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

Paper Details

Research Paper 01/07/2015
Views (152) Download (1)

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
Int. J. Agron. Agri. Res.7( 1), 125-133, July 2015.
Certificate: IJAAR 2015 [Generate Certificate]


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.


Alwala S, Suman A, Arro JA, Veremis JC, Kimbeng CA. 2006. Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm col- lections. Crop Science 46, 448–455.

Anuradha K, Agarwal S, Rao VY, Rao KV, Viraktamath BC, Sarla N. 2012. Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar×Swarna RILs. Gene 508, 233–240.

Berloo VR, Zhu A, Ursem R, Verbakel H, Gort G, Eeuwijk FAV. 2008. Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes. Theory of applied genetics 117, 89-101.

Benbouza H, Jacquemin JM, Baudoin JP, Mergeai G. 2006. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels, Biotechnologie, Agronomie, Société et Environnement 10, 77-81.

Bouis HE, Welch RM. 2010. Biofortification—a sustainable agricultural strategy for reducing micronutrient malnutrition in the global south. Crop Science 50, S20–S32.

Chandel G, Samuel P, Dubey M, Meena R. 2011. Insilico expression analysis of QTL specificcandidate genes for grain micronutrient (Fe/Zn) content using ESTs and MPSS signature analysis in rice (Oryza sativa L.) Journal of plant Genetics and Transgenics 2, 11–22.

Chen S, Chen G, Chen H, Wei Y, Li W, Liu Y, Liu D, Lan X, Zheng Y. 2011. Mapping stripe rust resistance gene YrSph derived from Tritium sphaerococcum Perc. with SSR, SRAP, and TRAP markers. Euphytica 185, 19-26.

Chenga D, Zhanga F, Liua L, Xua L, Chenb Y, Wanga X, Limeraa C, Yua R, Gonga Y. 2013. TRAP markers generated with resistant gene analog sequences and their application to genetic diversity analysis of radish germplasm. Scientia Horticulturae 161, 153–159.

Craig WJ, Am J, Clin. 1994. Iron status of vegetarians. American journal of Clinical Nutrition 59, 1233S–1237S.

Creste S, Accoroni KA, Pinto G, Vencosvskv LR, Gimenes R, Xavier MA, Landell MA, MGA. 2010. Genetic variability among sugarcane genotypes based on polymorphism in sucrose metabolism and drought tolerance genes. Euphytica 172, 435–446.

Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus 12, 13–15.

Hu J, Ochoa OE, Truco MJ, Vick BA. 2005. Application of the TRAP technique to lettuce (Lactuca sativa L.) genotyping. Euphytica 144, 225–235.

Hu J, Vick BA. 2003. Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Molecular Biology Reporter 21, 289–294.

Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS. 2000. Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theoretical and Applied Genetics 100, 1311-1320.

Kumar Y, Kwon SJ, Clarice J, Coyne, Jinguo Hu, Michael A. Grusak, Theodore J. Kisha, Sarker A. 2014. Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum L.) germplasm. Genetic Resource and Crop Evolution 61, 965–977.

Li G, Quiros CF. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theory Applied Genetics 103, 455–461.

Miklas PN, Hu J, Grunwald NJ, Larsen KM. 2006. Potential application of TRAP (target region amplified polymorphism) markers for mapping and tagging dis- ease resistance traits in common beans. Crop Science 46, 910–916.

Paltridge NG, Palmer LJ, Milham PJ, Guild GE, Stangoulis JC. 2012. Energy-dispersive X-ray fluorescence analysis of zinc and iron concentration in rice and pearl millet grain. Plant soil 361(1-2), 251-260.

Patel S, Patel NK. 2013. Candidate gene mapping: approach, methods and significance, American Journal of Research Communication 1(8), 199-204.

Pflieger S, Lefebvre V, Causse M. 2001. The candidate gene approach in plant genetics: a review. Molecular Breeding 7, 275–291.

Senadhira D, Graham RD. 1999. Genetic variation in iron and zinc concentrations in brown rice. Micronutrients in Agriculture 3, 10-12.

Shashidhar HE. 2008. Aerobic rice—an efficient water management strategy for rice production. In: Aswathanarayana, U. (Ed.), Food and Water Security. Taylor and Francis, London, UK. 131-139 p.

Soman R, Naveenkumar G, Pavan JK, Rajeswari A, Ashwathanarayana R, Berhanu DB, Shashidhar HE. 2014. Identification and Validation of Putative Candidate Gene Markers for Grain Iron Content in Recombinant Inbred Lines of Rice (Oryza sativa L.). International Journal of Agriculture Innovations and Research 3, 923-930.

Song X, Deng Z, Gong L, Hu J, Ma Q. 2012. Cloning and characterization of resistance gene candidate sequences and molecular marker development in gerbera (Gerbera hybrida). Scientia Horticulturae 45, 68–75.

Vos P, Hogers R, Bleeker M, Reijans M, Van der Lee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M. 1995. AFLP: a new technique for DNA finger-printing. Nucleic Acids Research 23, 4407-4414.

White PT. 1994. Rice: The essential harvest. National Geographic 185(5), 48–79.

Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SVM. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Research 18, 6231-6235.

World health organization. 1996. Trace elements in human nutrition and health. WHO report, Geneva, Switzerland.

Yue B, Cai X, Vick BA, Hu J. 2009. Genetic diversity and relationships among 177 public sunflower inbred lines assessed by TRAP markers. Crop Science 49, 1242–1249.