Molecular Plant Breeding 2024, Vol.15, No.5, 259-268 http://genbreedpublisher.com/index.php/mpb 264 be adapted to other traits and crops to enhance breeding outcomes (Sebastian et al., 2010). Combining MAS with conventional breeding methods, such as phenotypic selection and backcrossing, can enhance the overall effectiveness of breeding programs. This integrated approach can help accumulate favorable QTLs and improve complex traits (Miedaner and Korzun, 2012; Singh and Singh, 2015). The scalability of MAS depends on the availability of resources and the specific traits being targeted. While MAS has shown great promise in soybean breeding, its broader adoption will require continued advancements in genotyping technologies and the development of more robust markers for various traits (Francia et al., 2005; Collard and Mackill, 2008). 8 Technological Advancements to Support MAS 8.1 Advances in genome sequencing and genotyping platforms The advent of next-generation sequencing (NGS) technologies has significantly advanced the field of genome sequencing and genotyping, providing ultra-throughput sequences that have revolutionized plant genotyping and breeding. Genotyping-by-sequencing (GBS) is a notable application of NGS protocols, which combines molecular marker discovery and genotyping in a cost-effective manner. GBS involves the digestion of genomic DNA with restriction enzymes, followed by the ligation of barcode adapters, PCR amplification, and sequencing of the amplified DNA pool on a single lane of flow cells. This method has been successfully used in genome-wide association studies (GWAS), genomic diversity studies, genetic linkage analysis, and genomic selection in large-scale plant breeding programs (He et al., 2014). Additionally, high-throughput genotyping (HTG) platforms provide higher genome-wide marker density, which is crucial for the success of quantitative trait loci (QTL) and candidate gene identification in soybean improvement (Figure 1) (Bhat and Yu, 2021). Figure 1 Diagram showing the critical role of high-throughput phenotyping (HTP) and high-throughput genotyping (HTG) in the precise and accurate identification of quantitative trait loci (QTLs)/quantitative trait nucleotides (QTNs)/genes as well as genomic selection (GS)-based estimation of genomics-estimated breeding values (GEBVs) (Adopted from Bhat and Yu, 2021) 8.2 Application of genomic selection alongside MAS Genomic selection (GS) is a promising approach that complements marker-assisted selection (MAS) by using genome-wide markers to predict the breeding value of individuals. This method addresses the limitations of conventional phenotypic-based selection, which is often time-consuming and influenced by environmental factors. By integrating GS with MAS, breeders can achieve higher genetic gains per unit time and improve the efficiency of breeding programs. For instance, the use of high-throughput digital phenotyping (HTP) platforms alongside
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