Stability of grain zinc concentrations across lowland rice environments favors zinc biofortification breeding.

Introduction: One-third of the human population consumes insufficient zinc (Zn) to sustain a healthy life. Zn deficiency can be relieved by increasing the Zn concentration ([Zn]) in staple food crops through biofortification breeding. Rice is a poor source of Zn, and in countries predominantly relying on rice without sufficient dietary diversification, such as Madagascar, Zn biofortification is a priority. Methods: Multi-environmental trials were performed in Madagascar over two years, 2019 and 2020, to screen a total of 28 genotypes including local and imported germplasm. The trials were conducted in the highlands of Ankazomiriotra, Anjiro, and Behenji and in Morovoay, a location representative of the coastal ecosystem. Contributions of genotype (G), environment (E), and G by E interactions (GEIs) were investigated. Result: The grain [Zn] of local Malagasy rice varieties was similar to the internationally established grain [Zn] baseline of 18-20 µg/g for brown rice. While several imported breeding lines reached 50% of our breeding target set at +12 µg/g, only few met farmers' appreciation criteria. Levels of grain [Zn] were stable across E. The G effects accounted for a main fraction of the variation, 76% to 83% of the variation for year 1 and year 2 trials, respectively, while GEI effects were comparatively small, contributing 23% to 9%. This contrasted with dominant E and GEI effects for grain yield. Our results indicate that local varieties tested contained insufficient Zn to alleviate Zn malnutrition, and developing new Zn-biofortified varieties should therefore be a priority. GGE analysis did not distinguish mega-environments for grain [Zn], whereas at least three mega-environments existed for grain yield, differentiated by the presence of limiting environmental conditions and responsiveness to improved soil fertility. Discussion: Our main conclusion reveals that grain [Zn] seems to be under strong genetic control in the agro-climatic conditions of Madagascar. We could identify several interesting genotypes as potential donors for the breeding program, among those BF156, with a relatively stable grain [Zn] (AMMI stability value (ASV) = 0.89) reaching our target (>26 µg/g). While selection for grain yield, general adaptation, and farmers' appreciation would have to rely on multi-environment testing, selection for grain [Zn] could be centralized in earlier generations.

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.

QTL mapping for early root and shoot vigor of upland rice (Oryza sativa L.) under P deficient field conditions in Japan and Madagascar.

Upland rice production is limited by the low phosphorus (P) availability of many highly weathered tropical soils and P deficiency is likely to become increasingly limiting in future drier climates because P mobility decreases sharply with soil moisture. Good seedling root development will be crucial to cope with the combined effects of low P and water availability. Upland rice genebank accession DJ123 was used as a donor for P efficiency and root vigor traits in a cross with inefficient local variety Nerica4 and a set of backcross lines were used to characterize the seedling stage response of upland rice to low P availability and to identify associated QTL in field trials in Japan and Madagascar. Ten QTL were detected for crown root number, root, shoot and total dry weight per plant in a highly P deficient field in Japan using the BC1F3 generation. Of these, qPef9 on chromosome 9 affected multiple traits, increasing root number, root weight and total biomass, whereas a neighboring QTL on chromosome 9 (qPef9-2) increased shoot biomass. Field trials with derived BC1F5 lines in a low-P field in Madagascar confirmed a highly influential region on chromosome 9. However, qPef9-2 appeared more influential than qPef9, as the shoot and root biomass contrast between lines carrying DJ123 or Nerica4 alleles at qPef9-2 was +23.8% and +13.5% compared to +19.2% and +14.4% at qPef9. This advantage increased further during the growing season, leading to 46% higher shoot biomass at the late vegetative stage. Results suggest an introgression between 8.0 and 12.9 Mb on chromosome 9 from P efficient donor DJ123 can improve plant performance under P-limited conditions. The QTL identified here have practical relevance because they were confirmed in the target genetic background of the local variety Nerica4 and can therefore be applied directly to improve its performance.

Chemical and biochemical quality of organic and/ or mineral fertilization resources - A dataset from the Highlands of Madagascar.

A basic understanding of the fertilization resources (FR) characteristics is required to drive soil functions following the FR application, and to improve crop productivity. The datasets presented include the FR characteristics, i.e. their nutrient contents and biochemical quality, and their effects on soil in carbon (C) and nitrogen (N) mineralization. We selected nineteen FR from local farmers, from laboratory institution and from commercial producers. The soil used in experiment was sampled in Imerintsiatosika locality, located in the Central Highlands of Madagascar. Nutrient contents of FR were evaluated by measuring total carbon, nitrogen, phosphorus, potassium, calcium, magnesium and sulphur contents. Biochemical quality of the products was assayed by fractioning organic matter of organic resources in soluble compartments, hemicelluloses, celluloses and lignin equivalent. Laboratory incubations in microcosm experiments were conducted with the mixture of soil and fertilization resources to determine C and N mineralization rates. Carbon mineralization rate was measured using microgas chromatography, and nitrogen mineralization rates were analyzed by colorimetry on a continuous flow analyzer.

Organic resources from Madagascar: Dataset of chemical and near-infrared spectroscopy measurements.

Organic wastes originating from livestock, agro-industry or urban activities may represent true resources when recycled for new uses, for example, as soil improvers, organic fertilizers or bioenergy sources. The compositional characteristics of these organic resources (ORs) can vary considerably depending on origin, nature, processing, stage, and state. Despite being of potential interest to different stakeholders in a circular economy, the variability in OR characteristics and the difficulty of accessing reliable, fast and inexpensive analysis methods may curb the recycling of OR in the agriculture or bioenergy sectors. As is the case in other low-income countries, scarcity of data on OR characteristics and the difficulty in assessing these data (due to cost and the sparsity of laboratories) is particularly acute in Madagascar, thus impairing the rational utilization of OR in the agricultural or bioenergy sectors. Visible-near infrared spectroscopy (VIS-NIR) has proven to be suitable for the fast, reliable and low-cost determination of the composition of different ORs, usually through the development of calibration models based on one type of OR by single research or lab groups. It is challenging to develop VIS-NIR models based on several types of ORs encompassing a wide range of target characteristics. Another challenging issue is the extension of databases containing spectra acquired on different spectrometers to increase model genericity. In both cases, standardization can be performed to resolve the problem of developing models for diverse ORs whose spectra originate from different laboratories. To assess the ability to develop VIS-NIR models with as much genericity as possible, we built a large database containing a wide diversity of ORs produced in Madagascar. The data presented in this paper were obtained by chemical and spectral analyses of 1,000 ORs collected from five districts in Madagascar. The data are accompanied by fine-grained metadata defined by 32 descriptors of ORs, including origin (animal, agro-industrial, and urban); nature (manure, agro-industrial waste, and compost); farm type (smallholder and agricultural factory); exploitation type (smallholder farm, factory farm, on-farm compost facility, and town compost facility); diversity of animal feed, litter, sex, and age; and diversity of bedding material. The chemical properties (including the organic nitrogen, organic carbon, organic matter, inorganic matter, phosphorus, potassium, calcium, magnesium, zinc, copper, nickel, chromium, cadmium, and lead and soluble, hemicellulose, cellulose, lignin and cutin fractions) were analyzed following laboratory standards. The number of analyses performed ranged from 39 to 180 depending on the chemical property. VIS-NIR spectra were acquired using a Labspec spectrometer. To facilitate the merging of spectral data or the development of VIS-NIR models based on broad datasets, the spectra were presented in raw form and after standardization. The dataset is original in terms of sources and width. This dataset should be of particular interest to chemometricians, biogeochemists, agronomists, energy planners, hygienists and other professionals involved in recycling ORs for various new purposes in low-income countries and elsewhere.

Under pressure: Rapid lavaka erosion and floodplain sedimentation in central Madagascar.

Lavaka (gullies) are often considered as the prime indication of a currently ongoing human-induced environmental crisis in Madagascar's highlands. Yet, lavaka are known to have existed long before human arrival and account for the majority of the long-term sediment input into the highland rivers and floodplains. The role of anthropogenic disturbances in their formation therefore remains highly debated and it is unclear whether lavaka erosion has recently increased. Here, we address these questions by evaluating the dynamics of lavaka in the Lake Alaotra region (central Madagascar). An overall birth to stabilization ratio of 6.1 indicates a rapid lavaka population growth over the period 1949-2010s. Using data on lavaka development we calculated a mean lavaka population age of 410 ± 40 years and estimate that the disequilibrium started at 870 ± 430 cal. BP. Floodplain sedimentation starts to increase around 1000 cal. BP and peaks over the last 400 years, thereby independently confirming this time frame of increased lavaka activity. Lavaka population dynamics modelling shows that a strong increase in environmental pressure over the last centuries is needed to attain current disequilibrium levels. A general drying of the climate since 950 cal. BP in combination with the introduction of cattle and growing human presence around 1000 cal. BP will likely have triggered the increase in lavaka erosion. However, the recent acceleration cannot be explained by climatic changes alone and seems to be linked to increased anthropogenic pressure on the environment. As such, we offer a fresh and quantitatively supported perspective on lavaka dynamics and human impact in central Madagascar, where our methodology can be used in other locations where similar questions on geomorphic equilibrium need to be answered.

Corrigendum: QTL mapping for early root and shoot vigor of upland rice (Oryza sativa L.) under P deficient field conditions in Japan and Madagascar.

[This corrects the article DOI: 10.3389/fpls.2022.1017419.].

Soil microbial diversity drives the priming effect along climate gradients: a case study in Madagascar.

The priming effect in soil is proposed to be generated by two distinct mechanisms: 'stoichiometric decomposition' and/or 'nutrient mining' theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic and biotic soil descriptors were characterized including bacterial and fungal phylogenetic composition. Potential organic matter mineralization and PE were assessed 7 and 42 days after the beginning of incubation with 13C-enriched wheat straw. Both priming mechanisms were mainly driven by the mean annual temperature but in opposite directions. The priming effect generated by stoichiometric decomposition was fostered under colder climates, because of soil enrichment in less developed organic matter, as well as in fast-growing populations. Conversely, the priming effect generated by nutrient mining was enhanced under warmer climates, probably because of the lack of competition between slow-growing populations mining SOM and fast-growing populations for the energy-rich residue entering the soil. Our study leads to hypotheses about the consequences of climate change on both PE generation mechanisms and associated consequences on soil carbon sequestration.

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil.

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a (13)C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of (12)CO(2) and (13)CO(2) were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum.