Bioscience Methods 2024, Vol.15, No.5, 226-236 http://bioscipublisher.com/index.php/bm 229 development of superior varieties with combined resistance to diseases, pests, and improved nutritional quality, further increasing the economic returns (Moreau et al., 1997; Gupta et al., 2010). Several case studies illustrate the economic benefits of MAS in maize breeding. For example, the development of QPM using MAS not only improved the nutritional quality of maize but also demonstrated cost-effectiveness by reducing the breeding cycle time and minimizing genetic drag (Figure 1) (Babu et al., 2005; Kaur et al., 2020). Figure 1 A schematic representation of simultaneous conversion of four normal inbreds to QPM versions and development of QPM hybrids (Adapted from Kaur et al., 2020) Image caption: This diagram illustrates the process of improving maize varieties to obtain Quality Protein Maize (QPM) versions through marker-assisted selection (MAS). The diagram shows the backcross breeding process (BC) using different inbred lines (e.g., CML170, CML165, etc.), with foreground selection for the o2 gene, background selection, and phenotypic selection. After several generations of backcrossing, the diagram also shows the generation of hybrids and the evaluation of kernel quality and agronomic traits, ultimately leading to the development of improved QPM varieties (Adapted from Kaur et al., 2020) Another case study compared the efficiency of MAS and conventional phenotypic selection in maize. The study found that MAS significantly increased the rate of genetic gain and selection efficiency, particularly when combined with phenotypic selection. Although the initial costs of MAS were higher, the overall economic benefits, including increased yield and improved trait stability, justified the investment (Moreau et al., 2004). In conclusion, the integration of MAS in maize breeding programs offers substantial economic benefits by enhancing the efficiency and accuracy of selection, reducing breeding cycle times, and improving the overall quality and resilience of maize varieties. These advantages make MAS a valuable tool in modern plant breeding, with the potential to address both agronomic and nutritional challenges in maize production. 4 Challenges in the Integration of Genetic Markers 4.1 Technical challenges One of the primary technical challenges in integrating genetic markers is the accuracy of these markers. While platforms like genotyping by target sequencing (GBTS) have shown high consistency in marker genotypes and phylogenetic relationships, there are still limitations. For instance, the effectiveness of certain markers can be influenced by genetic background and environmental factors, which can lead to inaccuracies in marker-assisted
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