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Molecular characterization of rice (Oryza sativa L.) genotypes using target region amplification polymorphism (TRAP) markers in relation to grain iron content

Pavan J. Kundur, Prakash G. Patil, B.G. Harish, C.K. Ramesh, H.E. Shahidhar

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Int. J. Agron. Agri. Res.7(1), 125-133, July 2015


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In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 – 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity ( H ) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b+ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content rice varieties.


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Molecular characterization of rice (Oryza sativa L.) genotypes using target region amplification polymorphism (TRAP) markers in relation to grain iron content

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