Plant Gene and Traits 2024, Vol.15, No.4, 195-206 http://genbreedpublisher.com/index.php/pgt 201 8.2 Application of molecular markers and genomic tools to develop wilt-resistant chickpea varieties Recent advances in molecular breeding have significantly contributed to the development of Fusarium wilt-resistant chickpea varieties. The use of molecular markers, such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), has enabled the identification of quantitative trait loci (QTLs) associated with resistance to different races of Fusarium wilt (Sabbavarapu et al., 2013; Garg et al., 2018; Yadav et al., 2023). Marker-assisted backcrossing (MABC) has been employed to introgress resistance genes from donor parents into elite cultivars, resulting in the development of improved lines like Super Annigeri 1 and JG 74315-14 (Mannur et al., 2018). Additionally, genomic tools such as RNA-seq, proteomics, and metabolomics have provided deeper insights into the plant-pathogen interactions and the molecular basis of resistance (Figure 3) (Jha et al., 2020; Yadav et al., 2023). Figure 3 Integrated breeding, genetics, and “omics” scheme illustrating how to combat FW resistance in grain legume (Adopted from Jha et al., 2020) 8.3 Outcomes of the breeding program and lessons learned The molecular breeding programs have yielded several successful outcomes. For instance, the development of Super Annigeri 1 and improved JG 74 lines demonstrated enhanced resistance to Fusarium wilt and increased yield performance (Mannur et al., 2018). The identification of specific QTLs and linked markers has facilitated the rapid development of resistant cultivars through marker-assisted selection (MAS) (Sabbavarapu et al., 2013; Garg et al., 2018). One of the key lessons learned is the importance of integrating multiple genomic approaches to understand the complex nature of disease resistance and to develop robust resistant varieties (Jha et al., 2020; Yadav et al., 2023). Additionally, the need for high-throughput phenotyping and the challenges associated with it have been highlighted as critical areas for future improvement (Jha et al., 2020). 8.4 Potential for scaling similar breeding strategies to other legume crops The success of molecular breeding for Fusarium wilt resistance in chickpea provides a valuable framework that can be scaled to other legume crops. Similar strategies can be employed to tackle Fusarium wilt in other legumes such as faba bean and common bean, where molecular markers and genomic tools have already shown promise (Leitão et al., 2020; Mahmoud and El-Fatah, 2020). The principles of identifying resistance-associated QTLs, utilizing marker-assisted selection, and integrating omics approaches can be universally applied to enhance disease resistance across various legume species (Jha et al., 2020; Leitão et al., 2020; Mahmoud and El-Fatah, 2020). This approach not only improves crop resilience but also contributes to sustainable agricultural practices by reducing the reliance on chemical control measures. 9 Challenges and Limitations in Molecular Breeding for Resistance 9.1 Complex genetics of resistance traits in legumes The genetic basis of resistance traits in legumes is often complex and polygenic, making it challenging to identify and manipulate these traits effectively. For instance, resistance to rust in legumes such as faba bean, pea, chickpea, and lentil is typically incomplete and governed by multiple quantitative trait loci (QTLs), which complicates
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