated with disease resistance The identification and characterization of genomic regions and QTLs associated with disease resistance in wheat have been extensively studied. A meta-analysis of QTLs for resistance to multiple diseases, including septoria tritici blotch, fusarium head blight, and karnal bunt, identified 63 meta-QTLs (MQTLs) from 493 initial QTLs. These MQTLs were anchored to the reference physical map of wheat, and 38 of them were verified using marker-trait associations from GWAS. This study also identified 194 differentially expressed genes (DEGs) associated with disease resistance, providing valuable insights for fine mapping and marker-assisted breeding (Saini et al., 2021). In another study, a meta-QTL analysis of tan spot resistance in wheat identified 19 meta-QTLs from 104 initial QTLs. These meta-QTLs were clustered on an integrated linkage map, with three major QTLs located on chromosomes 2A, 3B, and 5A, showing large genetic effects and conferring resistance to multiple races of the pathogen. This analysis highlights the potential of integrating race-nonspecific QTLs to achieve high and stable resistance to tan spot in wheat (Liu et al., 2020). Additionally, a genome-wide association mapping study for pre-harvest sprouting resistance in European winter wheat identified novel QTLs on chromosomes 1A and 5B, with the latter showing pleiotropic effects on phenology and grain quality. This study underscores the complexity of resistance traits and the importance of considering pleiotropic effects in breeding programs (Dallinger et al., 2023). 2.3 Advances in wheat genomic resources: reference genome and diversity maps The development of wheat genomic resources, including reference genomes and diversity maps, has significantly advanced our understanding of the genetic basis of disease resistance. The recent surge in sequencing technologies
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