Plant Gene and Trait 2024, Vol.15, No.5, 253-264 http://genbreedpublisher.com/index.php/pgt 257 linked to resistance traits (Nazareno et al., 2023). In maize, a meta-analysis of QTLs for resistance to Fusarium and Gibberella ear rots identified stable QTLs that can be used in breeding programs to enhance disease resistance (Akohoue and Miedaner, 2022). These examples highlight the effectiveness of QTL mapping in identifying resistance genes, which can be applied to Welsh onion to improve its disease resistance profile. 4.2 Functional genomics approaches Functional genomics approaches, such as transcriptome sequencing and gene expression analysis, provide insights into the molecular mechanisms underlying disease resistance. These techniques help identify candidate genes that are differentially expressed in response to pathogen infection. For instance, transcriptome sequencing in Allium species has led to the identification of SNP markers linked to disease resistance, which are valuable for breeding programs aimed at improving onion cultivars (Scholten et al., 2016). In maize, co-expression analysis has revealed candidate genes associated with resistance to Fusarium and Gibberella ear rots, which can be targeted for functional validation (Akohoue and Miedaner, 2022). Applying similar approaches in Welsh onion can uncover key resistance genes and pathways, facilitating the development of resistant varieties. Functional genomics also involves the use of advanced techniques such as RNA interference (RNAi) and CRISPR/Cas9 to validate the function of candidate genes. For example, in rice, marker-assisted gene stacking has been used to combine multiple resistance genes into a single cultivar, enhancing its resistance to various biotic and abiotic stresses (Ludwików et al., 2015). This approach can be adapted for Welsh onion to pyramid multiple resistance genes, thereby providing broad-spectrum resistance to multiple diseases. By integrating functional genomics with traditional breeding methods, it is possible to accelerate the development of disease-resistant Welsh onion cultivars. 4.3 Validation of candidate genes The validation of candidate genes identified through gene mapping and functional genomics is a critical step in confirming their role in disease resistance. This involves the use of techniques such as quantitative PCR, gene knockout, and overexpression studies to assess the impact of these genes on disease resistance. For instance, in oat, candidate genes identified within QTL regions for crown rust resistance were validated using Polymerase Chain Reaction Allelic Competitive Extension (PACE) markers, confirming their association with resistance traits (Nazareno et al., 2023). Similarly, in maize, candidate genes within meta-QTL regions for Fusarium and Gibberella ear rots were validated through transcriptomic data, highlighting their potential for improving disease resistance (Akohoue and Miedaner, 2022). In Welsh onion, the validation of candidate genes can be achieved by developing specific markers for these genes and assessing their presence in resistant and susceptible lines. This can be complemented by functional studies to determine the role of these genes in the resistance mechanism. For example, SNP markers developed for Allium species have been used to map QTLs for resistance to Botrytis squamosa, providing a basis for marker-assisted breeding (Scholten et al., 2016). By validating candidate genes and incorporating them into breeding programs, it is possible to enhance the disease resistance and yield of Welsh onion cultivars. 5 Enhancing Disease Resistance through Breeding 5.1 Breeding strategies for disease resistance Conventional breeding techniques have long been employed to enhance disease resistance in crops, including Welsh onion. These methods typically involve selecting and crossbreeding plants that exhibit desirable traits, such as resistance to specific pathogens. However, conventional breeding can be time-consuming and labor-intensive, often requiring multiple generations to achieve significant improvements in disease resistance (Sharma and Cramer, 2023). Marker-assisted selection (MAS) has revolutionized the breeding process by enabling the identification and selection of disease-resistant traits at the molecular level. MAS utilizes molecular markers linked to resistance genes, allowing breeders to screen for these markers in early plant development stages. This accelerates the breeding process and increases the precision of selecting resistant varieties. For instance, the development of SNP
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