Development of potential intron polymorphic (PIP) markers in melon (Cucumis melo L.)

Potential intron polymorphic (PIP) marker is a newly developed species-specific, codominant, neutral, reliable and convenient marker technology. It has been applied in a variety of plants, but there has been no available information in melon. In this study, a total of 39,938 PIP markers were developed from the whole genome of melon, and these markers were evenly distributed on 12 chromosomes of melon. Most of these markers were far from the centromere region and distributed on both arms of the chromosomes, where the marker on chromosomes 5, 7, 8, 9, and 11 exhibited robust collinearity with genes located on other chromosomes. Using electronic PCR to validate these PIP molecular markers on the melon genome, 39,442 (98.76%) of the markers produced a single amplicon. In addition, 11 pairs of primers were randomly selected to be amplified in 20 melon genotypes, and 8% polyacrylamide gel electrophoresis was used to identify the products in order to confirm the availability and validity of PIP molecular markers in melon. Furthermore, PIP markers were applied to melon cultivar identification, and MCID (Manual Cultivar Identification Diagram) was constructed based on the polymorphic bands of PCR products, in which PIP-01 could completely distinguish 20 melon cultivars. The development of PIP markers of the melon provides important information for genetic analysis and breeding of melon. These markers can be used for linkage mapping, cultivar identification, genetic diversity analysis and comparative genomics research.