PCR-based single nucleotide polymorphism (SNP) genotyping for crop improvement-current status and future prospects

Single nucleotide polymorphisms (SNPs) represent the most abundant form of genetic variation within crop genomes, making them critical markers for plant breeding and crop improvement. Polymerase chain reaction (PCR)-based SNP genotyping methods have emerged as powerful tools for identifying and utilizing these genetic variations. This paper reviews the various PCR-based techniques used in SNP genotyping, including allele-specific PCR, real-time PCR, and high-resolution melting analysis. These methods are evaluated for their accuracy, efficiency, and cost-effectiveness in detecting SNPs. The application of these techniques in marker-assisted selection (MAS) and genomic selection (GS) is discussed, highlighting their role in accelerating breeding programs and developing crops with improved yield, disease resistance, and stress tolerance. Furthermore, advances in PCR technology and its integration with high-throughput sequencing platforms are explored, demonstrating how this convergence enhances SNP genotyping by improving accuracy, increasing throughput, and reducing costs. These innovations are making large-scale genotyping more accessible and scalable, thereby strengthening crop improvement programs.