Mechanisms of genotypic differences in tolerance of iron toxicity in field-grown rice

Iron (Fe) toxicity is a major constraint to rice yields in much of the world due to the greater solubility of reduced ferrous Fe in paddy soils compared with ferric Fe in aerobic soils and resulting excess uptake into the plants. There is genotypic variation in tolerance in Oryza gene pools, but so far only weak-effect alleles have been identified, largely because multiple critical physiological processes determine the tolerance. Most past research has been done in nutrient solution screens at the seedling stage, and not under field conditions over the full life cycle. We investigated tolerance mechanisms in a diverse set of genotypes under field conditions in a highly iron toxic soil in the Central Highlands of Madagascar. We made repeated plant samplings of young and old tissues throughout the growth period until maturity. Multiple mechanisms were involved, and the importance of different mechanisms changed between growth stages. Higher grain yields were mainly due to healthy vegetative growth, achieved either by reducing Fe uptake (exclusion) or by minimizing the effect of excess uptake through compartmentalization in older tissues and tissue tolerance. Exclusion mechanisms were relaxed during reproductive growth, leading to increased Fe accumulation in shoots. But tolerant genotypes were nonetheless able to grow well through a combination of Fe compartmentalization and tissue tolerance, so that grain filling could proceed relatively unimpeded. Tissue phosphorus (P) and potassium (K) concentrations were close to or below deficiency limits throughout growth. Exclusion by ferrous Fe oxidation in the rhizosphere will impede access of P and K ions to roots, but the differences in their tissue concentrations were much smaller than differences in growth rates, so growth rates evidently drove the uptake differences and responses to Fe toxicity were the more important constraints. There was no relation between grain yield and visual symptoms. To identify useful donors and markers for breeding it is important to develop screening protocols that capture the individual tolerance mechanisms, allowing for the effects of growth stage on their relative importance and expression, and possible interactions with other factors such as mineral nutrition. Selection for tolerance based on visual symptoms, particularly at the seedling stage, is overly simplistic, though it can be useful in the study of specific tolerance mechanisms

Magnesium supply alleviates iron toxicity-induced leaf bronzing in rice through exclusion and tissue-tolerance mechanisms

Introduction: Iron (Fe) toxicity is a widespread nutritional disorder in lowland rice causing growth retardation and leaf symptoms referred to as leaf bronzing. It is partly caused by an imbalance of nutrients other than Fe and supply of these is known to mitigate the toxicity. But the physiological and molecular mechanisms involved are unknown. Methods: We investigated the effect of magnesium (Mg) on Fe toxicity tolerance in a field study in the Central Highlands of Madagascar and in hydroponic experiments with excess Fe (300 mg Fe L-1). An RNA-seq analysis was conducted in a hydroponic experiment to elucidate possible mechanisms underlying Mg effects. Results and discussion: Addition of Mg consistently decreased leaf bronzing under both field and hydroponic conditions, whereas potassium (K) addition caused minor effects. Plants treated with Mg tended to have smaller shoot Fe concentrations in the field, suggesting enhanced exclusion at the whole-plant level. However, analysis of multiple genotypes showed that Fe toxicity symptoms were also mitigated without a concomitant decrease of Fe concentration, suggesting that increased Mg supply confers tolerance at the tissue level. The hydroponic experiments also suggested that Mg mitigated leaf bronzing without significantly decreasing Fe concentration or oxidative stress as assessed by the content of malondialdehyde, a biomarker for oxidative stress. An RNA-seq analysis revealed that Mg induced more changes in leaves than roots. Subsequent cis-element analysis suggested that NAC transcription factor binding sites were enriched in genes induced by Fe toxicity in leaves. Addition of Mg caused non-significant enrichment of the same binding sites, suggesting that NAC family proteins may mediate the effect of Mg. This study provides clues for mitigating Fe toxicity-induced leaf bronzing in rice

Overcoming phosphate deficiency in flooded rice in Madagascar

Phosphorus (P) is the major limiting nutrient for irrigated rice grown on highly weathered soils in Madagascar. In these soils, the total P is often very large but strongly fixed on the large amount of iron (Fe) oxyhydroxides. These soils have in addition a very high capacity to sorb soluble P fertilizer. Soil flooding is known to increase the P availability because of reductive dissolution of P-bearing Fe oxyhydroxides. In non-reduced system, addition of organic materials (OM) can improve efficiently the availability of P in such soils. The aim this study is to understand the mechanisms of P solubilization in flooded soils in order to elaborate a fertilization strategy in low-input farming system for a sustainable productivity. More focus will be on the understanding of OM input and P availability interactions, and soil factors explaining the extent of P solubilization. Soil incubations and greenhouse experiments with various soil samples will be done to study the underlying mechanisms and soil factors involved. Their results will be used to explain rice responses to treatments in field experiments and on farm trials.Acknowledgements i Summary iii Samenvatting vi List of abbreviations x List of symbols xii Table of contents xiv CHAPTER 1 The role of organic matter management in phosphorus availability to rice: introduction and research objectives 1 CHAPTER 2 Soil flooding and rice straw addition can increase isotopic exchangeable phosphorus in P-deficient tropical soils 21 CHAPTER 3 Effects of organic matter addition on phosphorous availability to flooded and non-flooded rice in a P-deficient tropical soil: a greenhouse study 39 CHAPTER 4 Effects of soil flooding and organic matter addition on plant accessible phosphorus in a tropical paddy soil: an isotope dilution study 57 CHAPTER 5 Pronounced rhizosphere mobilization of phosphorus by rice plants in flooded and non-flooded phosphorus deficient soils 75 CHAPTER 6 Farm yard manure application does not increase phosphorus availability to flooded rice grown in highly weathered soils: field experiments 93 CHAPTER 7 General conclusions and suggestions for future research 109 Bibliography 116 List of publications 126nrpages: 142status: publishe

Multiple-nutrient limitation of upland rainfed rice in ferralsols: a greenhouse nutrient-omission trial

International audienceTo optimize the nutrient management of upland rice production on tropical ferralsols, a greenhouse experiment was established using the multi-nutrient omission approach. A reciprocal soil origin-rice cultivar transplant experiment was also conducted to better understand the relative contributions of the soil origin and the rice cultivar in rice nutrient limitation. We tested the deficiency of seven major and secondary nutrients [nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), magnesium (Mg), and silicon (Si)] and a solution of six micronutrients (B, Mn, Cu, Co, Na, Mo) likely to limit the growth of two upland rice cultivars, Chhomrong Dan and Nerica 4, on two Ferralsols from the highlands of Madagascar. We found severe multiple nutrient deficiencies. For both cultivars, P, Ca, N, Mg omission significantly depressed the shoot and root dry biomass and their amounts in plant tissues. However, the main limiting nutrients were not the same in both soils. We conclude that the multinutrient deficiencies observed for rice growth in the Ferralsols are site-specific, even though P limitation appears to be in common, and requires a holistic consideration of the mineral fertility, including micronutrients

Vis-NIR Spectroscopy and PLS Regression with Waveband Selection for Estimating the Total C and N of Paddy Soils in Madagascar

Visible and near-infrared (Vis-NIR) diffuse reflectance spectroscopy with partial least squares (PLS) regression is a quick, cost-effective, and promising technology for predicting soil properties. The advantage of PLS regression is that all available wavebands can be incorporated in the model, while earlier studies indicate that PLS models include redundant wavelengths, and selecting specific wavebands can refine PLS analyses. This study evaluated the performance of PLS regression with waveband selection using Vis-NIR reflectance spectra to estimate the total carbon (TC) and total nitrogen (TN) in soils collected mainly from the surface of upland and lowland rice fields in Madagascar (n = 59; after outliers were removed). We used iterative stepwise elimination-based PLS (ISE-PLS) to estimate soil TC and TN and compared the predictive ability with standard full-spectrum PLS (FS-PLS). The predictive abilities were assessed using the coefficient of determination (R2), the root mean squared error of cross-validation (RMSECV), and the residual predictive deviation (RPD). Overall, ISE-PLS using first derivative reflectance (FDR) showed a better predictive accuracy than ISE-PLS for both TC (R2 = 0.972, RMSECV = 0.194, RPD = 5.995) and TN (R2 = 0.949, RMSECV = 0.019, RPD = 4.416) in the soil of Madagascar. The important wavebands for estimating TC (12.59% of all wavebands) and TN (3.55% of all wavebands) were selected from all 2001 wavebands over the 400–2400 nm range using ISE-PLS. These findings suggest that ISE-PLS based on Vis-NIR diffuse reflectance spectra can be used to estimate soil TC and TN contents in Madagascar with an improved predictive accuracy

Farm yard manure application mitigates aluminium toxicity and phosphorus deficiency for different upland rice genotypes

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Laboratory Visible and Near-Infrared Spectroscopy with Genetic Algorithm-Based Partial Least Squares Regression for Assessing the Soil Phosphorus Content of Upland and Lowland Rice Fields in Madagascar

As a laboratory proximal sensing technique, the capability of visible and near-infrared (Vis-NIR) diffused reflectance spectroscopy with partial least squares (PLS) regression to determine soil properties has previously been demonstrated. However, the evaluation of the soil phosphorus (P) content—a major nutrient constraint for crop production in the tropics—is still a challenging task. PLS regression with waveband selection can improve the predictive ability of a calibration model, and a genetic algorithm (GA) has been widely applied as a suitable method for selecting wavebands in laboratory calibrations. To develop a laboratory-based proximal sensing method, this study investigated the potential to use GA-PLS regression analyses to estimate oxalate-extractable P in upland and lowland soils from laboratory Vis-NIR reflectance data. In terms of predictive ability, GA-PLS regression was compared with iterative stepwise elimination PLS (ISE-PLS) regression and standard full-spectrum PLS (FS-PLS) regression using soil samples collected in 2015 and 2016 from the surface of upland and lowland rice fields in Madagascar (n = 103). Overall, the GA-PLS model using first derivative reflectance (FDR) had the best predictive accuracy (R2 = 0.796) with a good prediction ability (residual predictive deviation (RPD) = 2.211). Selected wavebands in the GA-PLS model did not perfectly match wavelengths of previously known absorption features of soil nutrients, but in most cases, the selected wavebands were within 20 nm of previously known wavelength regions. Bootstrap procedures (N = 10,000 times) using selected wavebands also confirmed the improvements in accuracy and robustness of the GA-PLS model compared to those of the ISE-PLS and FS-PLS models. These results suggest that soil oxalate-extractable P can be predicted from Vis-NIR spectroscopy and that GA-PLS regression has the advantage of tuning optimum bands for PLS regression, contributing to a better predictive ability

Phosphorus fertilization of Malagasy agronomic systems in the context of climate variability and change

National audienceFarmers in Madagascar are among the most vulnerable groups in the World. Malagasy agronomic systems are characterised by low to very low soil fertility resulting to food insecurity. The availability of phosphorus (P) is a key issue of climate change mitigation of agronomic systems, as P is the first limiting factor of agricultural productivity. In fact, combination of organic and inorganic phosphorus fertilisers allows overcoming P deficiency in rain fed rice and, at the same time, permit coping with the negative impacts of climate variability when farmers have to modify their conventional farming system and practices, such as the use of triple superphosphate or the delay in crop installation. The production of rain fed rice can be improved from 1t to 3t per ha using mixed organic and inorganic sources of phosphorus. A transformational change is needed for an effective support from the decision makers either in training than in financial and technical supports. The participatory action research is the way for scaling up research results in the field