Bioscience Methods 2024, Vol.15, No.5, 226-236 http://bioscipublisher.com/index.php/bm 228 markers have been used for high-resolution mapping and the identification of QTLs associated with important traits. Although these markers are less commonly used than SSRs and SNPs in modern breeding programs, they still offer valuable tools for specific applications where their unique characteristics are advantageous. By integrating various types of genetic markers, maize breeding programs can leverage the strengths of each marker system to enhance the efficiency and precision of breeding efforts. 3 Integration of Marker-Assisted Selection (MAS) in Maize Breeding 3.1 Basic principles of marker-assisted selection (MAS) Marker-Assisted Selection (MAS) is a process that uses molecular markers to select desirable traits in plant breeding. The fundamental principle of MAS involves identifying and using DNA markers that are closely linked to genes controlling important agronomic traits. These markers can be used to track the presence of these genes in breeding populations, thereby accelerating the selection process and improving the accuracy of breeding programs (Mohan et al., 1997; Collard et al., 2005; He et al., 2014). MAS integrates molecular genetics with traditional phenotypic selection, allowing breeders to make more informed decisions and achieve genetic gains more efficiently (Lande and Thompson, 1990; Francia et al., 2005). 3.2 Application of MAS in quality improvement Quality Protein Maize (QPM) is a notable example of MAS application in improving maize quality. QPM contains the opaque2 (o2) gene, which enhances the levels of essential amino acids like lysine and tryptophan, addressing the nutritional deficiencies of normal maize (Babu et al., 2005; Kaur et al., 2020). In a study, a two-generation marker-based backcross breeding program was employed to incorporate the o2 gene into an early maturing normal maize inbred line, V25. This program utilized flanking markers to optimize population size and ensure the recovery of the recurrent parent genome. The resulting BC2F3 lines showed significant enhancement in tryptophan concentration, demonstrating the effectiveness of MAS in developing QPM with desirable agronomic and biochemical traits (Babu et al., 2005). Another study focused on improving four maize inbred lines by introgressing the o2 allele using marker-assisted backcross breeding. The converted QPM lines exhibited high tryptophan content and maintained grain yield comparable to the original hybrids, highlighting the potential of MAS in tackling protein-energy malnutrition in developing countries (Kaur et al., 2020). 3.3 Application of MAS in resistance breeding MAS has been extensively used in breeding for disease and pest resistance in maize. By identifying markers linked to resistance genes, breeders can efficiently select for these traits, reducing the reliance on phenotypic screening, which can be time-consuming and less accurate (Moreau et al., 1997; Francia et al., 2005; Gupta et al., 2010). For instance, MAS has been applied to improve resistance to various pathogens and pests by incorporating resistance genes into elite maize lines. This approach not only accelerates the breeding process but also ensures the stability and durability of resistance traits across different environments (Moreau et al., 1997; Gupta et al., 2010). 3.4 Economic benefit analysis of MAS The economic benefits of MAS in maize breeding are significant. While the initial costs of developing and implementing MAS, including genotyping and marker development, can be high, the long-term benefits often outweigh these costs. MAS can substantially reduce the time required to develop new varieties, leading to faster commercialization and increased profitability (He et al., 2014; Francia et al., 2005; Hasan et al., 2021). MAS also enhances the precision of selection, reducing the number of breeding cycles needed to achieve desired traits. This efficiency translates into cost savings in terms of labor, field trials, and other resources (Lande and Thompson, 1990; Moreau et al., 2004). Additionally, the ability to stack multiple traits using MAS can lead to the
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