Challenges and opportunities to regulate mineral transport in rice

Iron (Fe) is an essential mineral for plants and its deficiency as well as toxicity severely affects plant growth and development. Although Fe is ubiquitous in mineral soils, its acquisition by plants is difficult to regulate particularly in acidic and alkaline soils. Under alkaline conditions, where lime is abundant, Fe and other mineral elements are sparingly soluble. In contrast, under low pH conditions, especially in paddy fields, Fe toxicity could occur. Fe uptake is complicated and could be integrated with copper (Cu), manganese (Mn), zinc (Zn), and cadmium (Cd) uptake. Plants have developed sophisticated mechanisms to regulate the Fe uptake from soil and its transport to root and above-ground parts. Here, we review recent developments in understanding metal transport and discuss strategies to effectively regulate metal transport in plants with a particular focus on rice.

The expression of OsPLA2-III and OsPPO genes in rice (Oryza sativa L.) under Fe toxicity stress

Lipids are an important biomolecule in plants because of their structural and functional roles in plant cells. Moreover, they could act as signal molecules in the defense system of plants suffering from biotic and abiotic stresses. Furthermore, plants develop various tolerance strategies to cope with iron (Fe) toxicity, for example, by involving genes in the detoxification process and other mechanisms. Therefore, the objective of this research was to investigate the expression of OsPLA2-III and OsPPO genes during Fe stress conditions. It was carried out using two-week-old seedlings of two rice varieties, namely, IR64 (Fe-sensitive variety) and Pokkali (Fe-tolerant variety). The seedlings were treated with 400 ppm FeSO4.7H2O in the nutrient culture solution and compared with control that received 1 ppm FeSO4.7H2O. Furthermore, leaf bronzing, chlorophyll content and relative expression of OsPLA2-III and OsPPO genes were observed. An in-silico study was also performed to predict the interaction between OsPLA2-III and OsPPO proteins. The results showed that the Fe toxicity induced leaf bronzing, decreased leaf chlorophyll content, and increased the expression levels of OsPLA2-III and OsPPO genes. Therefore, both genes were suggested to have a role in plant tolerance mechanism during Fe toxicity stress through the lipid signaling pathway.

Tolerance Mechanisms and Irrigation Management to Reduce Iron Stress in Irrigated Rice

Iron toxicity is a major nutritional disorder in rice plants, especially in flooded areas. The use of alternative crop management practices, such as soil drainage, may mitigate negative impacts of iron toxicity, since soil aeration that follows drainage can oxidize and precipitate potentially toxic Fe+2 into Fe3+. This study aimed to evaluate the impact of alternative water management on agronomical and physiological parameters in rice plants grown in a field location with iron toxicity history. Rice cultivars BR-IRGA 409 (sensitive) and IRGA 425 (resistant to iron toxicity) were tested. Irrigation management comprised three treatments: Continuous Irrigation (CI), one cycle of water Suppression (1S) and two cycles of water Suppression (2S). Evaluations included the ionic composition of soil solution and leaf tissues, grain yield, antioxidant responses and gene expression. Permanent soil flooding resulted in higher grain yield in plants from the resistant than from the sensitive genotype, which had higher malondialdehyde (MDA) concentrations in leaves. In contrast, two cycles of alternate soil drying resulted in equivalent grain yield and MDA concentrations in both genotypes. Resistance to iron toxicity in IRGA 425 plants seems related to limited Fe translocation to shoots, increased tolerance to oxidative stress in leaves and higher expression of Ferritin, OsGAP1, OsWRKY80 and Oryzain-α genes. Plants from the BR-IRGA 409 cultivar (sensitive to Fe toxicity) improved growth and yield under the interrupted irrigation treatments, probably due to lower Fe availability in the soil solution. Management of water irrigation successfully alleviated Fe toxicity in rice plants cultivated in field conditions.

The Effectiveness of Nutrient Culture Solutions with Agar Addition as An Evaluation Media of Rice Under Iron Toxicity Conditions

Background: Evaluation of the tolerance level of rice to iron (Fe) toxicity stress can be done using a hydroponic system in a nutrient culture solution under a controlled condition. This study aimed to obtain a nutrient culture solution that effective as a medium for evaluating the response of rice under Fe toxicity stress condition. Methods: This experiment was carried out by comparing the effectiveness of three kinds of nutrient culture media, namely Yoshida’s Half-Strength solution (HSY), Yoshida’s Half-Strength + 0.2% agar solution (HSYA), and Yoshida’s Full-Strength + 0.2% agar solution (FSYA) using two rice genotypes, Inpara 5 (sensitive to Fe toxicity) and Mahsuri (tolerant to Fe toxicity). Leaf bronzing level, plant dry weight, and pH of nutrient culture media were observed in this experiment. Results: The results showed that the stress response as represented by the bronzing score in Inpara 5 leaves was known to be higher than that of Mahsuri in the three nutrient culture media. The decrease of root and shoot dry weight in Inpara 5 was higher than that of Mahsuri. In addition, the decrease in the pH of nutrient culture solution media without an agar addition (HSY) occurred faster than the media with the agar addition (HSYA and FSYA). Conclusion: The HSYA and FSYA media exhibited a similar pattern of pH declining but causing significant differences in growth responses between Inpara 5 and Mashuri indicating the HSYA medium is considered more efficient compared to the FSYA medium because it only requires a smaller amount of agar.

The Tonoplast-Localized Transporter OsNRAMP2 is involved in Fe Homeostasis and affects Seed Germination in rice

Vacuolar storage of iron (Fe) is important for Fe homeostasis in plants. When sufficient, the excess Fe could be stored in vacuoles for remobilization in case of Fe deficiency. Although the mechanism of Fe remobilization from vacuoles is critical for crop development under low Fe stress, the transporters that mediate vacuolar Fe translocation into the cytosol in rice remains unknown. Here, we showed that under higher Fe 2+ concentrations, the Δccc1 yeast mutant transformed with rice natural resistance-associated macrophage protein 2 (OsNRAMP2) became more sensitive to Fe toxicity. In rice protoplasts and transgenic plants expressing Pro35S: OsNRAMP2-GFP, OsNRAMP2 was localized to tonoplast. Vacuolar Fe contents in osnramp2 knockdown lines were higher than in the wild-type, while the growth of osnramp2 knockdown plants was significantly influenced by Fe deficiency. Furthermore, the germination of osnramp2 knockdown plants was arrested. Inversely, the vacuolar Fe contents of Pro35S: OsNRAMP2-GFP lines were significantly lower than in the wild-type, and overexpression of OsNRAMP2 increased shoot biomass under Fe deficiency. Taken together, we propose that OsNRAMP2 transports Fe from the vacuole to the cytosol and plays a pivotal role in seed germination.

QTL underlying iron toxicity tolerance at seedling stage in backcross recombinant inbred lines (BRILs) population of rice using high density genetic map

Fe is a trace element considered to be essential for rice, and it drives several metabolic processes. Fe toxicity occurs due to excessive Fe ions (Fe2+) and which, disturb cellular homeostasis and dramatically reduces the rice yield. A set of 118 BRILs made from a cross of japonica cv.’02428’ and indica ‘Changhui 891’ was used with high density bin map constructed by using high quality SNP to identify the QTL for Fe toxicity tolerance. As a whole total of 23 QTL were identified for various seedling traits, 3 under control with phenotypic difference ranging from 14.21% to 62.46%, 11 QTL under stress with phenotypic difference ranging from 7.89% to 47.39% and 9 under stressed/control ratio with phenotypic variance ranging from 9.17% to 183.50%. LOD values of QTL ranging from 4.05 to 17.04 in control, 3.41 to 8.09 in stress and 2.84 to131.63 in stress/control ratio. Shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW), were used to estimate the degree of Fe tolerance. Many stable QTL, qSSDW-4, qSSDW-6, qRSDW-4 and qRSDW-6 affecting SDW were detected and beside this some new QTL, qRSFW-1, qRRFW-10 and qRRDW-1 were successfully identified significantly contributing to Fe toxicity tolerance in rice. The results of current study indicated that these novel regions could be transferred via markers assisted section and QTL pyramiding to develop Fe resistant lines in rice.

Population genetic structure and association mapping for iron toxicity tolerance in rice

Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.

Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.