Molecular Plant Breeding 2025, Vol.16, No.1, 35-43 http://genbreedpublisher.com/index.php/mpb 36 in improving key traits in soybean. The study will also explore recent advancements in MAS technology and its integration with other breeding techniques such as genomic selection and CRISPR/Cas9-based gene editing. 2 Principles and Techniques of Marker-Assisted Selection (MAS) 2.1 Genetic markers used in soybean breeding Simple sequence repeats (SSRs), also known as microsatellites, are short, repetitive DNA sequences that are highly polymorphic. SSRs have been widely used in soybean breeding due to their high level of polymorphism, co-dominant inheritance, and ease of detection. They are particularly useful for constructing genetic linkage maps and identifying quantitative trait loci (QTLs) associated with important agronomic traits (Campos-Rivero et al., 2017). SSR markers have been successfully applied in the early selection of individual plants with desirable traits, such as disease resistance and yield components. Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in genomes and have become the marker of choice for many plant breeding programs. SNPs offer several advantages, including high density across the genome, ease of automation, and the ability to provide high-resolution mapping. In soybean breeding, SNPs have been used extensively for genome-wide association studies (GWAS) and genomic selection (GS) to identify markers linked to traits such as yield, maturity, and seed composition (He et al., 2014; Ravelombola et al., 2021; Qin et al., 2022). The development of high-throughput genotyping platforms has further facilitated the use of SNPs in MAS. Quantitative trait loci (QTLs) are genomic regions that contain genes influencing quantitative traits, which are typically controlled by multiple genes. QTL mapping involves identifying the location and effect of these loci on traits of interest. In soybean, QTL mapping has been used to identify regions associated with traits such as plant height, seed weight, and protein content (Zhang et al., 2004; Takagi et al., 2013; Qin et al., 2022). The integration of QTL mapping with MAS allows breeders to select for multiple traits simultaneously, improving the efficiency of breeding programs (Collard et al., 2005; Francia et al., 2005). 2.2 Techniques and tools for MAS implementation High-throughput genotyping platforms, such as genotyping-by-sequencing (GBS), have revolutionized the field of plant breeding by enabling the rapid and cost-effective genotyping of large populations. GBS combines molecular marker discovery and genotyping in a single step, making it an ideal tool for MAS. This technique involves the digestion of genomic DNA with restriction enzymes, followed by the ligation of barcode adapters, PCR amplification, and sequencing. The resulting data can be used for GWAS, genetic diversity studies, and genomic selection (He et al., 2014; Ravelombola et al., 2021). Marker-assisted backcrossing (MABC) is a technique used to introgress specific genes or QTLs from a donor parent into the genetic background of an elite cultivar. This method involves selecting individuals that carry the desired marker alleles at each backcross generation, thereby accelerating the recovery of the recurrent parent genome. MABC has been successfully used in soybean breeding to incorporate traits such as disease resistance and improved yield (Francia et al., 2005). Genomic selection (GS) is a breeding approach that uses genome-wide marker data to predict the breeding values of individuals. Unlike traditional MAS, which focuses on a few markers linked to specific traits, GS considers the effects of all markers across the genome. This allows for the selection of individuals with superior genetic potential for complex traits. In soybean, GS has been shown to improve the accuracy of selection for traits such as yield and protein content, making it a valuable tool for modern breeding programs (Ravelombola et al., 2021; Qin et al., 2022). By integrating these principles and techniques, soybean breeders can enhance the efficiency and effectiveness of their breeding programs, ultimately leading to the development of superior cultivars with desirable agronomic traits.
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