Short Communication Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar × Swarna RILs K. Anuradha, Surekha Agarwal, Y. Venkateswara Rao, K.V. Rao, B.C. Viraktamath, N. Sarla ⁎ Directorate of Rice Research, Hyderabad, India abstract article info Article history: Accepted 30 July 2012 Available online 6 August 2012 Keywords: Candidate genes Biofortification Brown rice Iron Zinc Quantitative Trait Loci Identifying QTLs/genes for iron and zinc in rice grains can help in biofortification programs. 168 F 7 RILs de- rived from Madhukar × Swarna were used to map QTLs for iron and zinc concentrations in unpolished rice grains. Iron ranged from 0.2 to 224 ppm and zinc ranged from 0.4 to 104 ppm. Genome wide mapping using 101 SSRs and 9 gene specific markers showed 5 QTLs on chromosomes 1, 3, 5, 7 and 12 significantly linked to iron, zinc or both. In all, 14 QTLs were identified for these two traits. QTLs for iron were co-located with QTLs for zinc on chromosomes 7 and 12. In all, ten candidate genes known for iron and zinc homeostasis underlie 12 of the 14 QTLs. Another 6 candidate genes were close to QTLs on chromosomes 3, 5 and 7. Thus the high priority candidate genes for high Fe and Zn in seeds are OsYSL1 and OsMTP1 for iron, OsARD2, OsIRT1, OsNAS1, OsNAS2 for zinc and OsNAS3, OsNRAMP1, Heavy metal ion transport and APRT for both iron and zinc together based on our genetic mapping studies as these genes strictly underlie QTLs. Several elite lines with high Fe, high Zn and both were identified. © 2012 Elsevier B.V. All rights reserved. 1. Introduction Rice is the primary or secondary staple food for 50% of the world's population. In countries where rice is used as staple food, the per capita consumption is very high ranging from 62 to 190 kg/year (Chandel et al., 2011; Graham et al., 1999). However, rice is a poor source of essential micronutrients such as Iron (Fe) and Zinc (Zn) (Bouis and Welch, 2010). Biofortification has emerged as one possible solution to alleviate malnutrition and the development of new culti- vars with elevated concentration of Fe and Zn would be extremely useful (Zimmermann and Hurrell, 2002). Several studies have reported the evaluation of germplasm and advanced breeding lines for grain Fe and Zn content (Brar et al., 2011; Gregorio et al., 2000). 11,400 rice samples of brown (unpolished) and milled rice were eval- uated for Fe and Zn during 2006–2008 by Martínez et al. (2010). They found that brown rice had 10–11 ppm Fe and 20–25 ppm Zn while milled rice had 2–3 ppm Fe and 16–17 ppm Zn. It has been estimated that more than 70% of micronutrients are lost during polishing (Sellappan et al., 2009). It is suggested that the rice based diet should contain 14.5 ppm Fe (Johnson et al., 2011) and 24 ppm Zn (http:// www.harvestplus.org/content/zinc-rice-india). Several Quantitative Trait Loci (QTLs) for grain micronutrient con- tent including iron and zinc have been identified and mapped on rice chromosomes using molecular markers (Garcia-Oliveira et al., 2009; Lu et al., 2008; Norton et al., 2009). Chandel et al. (2011) reported QTLs for Fe and Zn and identified candidate genes governing iron and zinc concentrations in rice grains, based on EST and MPSS signatures using bioinformatic tools. Recently, over-expression of single rice genes such as OsNAS2 was reported to enhance the concentration of both iron (Johnson et al., 2011) and zinc (Lee et al., 2011). Deep-water rice varieties Madhukar and Jalmagna have high iron and zinc in endosperm (Gregorio et al., 2000). Jalmagna is floating rice grown in some regions of northern and eastern India. Madhukar is a leading improved and traditional variety of eastern India grown in flood prone areas and was released in 1967 from the state of Uttar Pradesh. It has the capacity to survive under complete submergence for 7–10 days. It is known as highly zinc efficient rice variety and has very high zinc density and slightly high iron density (Gregorio et al., 2000). It was identified and used as donor for submergence tolerance. Swarna (MTU 7029) is a popular rainfed lowland rice cultivar in South Gene 508 (2012) 233–240 Abbreviations: AC, amylose content; APRT, adenine phosphoribosyltransferase; ARD, acireductone deoxygenase; BAC, bacterial artificial chromosome; BILs, backcross inbred lines; BLAST, Basic Local Alignment Search Tool; BPH, brown plant hopper; Cd, cadmium; CIM, Composite Interval Mapping; cM, centimorgan; DNA, deoxyribonucleic acid; DRR, Directorate of Rice Research; EST, expressed sequence tag; Fe, iron; GGT, graphical genotyping; Hv, Hordeum vulgare; IM, Interval Mapping; IRGSP, International Rice Genome Sequencing Project; IRT, iron regulated transporters; LOD, logarithm of odds; MIM, Multiple Interval Mapping; MPSS, massively parallel signature sequencing; MTP, metal transport protein; NA, nicotianamine; NAS, nicotianamine synthase; NCBI, National Center for Biotechnology Information; NIL, near isogenic line; NRAMP, natural resistance associated macrophage protein; Os, Oryza sativa; ppm, parts per million; PS, phytosiderophores; QTL, Quantitative Trait Loci; RAP DB, The Rice Annotation Project Database (RAP DB); RILs, recombinant inbred lines; SAS, statistical analysis system; SMA, Single Marker Analysis; SSR, simple sequence repeat; TIGR, The Institute for Geno- mic Research; XRF, X-ray fluorescence; YSL, yellow stripe like; ZIP, zinc transporter; Zn, zinc; ZTP, zinc transporter family. ⁎ Corresponding author. Tel.: +91 40 24591225; fax: +91 40 24591217. E-mail addresses: sarla_neelamraju@yahoo.com, nsarla@drricar.org (N. Sarla). 0378-1119/$ – see front matter © 2012 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.gene.2012.07.054 Contents lists available at SciVerse ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene