Development of chromosome-specific potential intron polymorphism markers in watermelon

Intron length polymorphism (ILP) marker is one of the popular molecular markers. Despite the effectiveness of ILP markers in some plants has been reported, while none in watermelon compared to others marker systems. In this study, a genome-wide survey of intron length markers for watermelon genome-annotated genes was performed. According to the genomic information of watermelon, the intron position was extracted by comparison with Arabidopsis thaliana, and the primers were designed by ePrimer3. A total of 51,585 potential intron polymorphism (PIP) markers spanning 11 watermelon chromosomes were identified and designed. All these PIP markers on the watermelon genome were verified by ePCR, and 50,093 (98.51%) markers revealed single-locus amplification. The marker genes on chromosome 10 have the strongest collinearity with genes on other chromosomes. Further, two primers were randomly selected from the designed primers, and electrophoresis on 8% polyacrylamide gel was carried out in 48 watermelon cultivars demonstrated the potential utility of the developed markers. This study reported the development of PIP markers in watermelon for the first time, and provided abundant marker resources for genetic variation research, functional gene discovery and genome-assisted breeding of watermelon.