Molecular Plant Breeding 2024, Vol.15, No.6, 403-416 http://genbreedpublisher.com/index.php/mpb 408 5.2 Targeted editing of resistance genes to enhance disease resistance in wheat CRISPR-Cas9 has been effectively utilized to target and modify specific resistance genes in wheat, thereby enhancing its resistance to various pathogens. One common approach involves the knockout of susceptibility genes, which are essential for pathogen colonization, thus rendering the plant resistant to the disease (Schenke and Cai, 2020). Another strategy includes the precise modification of resistance genes to improve their efficacy against pathogens (Mushtaq et al., 2019; Schenke and Cai, 2020). For instance, targeted mutations in genes responsible for viral, fungal, and bacterial disease resistance have been successfully implemented in model plants and crops, including wheat (Borrelli et al., 2018). These targeted edits not only improve disease resistance but also maintain the overall health and yield of the crop (Wang et al., 2022). 5.3 Success stories: Wheat varieties with improved disease resistance through gene editing Several success stories highlight the potential of CRISPR-Cas9 in developing disease-resistant wheat varieties. For example, researchers have successfully edited wheat genes to confer resistance against powdery mildew, a common and devastating fungal disease (Borrelli et al., 2018; Mushtaq et al., 2019). By knocking out specific susceptibility genes, they were able to create wheat lines that showed significantly reduced disease symptoms and improved overall health (Schenke and Cai, 2020). Another notable achievement is the development of wheat varieties with enhanced resistance to rust diseases, which are caused by fungal pathogens and can lead to severe yield losses (Nascimento et al., 2023). These success stories demonstrate the practical applications of CRISPR-Cas9 in wheat breeding and its potential to address global food security challenges by developing robust, disease-resistant crops (Langner et al., 2018). 6 Whole-Genome Resequencing and Wheat Disease Resistance 6.1 Identifying resistance alleles using resequencing technology Whole-genome resequencing (WGR) has become a pivotal tool in identifying resistance alleles in wheat. By comparing multiple wheat genomes, researchers have uncovered extensive structural rearrangements and introgressions from wild relatives, which are crucial for disease resistance (Walkowiak et al., 2020). The use of WGR has enabled the identification of single-nucleotide polymorphisms (SNPs) across different genomic regions, including those associated with disease resistance genes. For instance, a study identified 3.3 million SNPs in the wheat genome, which can be used to develop high-throughput genotyping arrays for breeding programs (Rimbert et al., 2018). Additionally, molecular approaches such as allele mining and ecotilling have been employed to characterize the genetic variability of resistance loci, allowing for the identification of new resistance alleles (Kaur et al., 2008). 6.2 The relationship between genomic diversity and disease resistance Genomic diversity plays a crucial role in enhancing wheat disease resistance. Comparative genomic studies have shown that the genetic diversity among different wheat lines has been shaped by a complex breeding history aimed at improving resistance to various stresses, including diseases (Walkowiak et al., 2020). Studies on selective sweeps related to disease resistance genes highlight the impact of human selection on genomic diversity. Additionally, SNP-based diversity maps provide important insights into the geographic distribution of genetic diversity, which is essential for understanding the distribution of resistance alleles (Cavanagh et al., 2013). The creation of a wheat resistance gene atlas, which documents the sources of resistance, further underscores the importance of genomic diversity in breeding for durable disease resistance (Figure 2). Hafeez et al. (2021) emphasized the importance of dynamic diversity and rational stacking of R gene combinations in enhancing crop disease resistance. By integrating pathogen diversity information with gene-editing technologies, it is possible to effectively delay pathogen adaptation to resistance genes, contributing to the long-term management of crop disease resistance. 6.3 The role of resequencing in building the wheat disease resistance gene pool Resequencing technology has significantly contributed to the expansion of the wheat disease resistance gene pool. By generating high-quality genome assemblies, researchers have been able to identify and characterize resistance genes, such as the nucleotide-binding leucine-rich repeat (NLR) proteins, which are involved in disease resistance
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