The Role of Single Nucleotide Polymorphisms (SNPs) in Modern Plant Breeding: From Discovery to Application

The integration of molecular markers has significantly advanced the accuracy and speed of genetic analysis in plants, thereby accelerating the adoption of molecular breeding in field crops and forestry species. Among these, single nucleotide polymorphisms (SNPs) have emerged as the most widely utilized markers due to their high abundance across genomes and compatibility with high-throughput genotyping platforms. These functional markers hold great promise for enhancing the efficiency of marker-assisted selection (MAS) in crop improvement programs. Next-generation sequencing (NGS) technologies continue to play a transformative role in SNP genotyping, particularly for large-scale discovery applications. A key factor in scaling up SNP genotyping lies in minimizing the number of biochemical reactions required per assay. Therefore, the development of robust, multiplexed genotyping methods capable of amplifying numerous genomic loci simultaneously has become essential. Despite these advancements, there remains a gap in the availability of ultra-high-throughput and cost-efficient genotyping platforms suitable for routine use in applied breeding. This review highlights and evaluates four contemporary SNP genotyping assays and platforms, illustrating their roles in achieving scalable and accurate genotyping. Additionally, the paper provides an overview of current progress in SNP marker discovery, validation, and application in quantitative trait locus (QTL) analysis and modern plant breeding strategies.