Genic Markers Assessment of Four Qualitative Characteristics in DUS Testing of Rice Varieties

In this study the introduced functional (genic) markers for length, fragrance, amylose content, and gelatinization degree of rice grain were used in order to evaluate their applicability in distinctness testing of rice varieties under proposed model of BMT working group of UPOV convention. Therefore, five functional markers for grain length gene (two SSRs, one STS, one CAPS, and one ASP), four markers for fragrance gene (three STS, and one ASP), two markers for amylose content gene (one SSR and one CAPS), and two markers for gelatinization degree of grain length (one dCAPS, and one ASP) were evaluated for distinctness testing of 43 rice varieties. Results showed that among markers used for grain length, the PstI digested fragment of amplified SF28 marker could efficiently differentiate short length varieties (bearing allele C) from long ones (bearing allele A). Similar result were observed with detection of this SNP by ASP marker, however, the amplified fragments of two SSR markers were monomorphic between varieties and STS marker did not amplify in them. Among four markers utilized for grain fragrance, FMbadh2-E7 was the mere marker which could distinguish fragrant and non-fragrant varieties by an eight base pair length polymorphism. As regards the amylose content, the combination of (CT)17 motif of RM190 marker and Allele T (resulted from AccI digestion of W2 marker amplified fragment) could separate type IV varieties (16-20% amylose) from other groups. No association was found between two markers and gelatinization degree of rice grains, though there were significant differences between varieties. The results of this study indicates that the utilization of functional markers is effective for characterization of expensive and time-consuming traits like amylose content and scoring fragrance that relies on tester's olfactory.