Development of Sequence-Based DNA Markers for Evaluation of Phylogenetic Relationships in Korean Watermelon Varieties

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.