Identification of Polymorphic Markers by High-Resolution Melting (HRM) Assay for High-Throughput SNP Genotyping in Maize

The development of next generation sequencing (NGS) and high throughput genotyping are important techni-ques for the QTL mapping and genetic analysis of different crops. High-resolution melting (HRM) is an emerging technology used for detecting single-nucleotide polymorphisms (SNPs) in various species. However, its use is still limited in maize. The HRM analysis was integrated with SNPs to identify three types of populations (NIL popu-lation, RIL population and natural population), and the useful tags were screened. The patterns of temperature-shifted melting curves were investigated from the HRM analysis, and compared these with the kit. Among all 48 pairs of primers, 10 pairs of them were selected: six pairs of primers for the NIL population, three pairs of primers for the RIL population, and one pair of primer for the natural population. The marker for the natural population was developed with a matching rate of 80% for the plant height trait, based on the data of the phe-notypic characteristics measured in the field. This study provides an effective method for maize genotyping in the classification of maize germplasm resources, which can be applied to other plants for high-throughput SNP gen-otyping or further mapping.