Morphological and genetic diversity analysis of rice accessions (Oryza sativa L.) differing in iron toxicity tolerance

Fe toxicity in plants: Impacts and remediation

Fe is the fourth abundant element in the earth crust. Fe toxicity is not often discussed in plant science though it causes severe morphological and physiological disorders, including reduced germination percentage, interferes with enzymatic activities, nutritional imbalance, membrane damage, and chloroplast ultrastructure. It also causes severe toxicity to important biomolecules, which leads to ferroptotic cell death and induces structural changes in the photosynthetic apparatus, which results in retardation of carbon metabolism. However, some agronomic practices like soil remediation through chemicals, nutrients, and organic amendments and some breeding and genetic approaches can provide fruitful results in enhancing crop production in Fe-contaminated soils. Some quantitative trait loci have been reported for Fe tolerance in plants but the function of underlying genes is just emerging. Physiological and molecular mechanism of Fe uptake, translocation, toxicity, and remediation techniques are still under experimentation. In this review, the toxic effects of Fe on seed germination, carbon assimilation, water relations, nutrient uptake, oxidative damages, enzymatic activities, and overall plant growth and development have been discussed. The Fe dynamics in soil rhizosphere and role of remediation strategies, that is, biological, physical, and chemical, have also been described. Use of organic amendments, microbe, phytoremediation, and biological strategies is considered to be both cost and environment friendly for the purification of Fe-contaminated soil, while to ensure better crop yield and quality the manipulation of agronomic practices are suggested.

Morpho-physiological retardations due to iron toxicity involve redox imbalance rather than photosynthetic damages in tomato

Iron (Fe) toxicity is a major nutritional disorder that affects growth and yield in plants. Understanding the responses or damages due to Fe-toxicity may provide useful knowledge to improve tomato varieties. This study investigates the physiological and molecular responses in Fe-toxic tomato plants. The tomato plants were grown in separate hydroponic containers with two concentrations of Fe-EDTA (25 μM and 5 mM) in addition to the other nutrient elements. Fe-toxicity showed a severe reduction in growth parameters, which was accompanied by the increased electrolyte leakage and cell death in tomato. However, the SPAD score, quantum efficiency of PSII, and photosynthesis performance index did not show any changes in leaves, suggesting that damages due to Fe-toxicity are not related to the photosynthetic disturbance in tomato. The FCR (ferric chelate reductase) activity in root along with the Fe concentration in root and shoot significantly increased, being consistent with the upregulation of Fe-related genes (SlNramp1 and SlFRO1) in roots. It suggests that inefficiency to cope with elevated Fe is closely linked to Fe mobilization and uptake in roots of tomato. Consequently, this sensitive genotype was more prone to oxidative damages because of the inefficient antioxidant defense linked to antioxidant enzymes and metabolites. In conclusion, the growth retardation in Fe-toxic tomato is not related to photosynthetic inefficiency but highly associated with oxidative injuries in cells. These findings could be targeted in breeding or transgenic program to improve tomato plants sensitive to Fe toxicity.

Bridging old and new: diversity and evaluation of high iron-associated stress response of rice cultivated in West Africa

Adoption of rice varieties that perform well under high iron-associated (HIA) stress environments can enhance rice production in West Africa. This study reports the genetic characterization of 323 rice accessions and breeding lines cultivated in West Africa using genotyping-by-sequencing and their phenotypic response to HIA treatments in hydroponic solution (1500 mg l-1 FeSO4·7H2O) and hot-spot fields. The germplasm consisted of four genetic subpopulations: Oryza glaberrima (14%), O. sativa-japonica (7%), O. sativa-indica Group 1 (45%), and O. sativa-indica Group 2 (25%). Severe versus mild stress in the field was associated with a reduced SPAD value (12%), biomass (56%), and grain yield (57%), with leaf bronzing explaining 30% and 21% of the variation for biomass and grain yield, respectively. Association mapping using 175 indica genotypes identified 23 significant single nucleotide polymorphism (SNP) markers that mapped to 14 genomic regions. Genome-wide association study (GWAS) signals associated with leaf bronzing, a routinely used indicator of HIA stress, differed in hydroponic compared with field conditions. Contrastingly, six significant SNPs on chromosomes 8 and 9 were associated with the SPAD value under HIA stress in both field and hydroponic experiments, and a candidate potassium transporter gene mapped under the peak on chromosome 8. This study helps define criteria for assessing rice performance under HIA environments.

Genetic diversity and population structure analysis of Ghanaian and exotic cassava accessions using simple sequence repeat (SSR) markers

Genetic diversity is fundamentally important in crop improvement and provides plants with the capacity to meet the demands of changing environments. This work was carried out to assess the diversity and the extent of genetic relatedness among a number of assembled cassava (Manihot esculenta Crantz) accessions. We conducted a microsatellite marker analysis of 89 cassava accessions collected from Ghanaian and exotic sources. These accessions were assayed using 35 simple sequence repeat (SSR) markers. A total of 167 alleles were detected from 35 polymorphic markers with an average of 4.77 alleles per locus. High allelic frequency was detected across the accessions, ranging from 0.32 to 0.99 with an average of 0.62 per marker. Observed heterozygosity ranged from 0.03 - 0.97 across the accessions. Polymorphism information content (PIC) ranged from 0.03 to 0.78 with a mean of 0.45, indicating high level of polymorphism across the accessions. Comparatively, higher number of alleles, gene diversity and observed heterozygosity were detected among the local accessions compared with the exotic accessions indicating rich genetic diversity among them. Population structure analysis based on STRUCTURE identified two subpopulations and a large number of admixtures. Cluster analysis based on the neighbour joining algorithim further separated the collection into seven sub-groupings irrespective of geographical origin. This indicates the possible sharing of common genomic regions occurring across the accessions. High allelic frequency differences and levels of heterozygosity were observed among the germplasm. These findings indicated significant genetic variability in the germplasm to warrant selection.

Iron tolerance in rice: an efficient method for performing quick early genotype screening

Objectives

This study was conducted to establish a method for early, quick and cheap screening of iron excess tolerance in rice (Oryza sativa L.) cultivars.

Results

Based on the experiments, iron excess leads to reduction in shoot length (SL) and this can be a useful characteristic for adequate screening of tolerant genotypes. The sensitive genotypes Nipponbare and BR-IRGA 409 indicated higher accumulation of iron in their tissues while BRS-Agrisul and Epagri 108 also accumulated iron, but at lower concentrations. BR-IRGA 410 displayed an intermediate phenotype regarding iron accumulation. No changes in shoot Cu content can be observed when comparing treatments. On the other hand, an increase was seen for Zn and Mn when shoots are subjected to Fe²⁺ excess. Fe stress at a lower concentration than 7 mM increased Zn but decreased Mn contents in shoots of BR-IRGA 409. Strong positive correlations were found here for Fe × Zn (0.93); Fe × Mn (0.97) and Zn × Mn (0.92), probably due to the Fe-induced activation of bivalent cation transporters. Results show that genotypes scored as sensitive present higher concentration of Fe in shoots and this is an efficient method to characterize rice cultivars regarding iron response.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4362-5) contains supplementary material, which is available to authorized users.

Superior adaptation of aerobic rice under drought stress in Iran and validation test of linked SSR markers to major QTLs by MLM analysis across two years

Drought is one of the biggest challenges for rice (Oryza sativa L.) production in rainfed areas. Developing "aerobic rice" cultivars could be a valuable alternative to irrigated/rainfed areas. During 2010-2013, 115 rice genotypes, including non-local cultivars and aerobic rice genotypes, were evaluated and 31 rice genotypes were screened, while 21 Iranian lowland rice cultivars (52 genotypes) were investigated under non-stress and drought conditions at the University of Guilan, Rasht, Iran, in 2014 and 2017. The results revealed the superiority of high yielding genotypes, namely Neda (6.202 t ha^- 1), IR82639-B-B-140-1 (6.020 t ha^- 1), and IR82635-B-B-82-2 (5.75 t ha^- 1) under non-stress, Panda (4.512 t ha^- 1), and IR82639-B-B-140-1 (4.08 t ha^- 1), under drought stress conditions. Based on the molecular markers evaluation using identified SSR markers linked to major QTLs different important traits specially drought stress, IR 82639-B-B-140-1 showed the highest genetic distance with high-quality Iranian lowland cultivars, which could be considered as a donor for the development of new cultivars. Moreover, the assignment of rice genotypes based on Jaccard distance clustering was in agreement with the grouping of structure analysis. The validation test using MLM analysis in this natural population revealed the most important significant associations that were identified under drought conditions. These are: the associations between RM306, RM319, RM511, RM28166, and RM11943 with different grain yield (GY)-related traits simultaneously and stable across both years. These markers, which were verified in a natural population across 2 years, could be considered as the potential markers for use in marker-assisted breeding and to improve the grain yield of rice.

Mechanistic understanding of iron toxicity tolerance in contrasting rice varieties from Africa: 1. Morpho-physiological and biochemical responses

Iron (Fe) is a fundamental element involved in various plant metabolic processes. However, when Fe uptake is excessive, it becomes toxic to the plant and disrupts cellular homeostasis. The aim of this study was to determine the physiological and biochemical mechanisms underlying tolerance to Fe toxicity in contrasting rice varieties adapted to African environments. Four varieties (CK801 and Suakoko 8 (tolerant), Supa and IR64 (sensitive)) selected from our previous work were analysed in more detail, and the first part of this study reports morphological, physiological and biochemical responses induced by Fe toxicity in these four varieties. Morphological (shoot length, root length, number of lateral roots), physiological (photosynthesis rate, stomatal conductance, transpiration rate, fluorescence, relative water content and cell membrane stability) and biochemical (tissue Fe, chlorophyll pigments, soluble sugars, protein and starch) traits were measured, as appropriate, on both shoot and root tissues and at different time points during the stress period. Fe toxicity significantly (P≤0.05) reduced growth and metabolism of all the four varieties. Tolerant varieties showed more lateral roots than the sensitive ones, under Fe toxic conditions as well as higher photosynthesis rate, chlorophyll content and cell membrane stability. Strong dilution of Fe concentration in cells was identified, as one of the additional tolerance mechanisms used by CK801, whereas Suakoko 8 mainly used strong mobilisation of carbohydrates at the early stage of the stress period to anticipate metabolite shortage. Traits associated with Fe toxicity tolerance in this study could be specifically targeted in trait-based breeding programs of superior lowland rice varieties tolerant of Fe toxicity.

Understanding the regulation of iron nutrition: can it contribute to improving iron toxicity tolerance in rice?

Iron nutrition in plants is highly regulated in order to supply amounts sufficient for optimal growth while preventing deleterious effects. In response to iron deficiency, plants induce either reduction-based or chelation-based mechanisms to enhance iron uptake from the soil. Major physiological traits and genes involved in these mechanisms have been fairly well described in model plants like Arabidopsis thaliana (L. Heynh.) and rice (Oryza sativa L.). However, for rice, iron toxicity presents a major challenge worldwide and causes yield reductions because rice is widely cultivated in flooded soils. Nonetheless, rice employs different mechanisms of adaptation to iron-toxicity, which range from avoidance to tissue tolerance. The physiological and molecular bases of such mechanisms have not been fully investigated and their use in breeding for iron-toxicity tolerance remains limited. Efforts to precisely characterise iron-toxicity control mechanisms may help speed-up the development of tolerant rice varieties. Considering how far the understanding of iron dynamics in the soil and plants has progressed, we consider it valuable to exploit such knowledge to improve rice tolerance to iron toxicity. Here we present the mechanisms that regulate iron uptake from the rhizosphere to the plant tissues together with the possible regulators involved. In addition, a genetic model for iron-toxicity tolerance in rice, which hypothesises possible modulation of key genes involved in iron nutrition and regulation is presented. The possibility of incorporating such relevant regulators in breeding is also discussed.