Polymorphism and genotype-specific markers for Dichanthium identified by random amplified polymorphic DNA

Abstract

One hundred decamer arbitrary primers were tested for PCR based amplification of seven genotypes (IG2208-S-1, IG2177, IG2180, IG2178, IG2165-S-1-1, IG2165-1 and Local-1) of an apomictic grass, Dichanthium annulatum, with the aim of screening polymorphic primers and genotype-specific markers. Out of 100 decamer primers tested, 42 produced no amplification or smeared non scorable bands, 12 amplified only single band and 46 yielded more than one polymorphic bands. Thirty-two primers out of 46 selected showed high level of polymorphism, producing 3–15 reproducible bands each for the seven Dichanthium genotypes examined. Among the total of 307 amplified fragments 222 were polymorphic, 53 bands were unique to the genotypes and 32 were monomorphic. Thus, with selected primers sufficient polymorphism could be detected to allow identification of individual genotypes. Genetic similarities of RAPD profiles generated were estimated via a coefficient of DICE and then the data were processed by cluster analysis (UPGMA). The maximum similarities between two genotypes (IG2180 and IG2178) was 58% and these two made a cluster with genotype IG2177 having similarity of only 54%. It clearly corroborated existence of high levels of polymorphism in this grass though being apomictic in nature. Primers like OPE-16, OPG- 02, OPG-18, OPH-05, OPH-09, OPH-16, OPI-07 and OPF-06 found most informative as they produced specific bands pertaining to five out of seven genotypes. Polymerase chain reaction (PCR) offers a substantially simple, rapid and reliable method for identification of large number of Dichanthium genotypes once enough number of reproducible and suitable primers is screened.