Plant Gene and Trait 2024, Vol.15, No.5, 253-264 http://genbreedpublisher.com/index.php/pgt 261 7.3 Case studies of successful integration Several case studies demonstrate the successful integration of disease resistance and yield improvement in onion breeding programs. One notable example is the development of onion cultivars with resistance to Fusarium basal rot (FBR). Through artificial inoculation and selection, researchers have identified and advanced populations with improved FBR resistance, which has been validated over multiple years of testing. The use of conidial inoculation methods has accelerated the breeding process by enabling the precise identification of resistant individuals, which are then used to develop new cultivars with enhanced resistance and yield (Sharma and Cramer, 2023). Another successful case study involves the use of molecular markers to improve disease resistance and yield in onion. Researchers have identified SNP markers linked to resistance genes in related Allium species, such as Allium roylei and Allium fistulosum, and have successfully introgressed these genes into onion cultivars (Collins et al., 2018). This approach has led to the development of onion lines with improved resistance to diseases like Botrytis squamosa and Downy mildew, as well as enhanced yield traits (Scholten et al., 2016; Collins et al., 2018). These case studies underscore the effectiveness of integrating molecular tools and traditional breeding methods to achieve significant improvements in disease resistance and yield in Welsh onion. 8 Technical Challenges in Marker-Assisted Breeding 8.1 Limitations of molecular markers One of the primary limitations of molecular markers in marker-assisted breeding (MAB) is their effectiveness in detecting quantitative trait loci (QTL) with small effects. While molecular markers are highly effective for traits controlled by single major genes, their utility diminishes when dealing with complex traits governed by multiple minor genes. This is particularly relevant in the context of disease resistance, where quantitative resistance often involves numerous genes with small individual effects. For instance, in wheat and barley breeding, although many QTLs for disease resistance have been identified, their small individual effects and the prevalence of QTL-background interactions hinder the broad implementation of marker-assisted selection (MAS) (Miedaner and Korzun, 2012). Additionally, the development and validation of markers that are applicable across different breeding populations remain a significant challenge, as demonstrated in the case of lupin breeding for anthracnose resistance (Yang et al., 2008). Another limitation is the cost and labor associated with developing and validating molecular markers. High-throughput genotyping platforms and next-generation sequencing technologies have reduced these costs to some extent, but they still represent a significant investment, particularly for smaller breeding programs. Moreover, the integration of MAS into practical breeding programs is often constrained by the availability of diagnostic markers and the economic return on investment. For example, in small-grain cereal breeding, the low return on investment and the lack of diagnostic markers have been cited as major constraints (Miedaner and Korzun, 2012). Despite these challenges, advancements in genomic selection (GS) and the development of high-throughput genotyping platforms hold promise for overcoming some of these limitations in the future (Poland and Rutkoski, 2016; Collins et al., 2018). 8.2 Genetic diversity and marker availability Genetic diversity within breeding populations is crucial for the success of marker-assisted breeding programs. However, the availability of molecular markers that are polymorphic and informative across diverse genetic backgrounds is often limited. This is particularly challenging in crops like onion, where the biennial life cycle, cross-pollinated nature, and high inbreeding depression complicate the characterization and breeding of improved traits (Khosa et al., 2016). The identification and validation of single nucleotide polymorphism (SNP) markers in related species, such as Allium roylei and Allium fistulosum, have been instrumental in facilitating introgression breeding in onion, but the process remains complex and resource-intensive (Scholten et al., 2016). Furthermore, the development of markers that are broadly applicable across different breeding populations requires extensive validation. For example, in the case of lupin breeding for anthracnose resistance, multiple candidate markers were generated and validated across various cultivars to ensure their wide applicability before being converted into a routine implementable form (Yang et al., 2008). This process underscores the importance
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