Molecular Plant Breeding 2024, Vol.15, No.5, 259-268 http://genbreedpublisher.com/index.php/mpb 263 6.2 Limitations in identifying reliable markers for complex traits Identifying reliable markers for complex traits, such as yield and abiotic stress tolerance, poses a significant challenge in MAS. Complex traits are often controlled by multiple genes and are influenced by genotype-environment interactions, making it difficult to pinpoint specific markers that consistently correlate with the desired traits (Babu et al., 2004; Francia et al., 2005). The efficiency of MAS is further complicated by the variability in genetic gains across different generations, as markers that are effective in early generations may lead to the fixation of unfavorable alleles in later generations. This complexity necessitates a robust understanding of the genetic architecture of the traits and the development of sophisticated statistical models to accurately associate markers with phenotypic traits (Sebastian et al., 2010). 6.3 Difficulties in applying MAS in developing countries due to resource limitations The application of MAS in developing countries is often constrained by limited resources, including financial, technical, and infrastructural support. The high costs of marker development and genotyping, coupled with the need for advanced laboratory facilities and skilled personnel, make it challenging for developing countries to adopt MAS on a large scale (Collard and Mackill, 2008; Torres et al., 2010). Additionally, the lack of access to cutting-edge technologies and bioinformatics tools further hampers the effective implementation of MAS in these regions. As a result, the potential benefits of MAS in improving crop yields and resilience to environmental stresses remain largely untapped in developing countries, highlighting the need for international collaboration and investment to bridge this gap (Babu et al., 2004; He et al., 2014). 7 Case Study: Successful Application of MAS in Soybean Breeding 7.1 Description of a soybean breeding program using MAS One notable soybean breeding program utilizing marker-assisted selection (MAS) focused on developing pest-resistant and pod shattering-resistant varieties. Pod shattering is a significant issue in soybean cultivation, leading to substantial yield losses during harvest. The breeding program aimed to incorporate resistance to pod shattering by leveraging specific DNA markers associated with this trait. The KSS-SNP5 SNP marker on chromosome 16 was identified as a key marker for pod shattering resistance and was integrated into the MAS system for soybean breeding (Kim et al., 2020). 7.2 Breeding strategy, markers used, and outcomes The breeding strategy involved the use of the TaqMan SNP assay to detect the A/G allele of the KSS-SNP5 marker in various breeding materials, including F2:3 populations and yield trial stage breeding lines. The MAS prediction accuracy was evaluated by comparing genotyping data from the TaqMan assay with phenotype data obtained through the dry-oven method. The results demonstrated high prediction accuracy, with 92.5% and 96.2% accuracy in two F2:3 populations and breeding lines, respectively. Under severe conditions, the accuracy was 85% and 96% (Kim et al., 2020). Additionally, another study focused on improving grain yield in elite soybean populations using context-specific MAS (CSM). This approach involved detecting yield QTL within specific genetic and environmental contexts, modeling a target genotype, and selecting subline haplotypes that matched the target genotype. The selected subline haplotypes were then compared to their mother lines in yield trials across multiple environments and years. Statistically significant yield gains of up to 5.8% were confirmed in some of the selected sublines, and two improved sublines were released as new cultivars (Sebastian et al., 2010). 7.3 Lessons learned and key takeaways for future breeding efforts The successful application of MAS in soybean breeding programs has provided several key lessons and takeaways for future efforts. The use of specific markers, such as KSS-SNP5 for pod shattering resistance, can achieve high prediction accuracy, making MAS a reliable tool for selecting desirable traits (Kim et al., 2020). MAS allows for the efficient utilization of resources by enabling the selection of traits at early stages, thus expediting the breeding process. This efficiency is particularly beneficial for traits that are labor-intensive and time-consuming to evaluate phenotypically (Singh and Singh, 2015; Kim et al., 2020). The context-specific MAS approach demonstrated that considering the genetic and environmental contexts can lead to significant yield improvements. This approach can
RkJQdWJsaXNoZXIy MjQ4ODYzMg==