Molecular Plant Breeding 2024, Vol.15, No.6, 417-428 http://genbreedpublisher.com/index.php/mpb 420 breeding process. For instance, the use of GWAS in durum wheat has identified several QTLs associated with heat tolerance, which can be leveraged to improve disease resistance under stress conditions. The development of kompetitive allele-specific PCR markers for these QTLs further enhances the efficiency of breeding programs aimed at improving disease resistance (Sall et al., 2023). 3.2 Identification and transfer of resistance genes The identification and transfer of resistance genes in wheat have been greatly enhanced by genomics and genome-wide association studies (GWAS). These approaches have enabled the discovery of disease resistance genes and their integration into breeding materials. For example, the use of high-density SNP arrays in GWAS has revealed the genetic basis of heat tolerance in wheat, identifying significant marker-trait associations (MTAs) that can be used to develop heat-tolerant and disease-resistant genotypes (Ahmed et al., 2022a). Similarly, the assessment of functional diversity in germplasm pools through genome-wide approaches has identified alleles associated with desirable agronomic traits, including disease resistance (Dwivedi et al., 2017). The transfer of resistance genes from wild relatives and landraces into elite cultivars has also been a key strategy. The use of synthetic hexaploids and other exotic germplasm has introduced novel alleles for disease resistance into breeding programs (Ma and Cai, 2024). For instance, the mobilization of genetic variation from gene banks has led to the identification of new allelic variations for vernalization and glutenin genes, which are crucial for disease resistance and overall plant health (Sehgal et al., 2015). The integration of these genes into breeding pipelines has been facilitated by the development of effective DNA markers, making the process of heterologous gene transfer more efficient (Shumny et al., 2016). 3.3 Multigene resistance strategy for disease-resistant germplasm The multigene resistance strategy involves the integration of multiple resistance genes to develop germplasm with broad-spectrum disease resistance. Case studies have demonstrated the effectiveness of this approach in enhancing disease resistance in wheat. For example, the Indian Wheat Genomics Initiative has identified promising genotypes with high levels of biotic stress tolerance (Figure 2), which can be used to develop varieties with multigene resistance (Kumar et al., 2022). The use of genome editing technologies such as CRISPR-Cas9 has further enabled the fine-tuning of gene expression to enhance disease resistance traits. This technology allows for the precise modification of multiple genes, thereby improving the overall resistance of wheat cultivars to various diseases (Khadka et al., 2020a). Figure 2 Workflow for trait discovery in Indian germplasm through multi-layered integration of genotypic and phenotypic analysis (Adapted from Kumar et al., 2022) Image caption: The figure illustrates the preliminary screening of genetic resources (controlled trials, CT), including nutrient use efficiency (NUE), abiotic stress measurement (ASM), biotic stress measurement (BSM), and quality trait measurement (QTM). Genome-wide association studies (GWAS) or genomic selection (GS) are used to identify genotypes associated with specific traits, and the effects of these genotypes on phenotypes are ultimately validated through field trials (Adapted from Kumar et al., 2022) Another case study involves the use of synthetic hexaploids to introduce multiple resistance genes into wheat. These synthetic-derived lines have shown significant improvements in grain yield and resistance to biotic stresses,
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