Molecular Plant Breeding 2025, Vol.16, No.1, 35-43 http://genbreedpublisher.com/index.php/mpb 38 genetic gain. This approach has been successfully applied in various crops, including tomatoes, where it has expedited the breeding process by identifying genes and SNP markers associated with phenotypic variation (Varshney et al., 2013; Tiwari et al., 2022). 4.2 Use of high-density genetic maps High-density genetic maps are crucial for the effective implementation of MAS in soybean breeding. These maps provide detailed information on the location of genes and quantitative trait loci (QTLs) associated with important agronomic traits. Advances in next-generation sequencing (NGS) technologies have facilitated the development of dense genetic maps, enabling precise marker-trait associations. For instance, genotyping-by-sequencing (GBS) has been employed to create high-density maps that combine molecular marker discovery and genotyping, thus enhancing the resolution of genetic studies (He et al., 2014; Hasan et al., 2021). 4.3 Role of bioinformatics and computational tools Bioinformatics and computational tools play a pivotal role in analyzing and interpreting the vast amounts of data generated by NGS and other high-throughput genotyping methods. These tools are essential for managing large datasets, conducting genome-wide association studies (GWAS), and performing QTL mapping. The integration of bioinformatics in MAS has streamlined the identification of marker-trait associations and facilitated the development of robust breeding strategies. For example, bioinformatic pipelines are used to process GBS datasets, enabling the efficient discovery and genotyping of SNPs in crop genomes (He et al., 2014; Tiwari et al., 2022). 4.4 Recent advances in molecular markers Recent advancements in molecular markers have revolutionized MAS in soybean breeding. The development of various types of markers, such as single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs), and amplified fragment length polymorphisms (AFLPs), has provided breeders with powerful tools for genetic analysis. SNP markers, in particular, have gained prominence due to their abundance and high-throughput genotyping capabilities. These markers have been effectively used in the identification and mapping of genes associated with disease resistance, yield, and other important traits (Figure 1) (Francia et al., 2005; Hasan et al., 2021; Jing et al., 2024). Figure 1 A schematic drawing illustrating an example of genome editing for crop improvement through the CRISPR/Cas9 strategy (Adopted from Hasan et al., 2021)
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