Molecular Plant Breeding 2024, Vol.15, No.5, 259-268 http://genbreedpublisher.com/index.php/mpb 261 these genes in breeding programs. For example, MAS has been successfully used to pyramid resistance genes for various diseases in crops like rice, providing broad-spectrum resistance (Jena and Mackill, 2008; Haque et al., 2021). In common beans, MAS has facilitated the detection and selection of resistance genes for multiple pathogens, simplifying the breeding process and enhancing resistance to diseases such as angular leaf spot, anthracnose, and various viruses (Miklas et al., 2006). These advancements highlight the potential of MAS in developing soybean varieties with enhanced resistance to biotic stresses. 3.3 Resistance to abiotic stresses Abiotic stresses, including drought and salinity, pose significant challenges to soybean production. MAS has been instrumental in breeding for resistance to these stresses by identifying and incorporating QTL associated with stress tolerance. For instance, in rice, MAS has been used to pyramid genes conferring tolerance to submergence and salinity, resulting in varieties with improved stress resistance (Ludwików et al., 2015; Haque et al., 2021). Similarly, breeding programs for other crops have utilized MAS to combine traits such as root growth and phosphorus uptake mechanisms, addressing the complexity of abiotic stress resistance (Miklas et al., 2006; Araus et al., 2008). These strategies can be adapted to soybean breeding to enhance tolerance to abiotic stresses. 3.4 Enhancing nutritional quality and oil content Improving the nutritional quality and oil content of soybeans is another important objective in breeding programs. MAS has the potential to accelerate the selection of genotypes with desirable traits related to nutritional quality. For example, the integration of MAS in conventional breeding has been shown to improve grain quality traits in rice by monitoring the presence of specific genes linked to these traits (Jena and Mackill, 2008). Although the application of MAS for enhancing nutritional quality and oil content in soybeans is still evolving, the success in other crops suggests that similar approaches can be employed to achieve these goals in soybean breeding programs. 4 Molecular Markers and Their Development in Soybean 4.1 Overview of marker discovery and mapping technologies The discovery and development of molecular markers have significantly advanced plant breeding, particularly in crops like soybean. DNA markers, such as single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs), have become essential tools in marker-assisted selection (MAS). These markers facilitate the identification of genetic variations linked to desirable traits, thereby enhancing the efficiency and precision of breeding programs. The process of marker discovery involves several steps, including polymorphism detection, linkage analysis, and map construction. These steps are crucial for understanding the genetic architecture of traits and for developing reliable markers for MAS (Collard et al., 2005; Hasan et al., 2021). 4.2 Identification of quantitative trait loci (QTLs) linked to key agronomic traits Quantitative trait loci (QTLs) are genomic regions that contribute to the variation in quantitative traits, which are typically controlled by multiple genes. The identification of QTLs linked to key agronomic traits in soybean, such as protein content, disease resistance, and yield, is vital for improving these traits through MAS. Techniques like genome-wide association studies (GWAS) and linkage mapping have been employed to identify QTLs (Fu, 2024). For instance, a study identified 22 SNPs associated with protein content and five QTLs using various mapping approaches. Major QTLs were found on chromosomes 6 and 20, with significant implications for soybean breeding programs (Takagi et al., 2013; Qin et al., 2022). 4.3 Role of single nucleotide polymorphisms (SNPs) in MAS Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in genomes and play a crucial role in MAS. SNPs are highly informative markers due to their abundance and stability, making them ideal for high-resolution mapping and selection. In soybean breeding, SNPs have been used to identify and select for traits such as protein content, disease resistance, and yield. The integration of SNP markers into MAS pipelines has improved the accuracy and efficiency of selection processes. For example, SNP markers identified through GWAS and other mapping techniques have been used to enhance the genomic selection (GS) of protein content in soybean, demonstrating the practical applications of SNPs in MAS (Hasan et al., 2021; Qin et al., 2022).
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