A multiplex PCR system for testing the genetic purity of hybrid rice (Oryza sativa L.)

Commercial exploitation of rice hybrid for sustainable production and productivity largely depends on genetic purity of hybrid seed used. To detect genetic impurity in the hybrid seeds developed through the three-line system using wild abortive (WA) cytoplasmic-based male sterility, a multiplex PCR assay was designed . A total of six primers, namely, DRRM-Rf3-10, Rf4-STS, RM6100, CMS-WA, osWA352 and RMS-3-WA352 were designed based on fertility restorer genes Rf3, Rf4 and Wa352. The primer combinations having RF4-STS and CMS-WA markers of Rf4 and WA352 genes, respectively showed clear and distinct PCR banding patterns among the WA-cytoplasm possessing 31A, fertile restorer PK117 lines and their cognate hybrid rice, Ajay. This multiplex PCR will be useful for assessment of genetic purity of hybrid rice seeds.