High resolution melting curve analysis: an efficient method for fingerprinting of hybrid rice cultivars and their parental lines

Rice (Oryza sativa L.) is one of the most important crops in the world. It is essential to develop an efficient method to build the fingerprinting database of commercial hybrid rice cultivars and their parental lines in seed market for rapid and unambiguous cultivar identification and seed purity analysis as new similar cultivars increasing yearly. The objective of this investigation were to fingerprint three commercial hybrid rice cultivars and their parental lines using SSR molecular markers to develop an efficient fingerprinting method for rice cultivar identification and seed purity analysis in agriculture production. Three methods, agarose gel electrophoresis, capillary electrophoresis and high resolution melting curve analysis were used to fingerprinting three hybrid F1 rice cultivars and their parental lines. Out of the fourteen SSR primer pairs, nine primer pairs which produced stable, distinct and polymorphic amplifications as visualized on agarose gel were selected for capillary electrophoresis and high resolution melting curve analysis to compare their fingerprinting efficiency. Six (RM206, RM209, RM211, RM212, RM219, and RM297), four (RM72, RM209, RM212, and RM276) and six (RM190, RM206, RM211, RM212, RM219, and RM297) primer pairs were successfully used to fingerprint the three hybrid F1 rice cultivars, YLiangYou689, ZhuLiangYou06, and QianYou1, respectively. The result suggested that capillary electrophoresis and high resolution melting curve analysis could be used as potential, efficient and valuable methods for fingerprinting hybrid rice cultivars, and high resolution melting curve analysis should be given priority compared with capillary electrophoresis for its high accuracy and high efficiency.