Haplotype analysis of molecular markers linked to QTLs controlling Iron content in rice grains

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Research Paper 01/05/2015
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Haplotype analysis of molecular markers linked to QTLs controlling Iron content in rice grains

Shahrbanu Abutalebi, Mohammad-Hossein Fotokian, Mehrshad Zeinalabedini
J. Bio. Env. Sci.6( 5), 391-398, May 2015.
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Iron deficiency affects 2 billion people currently and the number is increasing. Biofortification of rice is one of the best approaches for solution this problem. Molecular marker techniques can greatly improve the efficacy of breeding programs to improve grain iron content and bioavailability in major staple crops such as rice. In the current study, the haplotype variation of three loci controlling iron content was evaluated using 50 genotypes and 14 associated microsatellite markers. The grain iron content analysis of a collection of 50 rice genotypes showed large variation from 9.06 (Sepidrud cultivar) to 50.55 (Mehr cultivar) mg.kg-1 indicating the existence of genetic potential to increase the content of this micronutrient in rice grain. Based on the results of genotyping RM276 indicated highest polymorphism information content (0.83). The haplotype diversity analysis showed, allelic pattern of 132-176-200 bp in the Norin22 and Shahak cultivars on chromosome 12 had the most similarity with haplotype of reference cultivar Mehr. This allele combination can be informative markers for improvement of iron content in rice grains through marker-assisted selection programs. Furthermore, the presence of allele combinations, different from reference haplotype in Dadras and Farideh cultivars (with high iron contents) indicated the presence of novel source of QTLs controlling grain iron content in Iranian rice cultivars.


Anandan A, Rajiv G, Eswaran R, Prakash M. 2011. Genotypic variation and relationships between quality traits and trace elements in traditional and improved rice (Oryza sativa L.) genotypes. Journal of Food Science 76, 122-130.

Anuradha K, Agarwal S, Rao YV, 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.

Balint AF, Kovacs G, Erdei L, Sutka J. 2001. Comparison of the Cu, Zn, Fe, Ca and Mg contents of the grains of wild, ancient and cultivated wheat species. Cereal Research Communications 29, 375-382.

Clemens S, Palmgren MG, Krämer U. 2002. A long way ahead: understanding and engineering plant metal accumulation. Trends in Plant Science 7,309-315.

Ensminger AH, Ensminger ME, Konlande JE, Robson JRK. 1995. The concise encyclopedia of foods and nutrition. Boca Raton, FL, USA.

Gregorio GB, Htut T. 2003. Micronutrient-dense rice: developing breeding tools at IRRI. Rice Science: Innovations and Impact for Livelihood. International Rice Research Institute, Philippines 371-378.

Gregorio GB, Senadhira D, Htut T, Graham RD. 2000. Breeding for trace mineral density in rice. Food and Nutrition Bulletin 21, 382-386.

Guerinot ML. 2001. Improving rice yields—ironing out the details. Nature Biotechnology 19, 417-418.

Ishikawa S, Abe T, Kuramata M, Yamaguchi M, Ando T, Yamamoto T. 2009. A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7. Journal of Experimental Botany 61, 923-934.

Johnson AA, Kyriacou B, Callahan DL, Carruthers L, Stangoulis J, Lombi E, Tester M. 2011. Constitutive overexpression of the OsNAS gene family reveals single-gene strategies for effective iron-and zinc-biofortification of rice endosperm. PLoS One 6, 24476.

Liu K, Muse SV. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128-2129.

Lu K, Li L, Zheng X, Zhang Z, Mou T, Hu Z. 2008. Quantitative trait loci controlling Cu, Ca, Zn, Mn, and Fe content in rice grains. Journal of Genetics 87, 305-310.

McCartney CA, Sommers DJ, Fedak G, Cao W. 2004. Haplotype diversity at Fusarium head blight resistance QTLs in wheat. Theoretical and Applied Genetics 109, 261-271.

Mohammadi-Nejad G, Singhb RK, Arzanic A, Rezaiec AM, Sabouri H, Gregoriob GB. 2010. Evaluation of salinity tolerance in rice genotypes. International Journal of Plant Production 4, 199-208.

Munson RD, Nelson WL. 1990. Principles and practices in plant analysis. In: Westerman RL, Ed. Soil testing and plant analysis, Soil Science Society of America, 359-388.

Ogbonnaya FC, Imtiaz M, DePauw RM. 2007. Haplotype diversity of preharvest sprouting QTLs in wheat. Genome 50, 107-118.

Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW. 1984. Ribosomal DNA sepacer-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences 81, 8014-8019.

Stangoulis JC, Huynh BL, Welch RM, Choi EY, Graham RD. 2007. Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content. Euphytica 154, 289-294.

Susanto U. 2008. Mapping of quantitative trait loci for high iron and zinc content in polished rice (Oryza Sativa L.) grain and some agronomic traits using simple sequence repeats markers, PhD thesis, Bogor agricultural University, Bogor.

Tiwari VK, Rawat N, Chhuneja P, Neelam K, Aggarwal R, Randhawa GS, Singh K. 2009. Mapping of quantitative trait loci for grain iron and zinc concentration in diploid A genome wheat. Journal of Heredity 100, 771-776.

Welch RM, Graham RD. 2004. Breeding for micronutrients in staple food crops from a human nutrition perspective. Journal of Experimental Botany 55, 353-364.

Yamamoto T, Yonemaru J, Yano M. 2009. Towards the understanding of complex traits in rice: Substantially or superficially? DNA research 16, 141-154.

Yano M, Sasaki T. 1997. Genetic and molecular dissection of quantitative traits in rice. Plant Molecular Biology 35, 145-153.