Differential effects of arsenite and arsenate on rice (Oryza sativa) plants differing in glutathione S-transferase gene expression.

Contamination of paddy soils with arsenic (As) can cause phytotoxicity in rice and increase the accumulation of arsenic in grains. The uptake and accumulation of As in rice depends on the different As species present in the soil. Plants detoxify As by conjugating and sequestering xenobiotic compounds into vacuoles using various enzymes. However, the severity of damage induced by arsenite (As(III)) and arsenate (As(V)), as well as the roles of glutathione S-transferase in detoxifying these As species in rice, are not fully understood. In this study, we developed plant materials overexpressing a glutathione S-transferase gene OsGSTU40 under the control of the maize UBIL promoter. Through systematic investigations of both wild-type Nipponbare (Oryza sativa L., ssp. japonica) and OsGSTU40 overexpression lines under chronic or acute stress of As, we aimed to understand the toxic effects of both As(III) and As(V) on rice plants at the vegetative growth stage. We hypothesized that (i) As(III) and As(V) have different toxic effects on rice plants and (ii) OsGSTU40 played positive roles in As toxicity tolerance. Our results showed that As(III) was more detrimental to plant growth than As(V) in terms of plant growth, biomass, and lipid peroxidation in both chronic and acute exposure. Furthermore, overexpression of OsGSTU40 led to better plant growth even though uptake of As(V), but not As(III), into shoots was enhanced in transgenic plants. In acute As(III) stress, transgenic plants exhibited a lower level of lipid peroxidation than wild-type plants. The element composition of plants was dominated by the different As stress treatments rather than by the genotype, while the As concentration was negatively correlated with phosphorus and silicon. Overall, our findings suggest that As(III) is more toxic to plants than As(V) and that glutathione S-transferase OsGSTU40 differentially affects plant reactions and tolerance to different species of arsenic.

Interactive effects of tropospheric ozone and blast disease (Magnaporthe oryzae) on different rice genotypes.

Rising tropospheric ozone concentrations can cause rice yield losses and necessitate the breeding of ozone-tolerant rice varieties. However, ozone tolerance should not compromise the resistance to important biotic stresses such as the rice blast disease. Therefore, we investigated the interactive effects of ozone and rice blast disease on nine different rice varieties in an experiment testing an ozone treatment, blast inoculation, and their interaction. Plants were exposed to an ozone concentration of 100 ppb for 7 h per day or ambient air throughout the growth period. Half of the plants were simultaneously infected with rice blast inoculum. Grain yield was significantly reduced in the blast treatment (17%) and ozone treatment (37%), while the combination of both stresses did not further decrease grain yields compared to ozone alone. Similar trends occurred for physiological traits such as vegetation indices, normalized difference vegetation index (NDVI), photochemical reflectance index (PRI), Lichtenthaler index 2 (Lic2), and anthocyanin reflectance index 1 (ARI1), as well as stomatal conductance and lipid peroxidation. Ozone exposure mitigated the formation of visible blast symptoms, while blast inoculation did not significantly affect visible ozone symptoms. Although different genotypes showed contrasting responses to the two types of stresses, no systematic pattern was observed regarding synergies or trade-offs under the two types of stresses. Therefore, we conclude that despite the similarities in physiological stress responses to ozone and blast, the tolerance to these stresses does not appear to be genetically linked in rice.

OsSWEET11b, a potential sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility.

SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by Transcription Activator-Like effectors (TALe) of Xanthomonas ssp. is key for virulence in rice, cassava and cotton. We identified OsSWEET11b with roles in male fertility and potential bacterial blight (BB) susceptibility in rice. While single ossweet11a or 11b mutants were fertile, double mutants were sterile. As clade III SWEETs can transport gibberellin (GA), a key hormone for spikelet fertility, sterility and BB susceptibility might be explained by GA transport deficiencies. However, in contrast with the Arabidopsis homologues, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility therefore are likely to depend on sucrose transport activity. Ectopic induction of OsSWEET11b by designer TALe enabled TALe-free Xanthomonas oryzae pv. oryzae (Xoo) to cause disease, identifying OsSWEET11b as a potential BB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence of Xoo. Notably, only three of six clade III SWEETs are targeted by known Xoo strains from Asia and Africa. The identification of OsSWEET11b is relevant for fertility and for protecting rice against emerging Xoo strains that target OsSWEET11b.

Identification of Promising Genotypes Through Systematic Evaluation for Arsenic Tolerance and Exclusion in Rice (Oryza sativa L.).

Rice remains a major staple food source for the rapidly growing world population. However, regular occurrences of carcinogenic arsenic (As) minerals in waterlogged paddy topsoil pose a great threat to rice production and consumers across the globe. Although As contamination in rice has been well recognized over the past two decades, no suitable rice germplasm had been identified to exploit in adaptive breeding programs. Therefore, this current study identified suitable rice germplasm for As tolerance and exclusion based on a variety of traits and investigated the interlinkages of favorable traits during different growth stages. Fifty-three different genotypes were systematically evaluated for As tolerance and accumulation. A germination screening assay was carried out to identify the ability of individual germplasm to germinate under varying As stress. Seedling-stage screening was conducted in hydroponics under varying As stress to identify tolerant and excluder genotypes, and a field experiment was carried out to identify genotypes accumulating less As in grain. Irrespective of the rice genotypes, plant health declined significantly with increasing As in the treatment. However, genotype-dependent variation in germination, tolerance, and As accumulation was observed among the genotypes. Some genotypes (WTR1-BRRI dhan69, NPT-IR68552-55-3-2, OM997, and GSR IR1-5-Y4-S1-Y1) showed high tolerance by excluding As in the shoot system. Arsenic content in grain ranged from 0.12 mg kg-1 in Huang-Hua-Zhan (indica) from China to 0.48 mg kg-1 in IRAT 109 (japonica) from Brazil. This current study provides novel insights into the performance of rice genotypes under varying As stress during different growth stages for further use in ongoing breeding programs for the development of As-excluding rice varieties for As-polluted environments.

High Throughput Analyses of Ascorbate-turnover Enzyme Activities in Rice (Oryza sativa L.) Seedlings.

Ascorbate (Vitamin C) fulfills various functions in plant photosynthesis and abiotic stress tolerance. The four key enzymes involved in the ascorbate-turnover pathway are ascorbate peroxidase, ascorbate oxidase, monodehydroascorbate reductase, and dehydroascorbate reductase. Several reports have shown the pivotal roles of these enzymes in plant development and stress tolerance. Therefore, reliable and rapid assay protocols are required for researchers to investigate their enzymatic activities during plant development and stress responses. Previously published methods for analyzing these enzymatic activities rely on cuvette spectrophotometers, which can only handle one sample per test, leading to a prolonged investigation. In this protocol, we employed a 96-well microplate reader to analyze at least eight samples with two technical replicates simultaneously. We analyzed two rice (Oryza sativa L.) genotypes with distinct ascorbate oxidase and dehydroascorbate reductase activities to demonstrate the assay process, including plant growth, sample preparation, reaction setup, and data analysis. Our protocol provides a high throughput method for investigating ascorbate turnover-related enzymatic activities in plants.

Chromosomal introgressions from Oryza meridionalis into domesticated rice Oryza sativa result in iron tolerance.

Iron (Fe) toxicity is one of the most common mineral disorders affecting rice (Oryza sativa) production in flooded lowland fields. Oryza meridionalis is indigenous to northern Australia and grows in regions with Fe-rich soils, making it a candidate for use in adaptive breeding. With the aim of understanding tolerance mechanisms in rice, we screened a population of interspecific introgression lines from a cross between O. sativa and O. meridionalis for the identification of quantitative trait loci (QTLs) contributing to Fe-toxicity tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL was highly tolerant despite very high shoot Fe concentrations. Physiological, biochemical, ionomic, and transcriptomic analyses showed that the tolerance of the introgression lines could partly be explained by higher relative Fe retention in the leaf sheath and culm. We constructed the interspecific hybrid genome in silico for transcriptomic analysis and identified differentially regulated introgressed genes from O. meridionalis that could be involved in shoot-based Fe tolerance, such as metallothioneins, glutathione S-transferases, and transporters from the ABC and MFS families. This work demonstrates that introgressions of O. meridionalis into the O. sativa genome can confer increased tolerance to excess Fe.

Development of marker-free rice with stable and high resistance to rice black-streaked dwarf virus disease through RNA interference.

The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Asia. RNA interference (RNAi) has been widely applied to develop antiviral varieties in plants. So far, only a few studies reported the application of RNAi in rice against RBSDV and most of them are lack of enough data to support its breeding potential, which limited the progress on developing RBSDV-resistant variety. In this study, we generated three RNAi constructs to specifically target three RBSDV genes (S1, S2 and S6), respectively. We confirmed that RNAi targeting RBSDV S6 conferred rice with almost full immunity to RBSDV through phenotyping test in eight consecutive years in both artificial inoculation and field trials, while RNAi of S1 or S2 only leads to partially increased resistance. The S6RNAi was also found conferring strong resistance to southern rice black-streaked dwarf virus (SRBSDV), a novel species closely related to RBSDV that outbroke recently in Southern China. In particular, no adverse effects on agronomical and developmental traits were found in S6RNAi transgenic lines. The marker-free transgenic lines with S6RNAi, driven by either maize ubiquitin-1 promoter or rice rbcS green tissue expression promoter, in elite rice background should have great potential in breeding of resistant varieties to both RBSDV and SRBSDV and provide a basis for further safety evaluation and commercial application.

Evaluation of rice wild relatives as a source of traits for adaptation to iron toxicity and enhanced grain quality.

Rice wild relatives (RWR) constitute an extended gene pool that can be tapped for the breeding of novel rice varieties adapted to abiotic stresses such as iron (Fe) toxicity. Therefore, we screened 75 Oryza genotypes including 16 domesticated O. sativa genotypes, one O. glaberrima, and 58 RWR representing 21 species, for tolerance to Fe toxicity. Plants were grown in a semi-artificial greenhouse setup, in which they were exposed either to control conditions, an Fe shock during the vegetative growth stage (acute treatment), or to a continuous moderately high Fe level (chronic treatment). In both stress treatments, foliar Fe concentrations were characteristic of Fe toxicity, and plants developed foliar stress symptoms, which were more pronounced in the chronic Fe stress especially toward the end of the growing season. Among the genotypes that produced seeds, only the chronic stress treatment significantly reduced yields due to increases in spikelet sterility. Moreover, a moderate but non-significant increase in grain Fe concentrations, and a significant increase in grain Zn concentrations were seen in chronic stress. Both domesticated rice and RWR exhibited substantial genotypic variation in their responses to Fe toxicity. Although no RWR strikingly outperformed domesticated rice in Fe toxic conditions, some genotypes scored highly in individual traits. Two O. meridionalis accessions were best in avoiding foliar symptom formation in acute Fe stress, while an O. rufipogon accession produced the highest grain yields in both chronic and acute Fe stress. In conclusion, this study provides the basis for using interspecific crosses for adapting rice to Fe toxicity.

Efficient Agrobacterium-mediated Transformation of The Elite-Indica Rice Variety Komboka.

Genetic transformation is crucial for both investigating gene functions and for engineering of crops to introduce new traits. Rice (Oryza sativa L.) is an important model in plant research, since it is the staple food for more than half of the world's population. As a result, numerous transformation methods have been developed for both indica and japonica rice. Since breeders continuously develop new rice varieties, transformation protocols have to be adapted for each new variety. Here we provide an optimized transformation protocol with detailed tips and tricks for a new African variety Komboka using immature embryos. In Komboka, we obtained an apparent transformation rate of up to 48% for GUS/GFP reporter gene constructs using this optimized protocol. This protocol is also applicable for use with other elite indica rice varieties.

Mapping of genomic regions associated with arsenic toxicity stress in a backcross breeding populations of rice (Oryza sativa L.).

BACKGROUND: Arsenic (As) is an unwanted toxic mineral that threatens the major rice-growing regions in the world, especially in South Asia. Rice production in Bangladesh and India depends on As-contaminated groundwater sources for irrigating paddy fields, resulting in elevated amounts of As in the topsoil. Arsenic accumulating in rice plants has a significant negative effect on human and animal health. Here, we present a quantitative trait locus (QTL) mapping study to identify candidate genes conferring As toxicity tolerance and accumulation in rice (Oryza sativa L.) seedlings. An early backcross breeding population consisting of 194 lines derived from a cross between WTR1 (indica) and Hao-an-nong (japonica) was grown in hydroponics for 25 days, from the seventh day exposed to an environmentally relevant concentration of 10 ppm As. RESULTS: Arsenic toxicity leads to significantly negative plant responses, including reduced biomass, stunted plant growth, reduced leaf chlorophyll content, and increased shoot As concentration ranging from 9 to 20 mg kg- 1. Marker-trait association was determined for seven As-related traits using 704 single nucleotide polymorphism (SNP) markers generated from a 6 K SNP-array. One QTL was mapped on chromosome 1 for relative chlorophyll content, two QTLs for As content in roots were mapped on chromosome 8, and six QTLs for As content in shoots were mapped on chromosomes 2, 5, 6, and 9. Using the whole-genome sequence of the parents, we narrowed down the number of candidate genes associated with the QTL intervals based on the existence of a non-synonymous mutation in genes between the parental lines. Also, by using publicly available gene expression profiles for As stress, we further narrowed down the number of candidate genes in the QTL intervals by comparing the expression profiles of genes under As stress and control conditions. Twenty-five genes showing transcription regulation were considered as candidate gene nominees for As toxicity-related traits. CONCLUSIONS: Our study provides insight into the genetic basis of As tolerance and uptake in the early seedling stage of rice. Comparing our findings with the previously reported QTLs for As toxicity stress in rice, we identified some novel and co-localized QTLs associated with As stress. Also, the mapped QTLs harbor gene models of known function associated with stress responses, metal homeostasis, and transporter activity in rice. Overall, our findings will assist breeders with initial marker information to develop suitable varieties for As-contaminated ecosystems.

Enhanced ascorbate level improves multi-stress tolerance in a widely grown indica rice variety without compromising its agronomic characteristics.

A biotechnological approach was adopted for increasing foliar ascorbate levels as a strategy to adapt a widely grown high yielding rice variety to multiple abiotic stresses. The variety IR64 (Oryza sativa L. ssp. indica) was engineered to express the ascorbate biosynthesis gene GDP-L-galactose phosphorylase (AcGGP) from kiwifruit (Actinidia chinensis Planch.) under the control of a leaf-specific promoter of the Leaf Panicle 2 (LP2) gene. Transgene expression increased foliar ascorbate levels up to >2.5 fold but did not lead to any changes in morphological traits (seed yield, sterility rate, grain weight, and biomass) in non-stress conditions. We then hypothesized that enhanced foliar ascorbate would confer multi-stress tolerance. Indeed transgenic lines were more tolerant to salinity in terms of lipid peroxidation and foliar symptoms, and to drought in terms of lipid peroxidation and post-drought recovery (number of dead leaves). A significantly better performance in ozone stress was seen only when ozone coincided with salinity. However, no differences between transgenic lines and wild types occurred when plants were subjected to toxicities in redox-active transition metals, i.e. iron and manganese, although plants showed clear symptoms of oxidative stress. Moreover, no differential response to zinc deficiency was observed, because the background genotype IR64 was not sensitive to this stress. Taken together, our study helps to identify stress conditions that can be mitigated by enhancing foliar ascorbate levels, and therefore facilitates an adaptive breeding approach for multiple stresses that would not imply any yield penalty.

Potassium Ion Channel Gene OsAKT1 Affects Iron Translocation in Rice Plants Exposed to Iron Toxicity.

Iron toxicity is one of the most widely spread mineral disorders in anaerobic soils, but the tolerance mechanisms in plants are poorly understood. Here we characterize the involvement of a rice potassium ion channel gene, OsAKT1, in Fe toxic conditions. Two knock-down lines of OsAKT1 together with azygos lines were investigated. Mutant lines did not differ from azygos lines regarding plant growth, gas exchange rate or chlorophyll fluorescence in control conditions. However, loss-of-function of OsAKT1 increased the sensitivity to excess Fe regarding leaf bronzing symptoms, reactive oxygen species generation, leaf spectral reflectance indices, and chlorophyll fluorescence. Fe toxicity leads to largely reduced uptake of other nutrients into shoots, which illustrates the complexity of Fe stress related to multiple mineral disorders. Less potassium uptake in the mutants compared to azygos lines co-occurred with higher amounts of Fe accumulated in the shoot tissues but not in the roots. These results were consistent with a higher level of Fe loaded into the xylem sap of mutants compared to azygos lines in the early phase of Fe toxicity. In conclusion, OsAKT1 is crucial for the tolerance of rice against Fe toxicity as K homeostasis affects Fe translocation from root to shoot.

Genome-wide association study to identify candidate loci and genes for Mn toxicity tolerance in rice.

Manganese (Mn) is an essential micro-nutrient for plants, but flooded rice fields can accumulate high levels of Mn2+ leading to Mn toxicity. Here, we present a genome-wide association study (GWAS) to identify candidate loci conferring Mn toxicity tolerance in rice (Oryza sativa L.). A diversity panel of 288 genotypes was grown in hydroponic solutions in a greenhouse under optimal and toxic Mn concentrations. We applied a Mn toxicity treatment (5 ppm Mn2+, 3 weeks) at twelve days after transplanting. Mn toxicity caused moderate damage in rice in terms of biomass loss and symptom formation despite extremely high shoot Mn concentrations ranging from 2.4 to 17.4 mg g-1. The tropical japonica subpopulation was more sensitive to Mn toxicity than other subpopulations. Leaf damage symptoms were significantly correlated with Mn uptake into shoots. Association mapping was conducted for seven traits using 416741 single nucleotide polymorphism (SNP) markers using a mixed linear model, and detected six significant associations for the traits shoot manganese concentration and relative shoot length. Candidate regions contained genes coding for a heavy metal transporter, peroxidase precursor and Mn2+ ion binding proteins. The significant marker SNP-2.22465867 caused an amino acid change in a gene (LOC_Os02g37170) with unknown function. This study demonstrated significant natural variation in rice for Mn toxicity tolerance and the possibility of using GWAS to unravel genetic factors responsible for such complex traits.

Responses of contrasting rice genotypes to excess manganese and their implications for lignin synthesis.

Manganese (Mn) toxicity is frequently encountered in crops grown on soils with low pH or low redox potential, and harmful to plant development and growth. This study aimed at exploring adaptive mechanisms to Mn toxicity in rice, and investigated the effects of Mn toxicity on shoot lignification. Sixteen rice genotypes were grown in hydroponic solutions and exposed to normal (0.5 mg dm-3) or toxic (5 mg dm-3) Mn concentrations for three weeks. Morphological responses to Mn toxicity included a significant reduction in shoot length and the formation of visible symptoms scored as leaf damage index (LDI). Based on shoot Mn concentrations in the Mn toxic treatment, genotypes were classified as Mn includers and excluders. Across different genotypes, shoot Mn concentrations were significantly negatively correlated with relative shoot length and positively correlated with LDI. Consequently, the most tolerant genotypes in terms of morphology were all excluders, while the most sensitive genotypes were includers. The sensitive genotypes were also more responsive to manganese in terms of lipid peroxidation than tolerant genotypes. Shoots of rice plants grown in the high Mn treatment showed a higher level of lignification measured as thioglycolic acid lignin (TGAL), especially among Mn includers. TGAL was positively correlated with shoot Mn concentration and the levels of phenolics. In contrast, peroxidase activity was not responsive to the Mn treatment and was not significantly correlated with shoot lignification. In conclusion, exclusion is a dominant tolerance mechanism to Mn toxicity in rice. Further, Mn stimulated lignin biosynthesis in rice, especially in genotypes that were unable to exclude Mn.

Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.).

Iron toxicity frequently affects lowland rice and leads to oxidative stress via the Fenton reaction. Tolerance mechanisms were investigated in contrasting genotypes: the intolerant IR29 and the tolerant recombinant inbred line FL483. Seedlings were exposed to 1000 mg L-1 ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (I) Iron uptake, partitioning and storage. The iron concentration and speciation in different plant tissues did not differ significantly between genotypes. Sub-cellular iron partitioning genes such as vacuolar iron transporters or ferritin showed no genotypic differences. (II) Antioxidant biosynthesis. Only one gene involved in carotenoid biosynthesis showed genotypic differences, but carotenoids are unlikely to scavenge the reactive oxygen species (ROS) involved in Fe toxicity, i.e. H2 O2 and hydroxyl radicals. (III) Enzymatic activities for ROS scavenging and antioxidants turnover. In shoots, glutathione-S-transferase and ascorbate oxidase genes showed genotypic differences, and consistently, the tolerant FL483 had lower dehydroascorbate reductase and higher ascorbate oxidase activity, suggesting that high rates ascorbate reduction confer sensitivity. This hypothesis was confirmed by application of exogenous reduced ascorbate or L-galactono-1,4-lactone, which increased lipid peroxidation under iron toxic conditions. Our results demonstrate in planta pro-oxidant activity of reduced ascorbate in the presence of iron.

Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.).

KEY MESSAGE: A genome-wide association study in rice yielded loci and candidate genes associated with tolerance to iron toxicity, and revealed biochemical mechanisms associated with tolerance in contrasting haplotypes. Iron toxicity is a major nutrient disorder affecting rice. Therefore, understanding the genetic and physiological mechanisms associated with iron toxicity tolerance is crucial in adaptive breeding and biofortification. We conducted a genome-wide association study (GWAS) by exposing a population of 329 accessions representing all subgroups of rice to ferrous iron stress (1000 ppm, 5 days). Expression patterns and sequence polymorphisms of candidate genes were investigated, and physiological hypotheses related to candidate loci were tested using a subset of contrasting haplotypes. Both iron including and excluding tolerant genotypes were observed, and shoot iron concentrations explained around 15.5 % of the variation in foliar symptom formation. GWAS for seven traits yielded 20 SNP markers exceeding a significance threshold of -log10 P > 4.0, which represented 18 distinct loci. One locus mapped for foliar symptom formation on chromosome 1 contained two putative glutathione-S-transferases, which were strongly expressed under iron stress and showed sequence polymorphisms in complete linkage disequilibrium with the most significant SNP. Contrasting haplotypes for this locus showed significant differences in dehydroascorbate reductase activity, which affected the plants' redox status under iron stress. We conclude that maintaining foliar redox homeostasis under iron stress represented an important tolerance mechanism associated with a locus identified through GWAS.

Genetic and physiological analysis of tolerance to acute iron toxicity in rice.

BACKGROUND: Fe toxicity occurs in lowland rice production due to excess ferrous iron (Fe(2+)) formation in reduced soils. To contribute to the breeding for tolerance to Fe toxicity in rice, we determined quantitative trait loci (QTL) by screening two different bi-parental mapping populations under iron pulse stresses (1,000 mg L(-1) = 17.9 mM Fe(2+) for 5 days) in hydroponic solution, followed by experiments with selected lines to determine whether QTLs were associated with iron exclusion (i.e. root based mechanisms), or iron inclusion (i.e. shoot-based mechanisms). RESULTS: In an IR29/Pokkali F8 recombinant inbred population, 7 QTLs were detected for leaf bronzing score on chromosome 1, 2, 4, 7 and 12, respectively, individually explaining 9.2-18.7% of the phenotypic variation. Two tolerant recombinant inbred lines carrying putative QTLs were selected for further experiments. Based on Fe uptake into the shoot, the dominant tolerance mechanism of the tolerant line FL510 was determined to be exclusion with its root architecture being conducive to air transport and thus the ability to oxidize Fe(2+) in rhizosphere. In line FL483, the iron tolerance was related mainly to shoot-based mechanisms (tolerant inclusion mechanism). In a Nipponbare/Kasalath/Nipponbare backcross inbred population, 3 QTLs were mapped on chromosomes 1, 3 and 8, respectively. These QTLs explained 11.6-18.6% of the total phenotypic variation. The effect of QTLs on chromosome 1 and 3 were confirmed by using chromosome segment substitution lines (SL), carrying Kasalath introgressions in the genetic background on Nipponbare. The Fe uptake in shoots of substitution lines suggests that the effect of the QTL on chromosome 1 was associated with shoot tolerance while the QTL on chromosome 3 was associated with iron exclusion. CONCLUSION: Tolerance of certain genotypes were classified into shoot- and root- based mechanisms. Comparing our findings with previously reported QTLs for iron toxicity tolerance, we identified co-localization for some QTLs in both pluse and chronic stresses, especially on chromosome 1.