Molecular Plant Breeding 2024, Vol.15, No.5, 259-268 http://genbreedpublisher.com/index.php/mpb 265 HTG can significantly enhance the precision and accuracy of phenotyping, thereby increasing the practical utility of genomics-assisted breeding (GAB) in soybean improvement (Bhat and Yu, 2021). Moreover, context-specific MAS (CSM) approaches have been developed to model target genotypes within specific genetic and environmental contexts, leading to significant yield gains in selected sublines (Sebastian et al., 2010). 8.3 Use of bioinformatics and computational tools to accelerate marker identification The integration of bioinformatics and computational tools is essential for analyzing and interpreting the vast datasets generated by advanced genotyping platforms. Bioinformatic pipelines are required to process GBS datasets, enabling the identification and genotyping of single nucleotide polymorphisms (SNPs) in crop genomes and populations (He et al., 2014). Additionally, the development of semi-automated pipelines that incorporate trait-associated SNP marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq), and decision-making processes has been demonstrated in grapevine breeding. This approach offers several advantages, including accuracy, flexibility, speed, high-throughput, low-cost, and easily automated analysis, making it broadly applicable to diverse crop species (Yang et al., 2016). Furthermore, comparative and functional genomic approaches, along with extensive mapping of resistance gene analogs (RGAs), can reveal new candidate genes and selectable markers for use in MAS, thereby facilitating the genetic improvement of crops (Francia et al., 2005; Torres et al., 2010). 9 Future Prospects for MAS in Soybean Breeding 9.1 Emerging trends in MAS The integration of marker-assisted selection (MAS) with advanced gene editing technologies such as CRISPR is a promising trend in soybean breeding. This combination can significantly enhance the precision and efficiency of breeding programs. CRISPR technology allows for targeted modifications at specific genomic loci, which, when combined with MAS, can accelerate the development of soybean varieties with desirable traits. For instance, the use of CRISPR in conjunction with MAS can facilitate the precise introduction of beneficial alleles identified through marker-assisted selection, thereby improving traits such as disease resistance and yield potential (Figure 2) (Ribaut and Ragot, 2006; Rosero et al., 2020). This integrated approach is expected to overcome some of the limitations of traditional breeding methods and enable the rapid development of superior soybean cultivars. Figure 2 Dual strategy of breeding for drought tolerance and the introduction of underutilized crops to make more resilient cropping systems to water deficiency conditions (Adopted from Rosero et al., 2020) 9.2 Potential for MAS to enhance climate-resilient soybean varieties The potential of MAS to enhance climate-resilient soybean varieties is substantial. Climate change poses significant challenges to agriculture, including increased frequency of droughts, floods, and extreme temperatures. MAS can be employed to identify and select for traits that confer resilience to these stresses. For example, MAS has been successfully used to improve drought tolerance in crops like maize, which can be translated to soybean breeding programs (Ribaut and Ragot, 2006). Additionally, integrating MAS with genomic selection (GS) and other advanced breeding techniques can further enhance the development of climate-smart soybean varieties that can withstand abiotic stresses while maintaining high yield and quality (Araus et al., 2008; Rosero et al., 2020; Sinha et al., 2023).
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