Utilizing RNA-Seq-Derived SNPs for KASP Marker Development in Maize.

Maize is the third most significant cereal crop, and most of its agronomic traits are quantitative in nature. The fine mapping of genes or quantitative trait loci (QTLs) associated with these traits is essential for marker-assisted selection (MAS) in maize breeding. Although significant progress has been made, there remains a lack of high-density, highly polymorphic single-nucleotide polymorphism (SNP) markers, especially competitive allele-specific PCR (KASP) SNP markers suitable for automated genotyping. The development of next-generation sequencing (NGS) platforms has generated vast amounts of whole-genome and transcriptome data, providing a valuable resource for identifying SNP loci for marker development. KASP markers, being cost-effective and reliable, provide a trustworthy molecular toolbox for the precise genetic analysis of major key agronomic traits and the rapid improvement of maize using MAS.