Identification of Microsatellite Heteroduplex Bands in Hybrid Rice

The genotypes of hybrid rice with their parental lines were analyzed using microsatellite markers and some non-parental bands were observed in hybrid (heterozygous) individuals. These nonparental bands could be due to formation of heteroduplex DNA between allelic sequences. To test this hypothesis two source of DNA material were used. Firstly DNA template was formed by combining of equal amounts of parental DNA before performing of PCR. Secondly, the PCR products of this step were used as source materials of template mixing experiment by combining of equal amounts of PCR products of parental lines. The results confirmed the formation of the extra bands in heterozygous individuals, and proven that these art-factorials are consequences of formation hetroduplex between allelic sequences. Heteroduplexes are double strand DNA that formed from two different alleles by mismatches. These bands can be detected in specific position on gel due to their different migrating rate compared to corresponding homoduplexes. In the present study, it was evident that heteroduplex bands can be diagnostic feature for identify heterozygote individuals from homozygote ones. Accordingly, heteroduplex bands derived from RM1 and RM171 microsatellite markers were used for identifying and genetic purity testing of hybrid rice genotypes. Overall, it is revealed that heteroduplex bands not only beneficial in fingerprinting hybrids rice, but also useful for detecting the off type seeds in the rice hybrids