27 results on '"Rellán-Álvarez R"'
Search Results
2. Changes in the proteomic and metabolic profiles of Beta vulgaris root tips in response to iron deficiency and resupply
- Author
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Álvarez-Fernández Ana, Zocchi Graziano, Wohlgemuth Gert, Rodríguez-Celma Jorge, Andaluz Sofía, Rellán-Álvarez Rubén, Fiehn Oliver, López-Millán Ana, and Abadía Javier
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Botany ,QK1-989 - Abstract
Abstract Background Plants grown under iron deficiency show different morphological, biochemical and physiological changes. These changes include, among others, the elicitation of different strategies to improve the acquisition of Fe from the rhizosphere, the adjustment of Fe homeostasis processes and a reorganization of carbohydrate metabolism. The application of modern techniques that allow the simultaneous and untargeted analysis of multiple proteins and metabolites can provide insight into multiple processes taking place in plants under Fe deficiency. The objective of this study was to characterize the changes induced in the root tip proteome and metabolome of sugar beet plants in response to Fe deficiency and resupply. Results Root tip extract proteome maps were obtained by 2-D isoelectric focusing polyacrylamide gel electrophoresis, and approximately 140 spots were detected. Iron deficiency resulted in changes in the relative amounts of 61 polypeptides, and 22 of them were identified by mass spectrometry (MS). Metabolites in root tip extracts were analyzed by gas chromatography-MS, and more than 300 metabolites were resolved. Out of 77 identified metabolites, 26 changed significantly with Fe deficiency. Iron deficiency induced increases in the relative amounts of proteins and metabolites associated to glycolysis, tri-carboxylic acid cycle and anaerobic respiration, confirming previous studies. Furthermore, a protein not present in Fe-sufficient roots, dimethyl-8-ribityllumazine (DMRL) synthase, was present in high amounts in root tips from Fe-deficient sugar beet plants and gene transcript levels were higher in Fe-deficient root tips. Also, a marked increase in the relative amounts of the raffinose family of oligosaccharides (RFOs) was observed in Fe-deficient plants, and a further increase in these compounds occurred upon short term Fe resupply. Conclusions The increases in DMRL synthase and in RFO sugars were the major changes induced by Fe deficiency and resupply in root tips of sugar beet plants. Flavin synthesis could be involved in Fe uptake, whereas RFO sugars could be involved in the alleviation of oxidative stress, C trafficking or cell signalling. Our data also confirm the increase in proteins and metabolites related to carbohydrate metabolism and TCA cycle pathways.
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- 2010
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3. Genetic mapping of maize metabolites using high-throughput mass profiling.
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González-Rodríguez T, Pérez-Limón S, Peniche-Pavía H, Rellán-Álvarez R, Sawers RJH, and Winkler R
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- Humans, Chromosome Mapping, Quantitative Trait Loci genetics, Genotype, Phenotype, Zea mays metabolism, Plant Breeding
- Abstract
Plant metabolites are the basis of human nutrition and have biological relevance in ecology. Farmers selected plants with favorable characteristics since prehistoric times and improved the cultivars, but without knowledge of underlying mechanisms. Understanding the genetic basis of metabolite production can facilitate the successful breeding of plants with augmented nutritional value. To identify genetic factors related to the metabolic composition in maize, we generated mass profiles of 198 recombinant inbred lines (RILs) and their parents (B73 and Mo17) using direct-injection electrospray ionization mass spectrometry (DLI-ESI MS). Mass profiling allowed the correct clustering of samples according to genotype. We quantified 71 mass features from grains and 236 mass features from leaf extracts. For the corresponding ions, we identified tissue-specific metabolic 'Quantitative Trait Loci' (mQTLs) distributed across the maize genome. These genetic regions could regulate multiple metabolite biosynthesis pathways. Our findings demonstrate that DLI-ESI MS has sufficient analytical resolution to map mQTLs. These identified genetic loci will be helpful in metabolite-focused maize breeding. Mass profiling is a powerful tool for detecting mQTLs in maize and enables the high-throughput screening of loci responsible for metabolite biosynthesis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)
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- 2023
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4. Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize.
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Hu H, Crow T, Nojoomi S, Schulz AJ, Estévez-Palmas JM, Hufford MB, Flint-Garcia S, Sawers R, Rellán-Álvarez R, Ross-Ibarra J, and Runcie DE
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- Alleles, Genetics, Population, Acclimatization, Zea mays genetics, Adaptation, Physiological genetics
- Abstract
Maize is a staple food of smallholder farmers living in highland regions up to 4,000 m above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggest the maize's adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2022
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5. Genome sequencing reveals evidence of adaptive variation in the genus Zea.
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Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS, Rellán-Álvarez R, Sawers RJH, Liu Q, Yin Y, Ye X, Yan J, Zhang Q, Zhang X, Wu S, Gui S, Wei W, Wang Y, Luo Y, Jiang C, Deng M, Jin M, Jian L, Yu Y, Zhang M, Yang X, Hufford MB, Fernie AR, Warburton ML, Ross-Ibarra J, and Yan J
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- Adaptation, Physiological genetics, Base Sequence, Alleles, Genetic Variation genetics, Zea mays genetics, Plant Breeding
- Abstract
Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2022
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6. ROOT PENETRATION INDEX 3, a major quantitative trait locus associated with root system penetrability in Arabidopsis.
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Bello Bello E, Rico Cambron TY, Ortiz Ramírez LA, Rellán Álvarez R, and Herrera-Estrella L
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- Agar pharmacology, Indoleacetic Acids pharmacology, Quantitative Trait Loci genetics, Soil, Arabidopsis
- Abstract
Soil mechanical impedance precludes root penetration, confining root system development to shallow soil horizons where mobile nutrients are scarce. Using a two-phase-agar system, we characterized Arabidopsis responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show a significant reduction in leaf area, root length, and elongation zone and an increment in root diameter, while those capable of penetrating show only minor morphological effects. Analyses using different auxin-responsive reporter lines, exogenous auxins, and inhibitor treatments suggest that auxin responsiveness and PIN-mediated auxin distribution play an important role in regulating root responses to mechanical impedance. The assessment of 21 Arabidopsis accessions revealed that primary root penetrability varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population derived from Landsberg erecta (Ler-0, with a high primary root penetrability) and Shahdara (Sha, with a low primary root penetrability) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3, ROOT PENETRATION INDEX 3 (q-RPI3), which accounted for 29.98% (logarithm of odds=8.82) of the total phenotypic variation. Employing an introgression line (IL-321) with a homozygous q-RPI3 region from Sha in the Ler-0 genetic background, we demonstrated that q-RPI3 plays a crucial role in root penetrability. This multiscale study reveals new insights into root plasticity during the penetration process in hard agar layers, natural variation, and genetic architecture behind primary root penetrability in Arabidopsis., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2022
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7. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time.
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Barnes AC, Rodríguez-Zapata F, Juárez-Núñez KA, Gates DJ, Janzen GM, Kur A, Wang L, Jensen SE, Estévez-Palmas JM, Crow TM, Kavi HS, Pil HD, Stokes RL, Knizner KT, Aguilar-Rangel MR, Demesa-Arévalo E, Skopelitis T, Pérez-Limón S, Stutts WL, Thompson P, Chiu YC, Jackson D, Muddiman DC, Fiehn O, Runcie D, Buckler ES, Ross-Ibarra J, Hufford MB, Sawers RJH, and Rellán-Álvarez R
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- Alleles, Chromosome Mapping, Genes, Plant, Genetic Linkage, Adaptation, Physiological, Flowers genetics, Flowers metabolism, Gene-Environment Interaction, Phosphatidylcholines metabolism, Phospholipases A1 classification, Phospholipases A1 genetics, Phospholipases A1 metabolism, Plant Proteins classification, Plant Proteins genetics, Plant Proteins metabolism, Zea mays genetics, Zea mays growth & development
- Abstract
Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.
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- 2022
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8. Demonstration of local adaptation in maize landraces by reciprocal transplantation.
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Janzen GM, Aguilar-Rangel MR, Cíntora-Martínez C, Blöcher-Juárez KA, González-Segovia E, Studer AJ, Runcie DE, Flint-Garcia SA, Rellán-Álvarez R, Sawers RJH, and Hufford MB
- Abstract
Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation ( Q
ST ) was greater than neutral allele frequency differentiation ( FST ) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces' native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland-adaptive. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)- Published
- 2022
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9. A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize.
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Perez-Limón S, Li M, Cintora-Martinez GC, Aguilar-Rangel MR, Salazar-Vidal MN, González-Segovia E, Blöcher-Juárez K, Guerrero-Zavala A, Barrales-Gamez B, Carcaño-Macias J, Costich DE, Nieto-Sotelo J, Martinez de la Vega O, Simpson J, Hufford MB, Ross-Ibarra J, Flint-Garcia S, Diaz-Garcia L, Rellán-Álvarez R, and Sawers RJH
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- Acclimatization, Genomics, Phenotype, Adaptation, Physiological genetics, Zea mays genetics, Zea mays metabolism
- Abstract
Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)
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- 2022
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10. The arches and spandrels of maize domestication, adaptation, and improvement.
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Abraham-Juárez MJ, Barnes AC, Aragón-Raygoza A, Tyson D, Kur A, Strable J, and Rellán-Álvarez R
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- Acclimatization, Adaptation, Physiological, Female, Humans, Poaceae, Selection, Genetic, Domestication, Zea mays genetics
- Abstract
People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
- Published
- 2021
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11. Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces.
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Wang L, Josephs EB, Lee KM, Roberts LM, Rellán-Álvarez R, Ross-Ibarra J, and Hufford MB
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- Alleles, Phenotype, Acclimatization genetics, Altitude, Zea mays genetics
- Abstract
Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
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- 2021
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12. Gene regulatory effects of a large chromosomal inversion in highland maize.
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Crow T, Ta J, Nojoomi S, Aguilar-Rangel MR, Torres Rodríguez JV, Gates D, Rellán-Álvarez R, Sawers R, and Runcie D
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- Adaptation, Physiological, Haplotypes, Polymorphism, Genetic, Transcriptome, Zea mays metabolism, Chromosome Inversion, Gene Expression Regulation, Plant, Zea mays genetics
- Abstract
Chromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying an inversion's role in adaptation. In this study, we used large-scale transcriptomic data to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m was introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. However, the specific genetic variants and traits that underlie this adaptation are not known. We created two families segregating for the standard and inverted haplotypes of Inv4m in a common genetic background and measured gene expression effects associated with the inversion across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m across the 9 tissues, including a strong effect on the expression of genes involved in photosynthesis and chloroplast physiology. Although we could not confidently identify the causal alleles within Inv4m, this research accelerates progress towards understanding this inversion and will guide future research on these important genomic features., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
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13. Inoculation with the mycorrhizal fungus Rhizophagus irregularis modulates the relationship between root growth and nutrient content in maize ( Zea mays ssp. mays L.).
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Ramírez-Flores MR, Bello-Bello E, Rellán-Álvarez R, Sawers RJH, and Olalde-Portugal V
- Abstract
Plant root systems play a fundamental role in nutrient and water acquisition. In resource-limited soils, modification of root system architecture is an important strategy to optimize plant performance. Most terrestrial plants also form symbiotic associations with arbuscular mycorrhizal fungi to maximize nutrient uptake. In addition to direct delivery of nutrients, arbuscular mycorrhizal fungi benefit the plant host by promoting root growth. Here, we aimed to quantify the impact of arbuscular mycorrhizal symbiosis on root growth and nutrient uptake in maize. Inoculated plants showed an increase in both biomass and the total content of twenty quantified elements. In addition, image analysis showed mycorrhizal plants to have denser, more branched root systems. For most of the quantified elements, the increase in content in mycorrhizal plants was proportional to root and overall plant growth. However, the increase in boron, calcium, magnesium, phosphorus, sulfur, and strontium was greater than predicted by root system size alone, indicating fungal delivery to be supplementing root uptake., Competing Interests: Rubén Rellán‐Álvarez is a review editor for Plant Direct., (© 2019 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd.)
- Published
- 2019
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14. Co-ordinated Changes in the Accumulation of Metal Ions in Maize (Zea mays ssp. mays L.) in Response to Inoculation with the Arbuscular Mycorrhizal Fungus Funneliformis mosseae.
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Ramírez-Flores MR, Rellán-Álvarez R, Wozniak B, Gebreselassie MN, Jakobsen I, Olalde-Portugal V, Baxter I, Paszkowski U, and Sawers RJH
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- Genotype, Ions, Metabolome, Plant Leaves metabolism, Plant Leaves microbiology, Plant Roots metabolism, Plant Roots microbiology, Principal Component Analysis, Zea mays genetics, Zea mays physiology, Glomeromycota physiology, Metals metabolism, Mycorrhizae physiology, Zea mays metabolism, Zea mays microbiology
- Abstract
Arbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of 19 elements was determined in the roots and leaves of a panel of 30 maize varieties, grown under phosphorus-limiting conditions, with or without inoculation with the fungus Funneliformis mosseae. Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a co-ordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants., (© The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2017
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15. Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences.
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Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, and Chitwood DH
- Abstract
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
- Published
- 2017
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16. Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate.
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Mora-Macías J, Ojeda-Rivera JO, Gutiérrez-Alanís D, Yong-Villalobos L, Oropeza-Aburto A, Raya-González J, Jiménez-Domínguez G, Chávez-Calvillo G, Rellán-Álvarez R, and Herrera-Estrella L
- Subjects
- Arabidopsis Proteins metabolism, Organic Anion Transporters metabolism, Transcription Factors metabolism, Arabidopsis growth & development, Iron metabolism, Malates metabolism, Meristem growth & development, Phosphates metabolism
- Abstract
Low phosphate (Pi) availability constrains plant development and seed production in both natural and agricultural ecosystems. When Pi is scarce, modifications of root system architecture (RSA) enhance the soil exploration ability of the plant and lead to an increase in Pi uptake. In Arabidopsis , an iron-dependent mechanism reprograms primary root growth in response to low Pi availability. This program is activated upon contact of the root tip with low-Pi media and induces premature cell differentiation and the arrest of mitotic activity in the root apical meristem, resulting in a short-root phenotype. However, the mechanisms that regulate the primary root response to Pi-limiting conditions remain largely unknown. Here we report on the isolation and characterization of two low-Pi insensitive mutants ( lpi5 and lpi6 ), which have a long-root phenotype when grown in low-Pi media. Cellular, genomic, and transcriptomic analysis of low-Pi insensitive mutants revealed that the genes previously shown to underlie Arabidopsis Al tolerance via root malate exudation, known as SENSITIVE TO PROTON RHIZOTOXICITY ( STOP1 ) and ALUMINUM ACTIVATED MALATE TRANSPORTER 1 ( ALMT1 ), represent a critical checkpoint in the root developmental response to Pi starvation in Arabidopsis thaliana Our results also show that exogenous malate can rescue the long-root phenotype of lpi5 and lpi6 Malate exudation is required for the accumulation of Fe in the apoplast of meristematic cells, triggering the differentiation of meristematic cells in response to Pi deprivation., Competing Interests: Conflict of interest statement: L.H.-E. and Leon V. Kochian were coauthors on a 2013 publication. This publication was a review article and did not involve any research collaboration.
- Published
- 2017
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17. Grasses suppress shoot-borne roots to conserve water during drought.
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Sebastian J, Yee MC, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP, and Dinneny JR
- Subjects
- Mutation, Plant Roots genetics, Plant Roots metabolism, Plant Shoots genetics, Plant Shoots metabolism, Poaceae genetics, Poaceae metabolism, Setaria Plant genetics, Setaria Plant growth & development, Setaria Plant metabolism, Soil, Zea mays genetics, Zea mays growth & development, Zea mays metabolism, Droughts, Plant Roots growth & development, Plant Shoots growth & development, Poaceae growth & development, Water metabolism
- Abstract
Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.
- Published
- 2016
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18. Environmental Control of Root System Biology.
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Rellán-Álvarez R, Lobet G, and Dinneny JR
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- Nitrogen metabolism, Phosphorus metabolism, Signal Transduction, Water metabolism, Acclimatization, Plant Roots growth & development, Plant Roots metabolism, Plants metabolism, Soil
- Abstract
The plant root system traverses one of the most complex environments on earth. Understanding how roots support plant life on land requires knowing how soil properties affect the availability of nutrients and water and how roots manipulate the soil environment to optimize acquisition of these resources. Imaging of roots in soil allows the integrated analysis and modeling of environmental interactions occurring at micro- to macroscales. Advances in phenotyping of root systems is driving innovation in cross-platform-compatible methods for data analysis. Root systems acclimate to the environment through architectural changes that act at the root-type level as well as through tissue-specific changes that affect the metabolic needs of the root and the efficiency of nutrient uptake. A molecular understanding of the signaling mechanisms that guide local and systemic signaling is providing insight into the regulatory logic of environmental responses and has identified points where crosstalk between pathways occurs.
- Published
- 2016
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19. Plant scientists: GM technology is safe.
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Fahlgren N, Bart R, Herrera-Estrella L, Rellán-Álvarez R, Chitwood DH, and Dinneny JR
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- China, Health, Humans, Plants, Genetically Modified genetics, United States, Zea mays genetics, Food, Genetically Modified adverse effects, Genetic Engineering statistics & numerical data, Plants, Genetically Modified adverse effects
- Published
- 2016
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20. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems.
- Author
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Rellán-Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, and Dinneny JR
- Subjects
- Genes, Reporter, Luminescence, Image Processing, Computer-Assisted methods, Optical Imaging methods, Plant Roots growth & development, Soil
- Abstract
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.
- Published
- 2015
- Full Text
- View/download PDF
21. Iron-dependent modifications of the flower transcriptome, proteome, metabolome, and hormonal content in an Arabidopsis ferritin mutant.
- Author
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Sudre D, Gutierrez-Carbonell E, Lattanzio G, Rellán-Álvarez R, Gaymard F, Wohlgemuth G, Fiehn O, Alvarez-Fernández A, Zamarreño AM, Bacaicoa E, Duy D, García-Mina JM, Abadía J, Philippar K, López-Millán AF, and Briat JF
- Subjects
- Arabidopsis chemistry, Arabidopsis genetics, Arabidopsis growth & development, Arabidopsis Proteins chemistry, Arabidopsis Proteins metabolism, Electrophoresis, Gel, Two-Dimensional, Ferritins metabolism, Flowers chemistry, Flowers genetics, Flowers growth & development, Flowers metabolism, Gene Expression Regulation, Plant, Mass Spectrometry, Mutation, Proteome chemistry, Proteome genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Ferritins genetics, Iron metabolism, Metabolome, Plant Growth Regulators metabolism, Proteome metabolism, Transcriptome
- Abstract
Iron homeostasis is an important process for flower development and plant fertility. The role of plastids in these processes has been shown to be essential. To document the relationships between plastid iron homeostasis and flower biology further, a global study (transcriptome, proteome, metabolome, and hormone analysis) was performed of Arabidopsis flowers from wild-type and triple atfer1-3-4 ferritin mutant plants grown under iron-sufficient or excess conditions. Some major modifications in specific functional categories were consistently observed at these three omic levels, although no significant overlaps of specific transcripts and proteins were detected. These modifications concerned redox reactions and oxidative stress, as well as amino acid and protein catabolism, this latter point being exemplified by an almost 10-fold increase in urea concentration of atfer1-3-4 flowers from plants grown under iron excess conditions. The mutant background caused alterations in Fe-haem redox proteins located in membranes and in hormone-responsive proteins. Specific effects of excess Fe in the mutant included further changes in these categories, supporting the idea that the mutant is facing a more intense Fe/redox stress than the wild type. The mutation and/or excess Fe had a strong impact at the membrane level, as denoted by the changes in the transporter and lipid metabolism categories. In spite of the large number of genes and proteins responsive to hormones found to be regulated in this study, changes in the hormonal balance were restricted to cytokinins, especially in the mutant plants grown under Fe excess conditions.
- Published
- 2013
- Full Text
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22. Nicotianamine functions in the Phloem-based transport of iron to sink organs, in pollen development and pollen tube growth in Arabidopsis.
- Author
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Schuler M, Rellán-Álvarez R, Fink-Straube C, Abadía J, and Bauer P
- Subjects
- Arabidopsis genetics, Arabidopsis growth & development, Azetidinecarboxylic Acid metabolism, Biological Transport, Citrates metabolism, Flowers metabolism, Gene Expression Regulation, Plant, Mutation, Phloem metabolism, Plant Development, Plant Leaves genetics, Plant Leaves metabolism, Plant Roots metabolism, Pollen genetics, Pollen metabolism, Pollen Tube growth & development, Pollen Tube metabolism, Zinc metabolism, Arabidopsis metabolism, Azetidinecarboxylic Acid analogs & derivatives, Iron metabolism, Pollen growth & development
- Abstract
The metal chelator nicotianamine promotes the bioavailability of Fe and reduces cellular Fe toxicity. For breeding Fe-efficient crops, we need to explore the fundamental impact of nicotianamine on plant development and physiology. The quadruple nas4x-2 mutant of Arabidopsis thaliana cannot synthesize any nicotianamine, shows strong leaf chlorosis, and is sterile. To date, these phenotypes have not been fully explained. Here, we show that sink organs of this mutant were Fe deficient, while aged leaves were Fe sufficient. Upper organs were also Zn deficient. We demonstrate that transport of Fe to aged leaves relied on citrate, which partially complemented the loss of nicotianamine. In the absence of nicotianamine, Fe accumulated in the phloem. Our results show that rather than enabling the long-distance movement of Fe in the phloem (as is the case for Zn), nicotianamine facilitates the transport of Fe from the phloem to sink organs. We delimit nicotianamine function in plant reproductive biology and demonstrate that nicotianamine acts in pollen development in anthers and pollen tube passage in the carpels. Since Fe and Zn both enhance pollen germination, a lack of either metal may contribute to the reproductive defect. Our study sheds light on the physiological functions of nicotianamine.
- Published
- 2012
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23. Oxidative stress is a consequence, not a cause, of aluminum toxicity in the forage legume Lotus corniculatus.
- Author
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Navascués J, Pérez-Rontomé C, Sánchez DH, Staudinger C, Wienkoop S, Rellán-Álvarez R, and Becana M
- Subjects
- Antioxidants metabolism, Carboxylic Acids metabolism, Gene Expression Regulation, Plant drug effects, Genes, Plant genetics, Lotus genetics, Lotus growth & development, Metabolomics, Nutritional Physiological Phenomena drug effects, Plant Leaves drug effects, Plant Leaves genetics, Plant Leaves metabolism, Plant Proteins genetics, Plant Proteins metabolism, Plant Roots cytology, Plant Roots drug effects, Plant Roots genetics, Plant Roots metabolism, Protein Isoforms metabolism, Proteome metabolism, Proteomics, RNA, Messenger genetics, RNA, Messenger metabolism, Reactive Oxygen Species metabolism, Stress, Physiological drug effects, Stress, Physiological genetics, Aluminum toxicity, Lotus drug effects, Lotus metabolism, Oxidative Stress drug effects
- Abstract
• Aluminum (Al) toxicity is a major limiting factor of crop production on acid soils, but the implication of oxidative stress in this process is controversial. A multidisciplinary approach was used here to address this question in the forage legume Lotus corniculatus. • Plants were treated with low Al concentrations in hydroponic culture, and physiological and biochemical parameters, together with semiquantitative metabolic and proteomic profiles, were determined. • The exposure of plants to 10 μM Al inhibited root and leaf growth, but had no effect on the production of reactive oxygen species or lipid peroxides. By contrast, exposure to 20 μM Al elicited the production of superoxide radicals, peroxide and malondialdehyde. In response to Al, there was a progressive replacement of the superoxide dismutase isoforms in the cytosol, a loss of ascorbate and consistent changes in amino acids, sugars and associated enzymes. • We conclude that oxidative stress is not a causative factor of Al toxicity. The increased contents in roots of two powerful Al chelators, malic and 2-isopropylmalic acids, together with the induction of an Al-activated malate transporter gene, strongly suggest that both organic acids are implicated in Al detoxification. The effects of Al on key proteins involved in cytoskeleton dynamics, protein turnover, transport, methylation reactions, redox control and stress responses underscore a metabolic dysfunction, which affects multiple cellular compartments, particularly in plants exposed to 20 μM Al., (© 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.)
- Published
- 2012
- Full Text
- View/download PDF
24. Metabolite profile changes in xylem sap and leaf extracts of strategy I plants in response to iron deficiency and resupply.
- Author
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Rellán-Álvarez R, El-Jendoubi H, Wohlgemuth G, Abadía A, Fiehn O, Abadía J, and Alvarez-Fernández A
- Abstract
The metabolite profile changes induced by Fe deficiency in leaves and xylem sap of several Strategy I plant species have been characterized. We have confirmed that Fe deficiency causes consistent changes both in the xylem sap and leaf metabolite profiles. The main changes in the xylem sap metabolite profile in response to Fe deficiency include consistent decreases in amino acids, N-related metabolites and carbohydrates, and increases in TCA cycle metabolites. In tomato, Fe resupply causes a transitory flush of xylem sap carboxylates, but within 1 day the metabolite profile of the xylem sap from Fe-deficient plants becomes similar to that of Fe-sufficient controls. The main changes in the metabolite profile of leaf extracts in response to Fe deficiency include consistent increases in amino acids and N-related metabolites, carbohydrates and TCA cycle metabolites. In leaves, selected pairs of amino acids and TCA cycle metabolites show high correlations, with the sign depending of the Fe status. These data suggest that in low photosynthesis, C-starved Fe-deficient plants anaplerotic reactions involving amino acids can be crucial for short-term survival.
- Published
- 2011
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25. Towards a knowledge-based correction of iron chlorosis.
- Author
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Abadía J, Vázquez S, Rellán-Álvarez R, El-Jendoubi H, Abadía A, Alvarez-Fernández A, and López-Millán AF
- Subjects
- Chloroplasts metabolism, Ethylenediamines metabolism, FMN Reductase metabolism, Ferric Compounds analysis, Homeostasis, Iron analysis, Iron Chelating Agents metabolism, Mitochondria metabolism, Phloem metabolism, Plant Diseases prevention & control, Plant Leaves metabolism, Plant Proteins metabolism, Protein Transport, Prunus metabolism, Soil chemistry, Xylem metabolism, Crops, Agricultural metabolism, Ferric Compounds metabolism, Fertilizers, Iron metabolism
- Abstract
Iron (Fe) deficiency-induced chlorosis is a major nutritional disorder in crops growing in calcareous soils. Iron deficiency in fruit tree crops causes chlorosis, decreases in vegetative growth and marked fruit yield and quality losses. Therefore, Fe fertilizers, either applied to the soil or delivered to the foliage, are used every year to control Fe deficiency in these crops. On the other hand, a substantial body of knowledge is available on the fundamentals of Fe uptake, long and short distance Fe transport and subcellular Fe allocation in plants. Most of this basic knowledge, however, applies only to Fe deficiency, with studies involving Fe fertilization (i.e., with Fe-deficient plants resupplied with Fe) being still scarce. This paper reviews recent developments in Fe-fertilizer research and the state-of-the-art of the knowledge on Fe acquisition, transport and utilization in plants. Also, the effects of Fe-fertilization on the plant responses to Fe deficiency are reviewed. Agronomical Fe-fertilization practices should benefit from the basic knowledge on plant Fe homeostasis already available; this should be considered as a long-term goal that can optimize fertilizer inputs, reduce grower's costs and minimize the environmental impact of fertilization., (Copyright © 2011 Elsevier Masson SAS. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
26. Metabolic response in roots of Prunus rootstocks submitted to iron chlorosis.
- Author
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Jiménez S, Ollat N, Deborde C, Maucourt M, Rellán-Álvarez R, Moreno MÁ, and Gogorcena Y
- Subjects
- Chromatography, Liquid, Magnetic Resonance Spectroscopy, Spectrometry, Mass, Electrospray Ionization, Iron metabolism, Plant Roots metabolism, Prunus metabolism
- Abstract
Iron deficiency induces several responses to iron shortage in plants. Metabolic changes occur to sustain the increased iron uptake capacity of Fe-deficient plants. We evaluated the metabolic changes of three Prunus rootstocks submitted to iron chlorosis and their different responses for tolerance using measurements of metabolites and enzymatic activities. The more tolerant rootstocks Adesoto (Prunus insititia) and GF 677 (Prunus amygdalus×Prunus persica), and the more sensitive Barrier (P. persica×Prunus davidiana) were grown hydroponically in iron-sufficient and -deficient conditions over two weeks. Sugar, organic and amino acid concentrations of root tips were determined after two weeks of iron shortage by proton nuclear magnetic resonance spectroscopy of extracts. Complementary analyses of organic acids were performed by liquid chromatography coupled to mass spectrometry. The major soluble sugars found were glucose and sucrose. The major organic acids were malic and citric acids, and the major amino acid was asparagine. Iron deficiency increased root sucrose, total organic and amino acid concentrations and phosphoenolpyruvate carboxylase activity. After two weeks of iron deficiency, the malic, citric and succinic acid concentrations increased in the three rootstocks, although no significant differences were found among genotypes with different tolerance to iron chlorosis. The tolerant rootstock Adesoto showed higher total organic and amino acid concentrations. In contrast, the susceptible rootstock Barrier showed lower total amino acid concentration and phosphoenolpyruvate carboxylase activity values. These results suggest that the induction of this enzyme activity under iron deficiency, as previously shown in herbaceous plants, indicates the tolerance level of rootstocks to iron chlorosis. The analysis of other metabolic parameters, such as organic and amino acid concentrations, provides complementary information for selection of genotypes tolerant to iron chlorosis., (Copyright © 2010 Elsevier GmbH. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
27. Rapid alteration of cellular redox homeostasis upon exposure to cadmium and mercury in alfalfa seedlings.
- Author
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Ortega-Villasante C, Hernández LE, Rellán-Álvarez R, Del Campo FF, and Carpena-Ruiz RO
- Subjects
- Cadmium metabolism, Gene Expression drug effects, Kinetics, Medicago sativa drug effects, Medicago sativa growth & development, Mercury metabolism, Oxidation-Reduction, Oxidative Stress, Plant Proteins genetics, Plant Proteins metabolism, Plant Proteins physiology, Reactive Oxygen Species metabolism, Reverse Transcriptase Polymerase Chain Reaction, Seedlings drug effects, Seedlings growth & development, Cadmium pharmacology, Homeostasis drug effects, Medicago sativa metabolism, Mercury pharmacology, Seedlings metabolism
- Abstract
Here, the kinetics of oxidative stress responses of alfalfa (Medicago sativa) seedlings to cadmium (Cd) and mercury (Hg) (0, 3, 10 and 30 microm) exposure, expanding from a few minutes to 24 h, were studied. Intracellular oxidative stress was analysed using 2',7'-dichlorofluorescin diacetate and extracellular hydrogen peroxide (H(2)O(2)) production was studied with Amplex Red. Growth inhibition, concentrations of ascorbate, glutathione (GSH), homoglutathione (hGSH), Cd and Hg, ascorbate peroxidase (APX) activity, and expression of genes related to GSH metabolism were also determined. Both Cd and Hg increased cellular reactive oxygen species (ROS) production and extracellular H(2)O(2) formation, but in different ways. The increase was mild and slow with Cd, but more rapid and transient with Hg. Hg treatments also caused a higher cell death rate, significant oxidation of hGSH, as well as increased APX activity and transient overexpression of glutathione reductase 2, glutamylcysteinyl synthetase, and homoglutathione synthetase genes. However, Cd caused minor alterations. Hg accumulation was one order of magnitude higher than Cd accumulation. The different kinetics of early physiological responses in vivo to Cd and Hg might be relevant to the characterization of their mechanisms of toxicity. Thus, high accumulation of Hg might explain the metabolism poisoning observed in Hg-treated seedlings.
- Published
- 2007
- Full Text
- View/download PDF
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