@article{he_gage_rellan-alvarez_xiang_2024, title={Swin-Roleaf: A new method for characterizing leaf azimuth angle in large-scale maize plants}, volume={224}, ISSN={["1872-7107"]}, url={https://doi.org/10.1016/j.compag.2024.109120}, DOI={10.1016/j.compag.2024.109120}, journal={COMPUTERS AND ELECTRONICS IN AGRICULTURE}, author={He, Weilong and Gage, Joseph L. and Rellan-Alvarez, Ruben and Xiang, Lirong}, year={2024}, month={Sep} }
 @article{perez-limón_li_cintora-martinez_aguilar-rangel_salazar-vidal_gonzález-segovia_blöcher-juárez_guerrero-zavala_barrales-gamez_carcaño-macias_et al._2022, title={A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize}, volume={12}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkab447}, DOI={10.1093/g3journal/jkab447}, abstractNote={AbstractGenerations 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.}, number={3}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={Perez-Limón, Sergio and Li, Meng and Cintora-Martinez, G Carolina and Aguilar-Rangel, M Rocio and Salazar-Vidal, M Nancy and González-Segovia, Eric and Blöcher-Juárez, Karla and Guerrero-Zavala, Alejandro and Barrales-Gamez, Benjamin and Carcaño-Macias, Jessica and et al.}, editor={Akhunov, E DEditor}, year={2022}, month={Jan} }
 @article{hu_crow_nojoomi_schulz_estévez-palmas_hufford_flint-garcia_sawers_rellán-álvarez_ross-ibarra_et al._2022, title={Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize}, volume={39}, ISSN={0737-4038 1537-1719}, url={http://dx.doi.org/10.1093/molbev/msac239}, DOI={10.1093/molbev/msac239}, abstractNote={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.}, number={11}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Hu, Haixiao and Crow, Taylor and Nojoomi, Saghi and Schulz, Aimee J and Estévez-Palmas, Juan M and Hufford, Matthew B and Flint-Garcia, Sherry and Sawers, Ruairidh and Rellán-Álvarez, Rubén and Ross-Ibarra, Jeffrey and et al.}, editor={Wittkopp, PatriciaEditor}, year={2022}, month={Nov} }
 @article{barnes_rodriguez-zapata_juarez-nunez_gates_janzen_kur_wang_jensen_estevez-palmas_crow_et al._2022, title={An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time}, volume={119}, ISSN={["1091-6490"]}, url={http://dx.doi.org/10.1073/pnas.2100036119}, DOI={10.1073/pnas.2100036119}, abstractNote={Native Americans domesticated maize (Zea maysssp.mays) from lowland teosinteparviglumis(Zea maysssp.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 identifyHigh 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 atHPC1,with the highlandHPC1allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maizeHPC1variant 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 ofHPC1via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highlandHPC1allele entered cultivated maize by introgression from the wild highland teosinteZea maysssp.mexicanaand has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus,HPC1introgressed from teosintemexicanaunderlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.}, number={27}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Barnes, Allison C. and Rodriguez-Zapata, Fausto and Juarez-Nunez, Karla A. and Gates, Daniel J. and Janzen, Garrett M. and Kur, Andi and Wang, Li and Jensen, Sarah E. and Estevez-Palmas, Juan M. and Crow, Taylor M. and et al.}, year={2022}, month={Jul} }
 @article{janzen_aguilar-rangel_cintora-martinez_blocher-juarez_gonzalez-segovia_studer_runcie_flint-garcia_rellan-alvarez_sawers_et al._2022, title={Demonstration of local adaptation in maize landraces by reciprocal transplantation}, volume={4}, ISSN={["1752-4571"]}, DOI={10.1111/eva.13372}, abstractNote={AbstractPopulations 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 (QST) 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.}, journal={EVOLUTIONARY APPLICATIONS}, author={Janzen, Garrett M. and Aguilar-Rangel, Maria Rocio and Cintora-Martinez, Carolina and Blocher-Juarez, Karla Azucena and Gonzalez-Segovia, Eric and Studer, Anthony J. and Runcie, Daniel E. and Flint-Garcia, Sherry A. and Rellan-alvarez, Ruben and Sawers, Ruairidh J. H. and et al.}, year={2022}, month={Apr} }
 @article{gonzález-rodríguez_pérez-limón_peniche-pavía_rellán-álvarez_sawers_winkler_2023, title={Genetic mapping of maize metabolites using high-throughput mass profiling}, volume={326}, ISSN={0168-9452}, url={http://dx.doi.org/10.1016/j.plantsci.2022.111530}, DOI={10.1016/j.plantsci.2022.111530}, abstractNote={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.}, journal={Plant Science}, publisher={Elsevier BV}, author={González-Rodríguez, Tzitziki and Pérez-Limón, Sergio and Peniche-Pavía, Héctor and Rellán-Álvarez, Rubén and Sawers, Ruairidh J.H. and Winkler, Robert}, year={2023}, month={Jan}, pages={111530} }
 @article{chen_luo_jin_yang_liu_peng_li_phillips_cameron_bernal_et al._2022, title={Genome sequencing reveals evidence of adaptive variation in the genus Zea}, volume={10}, ISSN={["1546-1718"]}, DOI={10.1038/s41588-022-01184-y}, abstractNote={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.}, journal={NATURE GENETICS}, author={Chen, Lu and Luo, Jingyun and Jin, Minliang and Yang, Ning and Liu, Xiangguo and Peng, Yong and Li, Wenqiang and Phillips, Alyssa and Cameron, Brenda and Bernal, Julio S. and et al.}, year={2022}, month={Oct} }
 @article{bello bello_rico cambron_abril ortiz ramirez_rellan alvarez_herrera-estrella_2022, title={ROOT PENETRATION INDEX 3, a major quantitative trait locus associated with root system penetrability in Arabidopsis}, volume={5}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erac188}, abstractNote={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.}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Bello Bello, Elohim and Rico Cambron, Thelma Y. and Abril Ortiz Ramirez, Lesly and Rellan alvarez, Ruben and Herrera-Estrella, Luis}, year={2022}, month={May} }
 @article{janzen_aguilar-rangel_cíntora-martínez_blöcher-juárez_gonzález-segovia_studer_runcie_flint-garcia_rellán-álvarez_sawers_et al._2021, title={Demonstration of local adaptation of maize landraces by reciprocal transplantation}, url={https://doi.org/10.1101/2021.03.25.437076}, DOI={10.1101/2021.03.25.437076}, abstractNote={AbstractPopulations 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, as well as reported highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparison 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. While population genetic structure largely recapitulates drift during post-domestication dispersal, landrace phenotypes reflect adaptations to native elevation. Quantitative traitQSTwas greater than neutralFSTfor many traits, signaling divergent 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 our Mexican sites. Highland populations expressed generally higher anthocyanin pigmentation than lowland populations, and more so in the highland site than in the lowland site. Macrohair density was largely non-plastic, and Mexican landraces and highland landraces were generally more pilose. Analysis ofδ13C indicated that lowland populations may have lower WUE. Each population demonstrated garden-specific correlations between highland trait expression and fitness, with stronger positive correlations in the highland site.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.}, author={Janzen, Garrett M. and Aguilar-Rangel, María Rocío and Cíntora-Martínez, Carolina and Blöcher-Juárez, Karla Azucena and González-Segovia, Eric and Studer, Anthony J. and Runcie, Daniel E. and Flint-Garcia, Sherry A. and Rellán-Álvarez, Rubén and Sawers, Ruairidh J. H. and et al.}, year={2021}, month={Mar} }
 @article{wang_josephs_lee_roberts_rellán-álvarez_ross-ibarra_hufford_2021, title={Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces}, volume={38}, ISSN={1537-1719}, url={http://dx.doi.org/10.1093/molbev/msab119}, DOI={10.1093/molbev/msab119}, abstractNote={AbstractConvergent 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.}, number={9}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Wang, Li and Josephs, Emily B and Lee, Kristin M and Roberts, Lucas M and Rellán-Álvarez, Rubén and Ross-Ibarra, Jeffrey and Hufford, Matthew B}, editor={Purugganan, MichaelEditor}, year={2021}, month={Apr}, pages={3567–3580} }
 @article{bello_cambron_álvarez_estrella_2021, title={ROOT PENETRATION INDEX 3, a major quantitative trait locus (QTL) associated with root system penetrability in Arabidopsis}, url={https://doi.org/10.1101/2021.12.23.473296}, DOI={10.1101/2021.12.23.473296}, abstractNote={AbstractSoil 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 thaliana responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show drastic changes in shoot and root morphology, while those capable of penetrating have only minor morphological effects. The assessment of 21 Arabidopsis accessions revealed that primary root penetrability (PRP) varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population (RIL) derived from Landsberg erecta (Ler-0, with a high PRP) and Shahdara (Sha, with a low PRP) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3 (q-RPI3), which accounted for 29.98% (LOD = 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 revels new insights into root plasticity during the penetration process in hard agar layers, natural variation and genetic architecture behind primary root penetrability in Arabidopsis.HighlightWe found a wide natural variation in the capacity of Arabidopsis accessions to penetrate hard agar layers. Using a Ler-0 x Sha recombinant inbred population, a major-effect QTL (q-RPI3) strongly associated with root penetrability of compact agar layers was identified.}, author={Bello, Elohim Bello and Cambron, Thelma Y. Rico and Álvarez, Rubén Rellán and Estrella, Luis Herrera}, year={2021}, month={Dec} }
 @book{barnes_rodrı́guez-zapata fausto_blöcher-juárez_gates_kur_wang_janzen_jensen_estévez-palmas_crow_et al._2021, title={Teosinte introgression modulates phosphatidylcholine levels and induces early maize flowering time}, volume={1}, url={http://dx.doi.org/10.1101/2021.01.25.426574}, DOI={10.1101/2021.01.25.426574}, abstractNote={AbstractNative Americans domesticated maize (Zea maysssp.mays) from lowland teosinteparviglumis(Zea maysssp.parviglumis) in the warm Mexican southwest and brought it to the highlands of México 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 identifyHigh 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 atHPC1, with the highlandHPC1allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maizeHPC1variant 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 ofHPC1via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highlandHPC1allele entered cultivated maize by introgression from the wild highland teosinteZea maysssp.mexicanaand has been maintained in maize breeding lines from the Northern US, Canada and Europe. Thus,HPC1introgressed from teosintemexicanaunderlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.}, journal={[]}, institution={Cold Spring Harbor Laboratory}, author={Barnes, Allison C and Rodrı́guez-Zapata Fausto and Blöcher-Juárez, Karla A and Gates, Dan J and Kur, Andi and Wang, Li and Janzen, Garrett M and Jensen, Sarah E and Estévez-Palmas, Juan M and Crow, Taylor M and et al.}, year={2021}, month={Jan} }
 @misc{abraham-juarez_barnes_aragon-raygoza_tyson_kur_strable_rellan-alvarez_2021, title={The arches and spandrels of maize domestication, adaptation, and improvement}, volume={64}, ISSN={["1879-0356"]}, url={https://doi.org/10.1016/j.pbi.2021.102124}, DOI={10.1016/j.pbi.2021.102124}, abstractNote={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.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, publisher={Elsevier BV}, author={Abraham-Juarez, Maria Jazmin and Barnes, Allison C. and Aragon-Raygoza, Alejandro and Tyson, Destiny and Kur, Andi and Strable, Josh and Rellan-Alvarez, Ruben}, year={2021}, month={Dec} }
 @article{crow_ta_nojoomi_aguilar-rangel_torres rodríguez_gates_rellán-álvarez_sawers_runcie_2020, title={Gene regulatory effects of a large chromosomal inversion in highland maize}, volume={16}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1009213}, DOI={10.1371/journal.pgen.1009213}, abstractNote={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.}, number={12}, journal={PLOS Genetics}, publisher={Public Library of Science (PLoS)}, author={Crow, Taylor and Ta, James and Nojoomi, Saghi and Aguilar-Rangel, M. Rocío and Torres Rodríguez, Jorge Vladimir and Gates, Daniel and Rellán-Álvarez, Rubén and Sawers, Ruairidh and Runcie, Daniel}, editor={Springer, Nathan M.Editor}, year={2020}, month={Dec}, pages={e1009213} }
 @book{wang_josephs_lee_roberts_rellán-álvarez_ross-ibarra_hufford_2020, title={Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces}, url={http://dx.doi.org/10.1101/2020.07.31.227629}, DOI={10.1101/2020.07.31.227629}, abstractNote={AbstractConvergent 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 strong evidence of parallel adaptation at the level of individual SNPs, genes and pathways in four independent highland maize populations, even though most SNPs show unique patterns of local adaptation. The majority of selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands. 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.}, number={227629227629}, author={Wang, Li and Josephs, Emily B. and Lee, Kristin M. and Roberts, Lucas M. and Rellán-Álvarez, Rubén and Ross-Ibarra, Jeffrey and Hufford, Matthew B.}, year={2020}, month={Aug} }
 @misc{gene regulatory effects of a large chromosomal inversion in highland maize_2019, url={http://dx.doi.org/10.1101/861583}, DOI={10.1101/861583}, abstractNote={AbstractChromosomal 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 that underlie an inversion’s role in adaption. In this study, we explore how large-scale transcriptomic data can be used 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 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. First, using a large publicly available association mapping panel, we confirmed that Inv4m is associated with locally adaptive agronomic phenotypes, but only in highland fields. Second, we created two families segregating for standard and inverted haplotypess of Inv4m in a isogenic B73 background, and measured gene expression variation association with Inv4m 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, and speculate that the genetic basis of its effects on adaptive traits is distributed across many separate functional variants.Author SummaryChromosomal inversions are an important type of genomic structural variant. However, mapping causal alleles within their boundaries is difficult because inversions suppress recombination between homologous chromosomes. This means that inversions, regardless of their size, are inherited as a unit. We leveraged the high-dimensional phenotype of gene expression as a tool to study the genetics of a large chromosomal inversion found in highland maize populations in Mexico - Inv4m. We grew plants carrying multiple versions of Inv4m in a common genetic background, and quantified the transcriptional reprogramming induced by alternative alleles at the locus. Inv4m has been shown in previous studies to have a large effect on flowering, but we show that the functional variation within Inv4m affects many developmental and physiological processes.Author ContributionsT. Crow, R. Rellan-Alvarez, R. Sawers and D. Runcie conceived and designed the experiment. M. Aguilar-Rangel, J. Rodrǵuez, R. Rellan-Alvarez and R. Sawers generated the segregating families. T. Crow, J. Ta, S. Nojoomi, M. Aguilar-Rangel, J. Rodrǵuez D. Gates, D. Runcie performed the experiment. T. Crow, D. Gates, D. Runcie analyzed the data. T. Crow, D. Runcie wrote the original manuscript, and R. Rellan-Alvarez and R. Sawers provided review and editing.}, journal={[Biorxiv]}, year={2019}, month={Dec} }
 @article{rosario ramirez-flores_bello-bello_rellan-alvarez_sawers_olalde-portugal_2019, title={Inoculation with the mycorrhizal fungus Rhizophagus irregularis modulates the relationship between root growth and nutrient content in maize (Zea mays ssp. mays L.)}, volume={3}, ISSN={["2475-4455"]}, DOI={10.1002/pld3.192}, abstractNote={AbstractPlant 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.}, number={12}, journal={PLANT DIRECT}, author={Rosario Ramirez-Flores, M. and Bello-Bello, Elohim and Rellan-Alvarez, Ruben and Sawers, Ruairidh J. H. and Olalde-Portugal, Victor}, year={2019}, month={Dec} }
 @article{gates_runcie_janzen_navarro_willcox_sonder_snodgrass_rodríguez-zapata_sawers_rellán-álvarez_et al._2019, title={Single-gene resolution of locally adaptive genetic variation in Mexican maize}, volume={7}, url={http://dx.doi.org/10.1101/706739}, DOI={10.1101/706739}, abstractNote={AbstractThreats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.}, journal={[Biorxiv]}, publisher={Cold Spring Harbor Laboratory}, author={Gates, Daniel J and Runcie, Dan and Janzen, Garrett M. and Navarro, Alberto Romero and Willcox, Martha and Sonder, Kai and Snodgrass, Samantha J. and Rodríguez-Zapata, Fausto and Sawers, Ruairidh J. H. and Rellán-Álvarez, Rubén and et al.}, year={2019}, month={Jul} }
 @article{ramírez-flores_rellán-álvarez_wozniak_gebreselassie_jakobsen_olalde-portugal_baxter_paszkowski_sawers_2017, title={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}, volume={58}, ISSN={0032-0781 1471-9053}, url={http://dx.doi.org/10.1093/pcp/pcx100}, DOI={10.1093/pcp/pcx100}, abstractNote={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 nineteen elements was determined in the roots and leaves of a panel of thirty 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 coordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants. Abbreviations NC non-colonized M mycorrhizal SDW shoot dry weight ICP-MS inductively coupled plasma mass spectrometry PC principal component}, number={10}, journal={Plant and Cell Physiology}, publisher={Oxford University Press (OUP)}, author={Ramírez-Flores, M Rosario and Rellán-Álvarez, Rubén and Wozniak, Barbara and Gebreselassie, Mesfin-Nigussie and Jakobsen, Iver and Olalde-Portugal, Víctor and Baxter, Ivan and Paszkowski, Uta and Sawers, Ruairidh J H}, year={2017}, month={Aug}, pages={1689–1699} }
 @misc{rellan-alvarez_2017, title={Convergent phospholipid metabolism in highland adapted maize?}, author={Rellan-Alvarez, R}, year={2017} }
 @misc{rellan-alvarez_2017, title={Identification of phospholipid metabolic patterns involved in maize adaptation to highland conditions}, author={Rellan-Alvarez, R.}, year={2017} }
 @misc{rellan-alvarez_2017, title={Identification of phospholipid metabolic patterns involved in maize adaptation to low phosphorus and cold conditions}, author={Rellan-Alvarez, R.}, year={2017} }
 @article{mora-macías_ojeda-rivera_gutiérrez-alanís_yong-villalobos_oropeza-aburto_raya-gonzález_jiménez-domínguez_chávez-calvillo_rellán-álvarez_herrera-estrella_et al._2017, title={Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate}, volume={114}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1701952114}, DOI={10.1073/pnas.1701952114}, abstractNote={Significance
          
            Phosphate (Pi) deficiency constrains plant development and productivity in both natural and agricultural ecosystems. An interaction among Pi and Fe availability controls the developmental program that allows the
            Arabidopsis
            root system to more effectively explore the topsoil where Pi accumulates. Analysis of mutants unable to establish root architecture responses to low Pi allowed the identification of mutant alleles of
            STOP1
            (a transcription factor) and
            ALMT1
            (a malate transporter), two genes previously reported to play a role in the malate-mediated tolerance to toxic levels of aluminum. We show that these genes underlie a malate-exudation–dependent mechanism of Fe relocation in the root apical meristem that is essential for reprogramming root growth under low-Pi conditions.
          }, number={17}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Mora-Macías, Javier and Ojeda-Rivera, Jonathan Odilón and Gutiérrez-Alanís, Dolores and Yong-Villalobos, Lenin and Oropeza-Aburto, Araceli and Raya-González, Javier and Jiménez-Domínguez, Gabriel and Chávez-Calvillo, Gabriela and Rellán-Álvarez, Rubén and Herrera-Estrella, Luis and et al.}, year={2017}, month={Apr}, pages={E3563–E3572} }
 @article{bucksch_atta-boateng_azihou_battogtokh_baumgartner_binder_braybrook_chang_coneva_dewitt_et al._2017, title={Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences}, volume={8}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2017.00900}, DOI={10.3389/fpls.2017.00900}, abstractNote={Plant morphology is inherently mathematical in that morphology describes plant form and architecture with geometrical and topological descriptors. The geometries and topologies of leaves, flowers, roots, shoots and their spatial arrangements have fascinated plant biologists and mathematicians alike. Beyond providing aesthetic inspiration, quantifying plant morphology has become pressing in an era of climate change and a growing human population. Modifying plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems with fewer natural resources. In this white paper, we begin with an overview of the mathematical models applied to quantify patterning in plants. We then explore fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leafs in air streams. We end with a discussion concerning the incorporation of plant morphology into educational programs. This strategy focuses on synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. This white paper arose from bringing mathematicians and biologists together at the National Institute for Mathematical and Biological Synthesis (NIMBioS) workshop titled “Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences” held at the University of Tennessee, Knoxville in September, 2015. Never has the need to quantify plant morphology been more imperative. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Bucksch, Alexander and Atta-Boateng, Acheampong and Azihou, Akomian F. and Battogtokh, Dorjsuren and Baumgartner, Aly and Binder, Brad M. and Braybrook, Siobhan A. and Chang, Cynthia and Coneva, Viktoirya and DeWitt, Thomas J. and et al.}, year={2017}, month={Jun} }
 @inproceedings{rellan-alvarez_2017, title={The Role of Phospholipid Metabolism in Maize Adaptation to Low Phosphorus and Cold Conditions}, author={Rellan-Alvarez, R}, year={2017} }
 @misc{rellan-alvarez_2017, title={Towards and understanding of maize adaptation to highlands using a combination of lipidomics and quantitative and population genetics}, author={Rellan-Alvarez, R}, year={2017} }
 @article{rellán-álvarez_lobet_dinneny_2016, title={Environmental Control of Root System Biology}, volume={67}, url={http://dx.doi.org/10.1146/annurev-arplant-043015-111848}, DOI={10.1146/annurev-arplant-043015-111848}, abstractNote={ 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. }, note={PMID: 26905656}, number={1}, journal={Annual Review of Plant Biology}, author={Rellán-Álvarez, Rubén and Lobet, Guillaume and Dinneny, José R.}, year={2016}, pages={null} }
 @article{sebastian_yee_viana_rellán-?lvarez_feldman_priest_trontin_lee_jiang_baxter_et al._2016, title={Grasses suppress shoot-borne roots to conserve water during drought}, volume={113}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84982743617&partnerID=MN8TOARS}, DOI={10.1073/pnas.1604021113}, abstractNote={Significance
          Grasses, whose members constitute key food and bioenergy crops worldwide, use unique developmental programs to establish the root system from the shoot. Shoot-borne crown roots originate near the soil surface and provide the main conduits through which the plant takes up water and nutrients. We show that crown root development is the major target of drought stress signaling. Water deficit-triggered crown root arrest provides an important mechanism to conserve water under drought, and this response is widely conserved across grass species. Substantial phenotypic variation exists in maize for this trait, which may be a useful target in breeding efforts to improve drought tolerance.}, number={31}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Sebastian, J. and Yee, M.-C. and Viana, W.G. and Rellán-?lvarez, R. and Feldman, M. and Priest, H.D. and Trontin, C. and Lee, T. and Jiang, H. and Baxter, I. and et al.}, year={2016}, pages={8861–8866} }
 @misc{rellan-alvarez_2016, title={Invited seminar Multidimensional mapping of root responses to soil environmental cues using a luminescence-based imaging system}, author={Rellan-Alvarez, R}, year={2016} }
 @article{fahlgren_bart_herrera-estrella_rellan-alvarez_chitwood_dinneny_2016, title={Plant scientists: GM technology is safe}, volume={351}, ISSN={0036-8075 1095-9203}, url={http://dx.doi.org/10.1126/science.351.6275.824-a}, DOI={10.1126/science.351.6275.824-a}, abstractNote={The American Society of Plant Biologists (ASPB) “supports the continued responsible use of genetic engineering… as an effective tool for advancing food security and reducing the negative environmental impacts of agriculture” ([ 1 ][1]). A recent petition advocating the ASPB position collected}, number={6275}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Fahlgren, N. and Bart, R. and Herrera-Estrella, L. and Rellan-Alvarez, R. and Chitwood, D. H. and Dinneny, J. R.}, year={2016}, month={Feb}, pages={824–824} }
 @inproceedings{rellan-alvarez_2016, title={The role of polar lipid metabolism reorganization in maize adaptation to low phosphorus soils of the Trans-Mexican volcanic belt highlands}, author={Rellan-Alvarez, R}, year={2016} }
 @misc{rellan-alvarez_2016, title={Towards a faster, more open and collaborative science. The future of scientific publishing beyond journals and impact factors}, author={Rellan-Alvarez, r}, year={2016} }
 @article{rellán-álvarez_lobet_lindner_pradier_sebastian_yee_geng_trontin_larue_schrager-lavelle_et al._2015, title={GLO-Roots: An imaging platform enabling multidimensional characterization of soil-grown root systems}, volume={4}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84943802725&partnerID=MN8TOARS}, DOI={10.7554/eLife.07597}, abstractNote={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.}, number={AUGUST2015}, journal={eLife}, publisher={eLife Sciences Organisation, Ltd.}, author={Rellán-Álvarez, Rubén and Lobet, Guillaume and Lindner, Heike and Pradier, Pierre-Luc and Sebastian, Jose and Yee, Muh-Ching and Geng, Yu and Trontin, Charlotte and LaRue, Therese and Schrager-Lavelle, Amanda and et al.}, year={2015} }
 @misc{rellan-alvarez_2015, title={Multidimensional mapping of root responses to soil environmental cues using a luminescence-based imaging system}, author={Rellan-Alvarez, R}, year={2015} }
 @inproceedings{rellan-alvarez_2015, title={Roundtable Organization Emerging technologies for root systems scale imaging and phenotyping}, author={Rellan-Alvarez, R}, year={2015} }
 @inproceedings{rellan-alvarez_2015, title={Towards a root system level understanding of how plants adjust root function and shape and integrate heterogeneous environmental cues}, author={Rellan-Alvarez, R}, year={2015} }
 @misc{rellan-alvarez_2014, title={Growth and Luminescence Observatory of Roots (GLO-Roots) A platform for the Analysis of Root Structure and Physiology in Soil}, author={Rellan-Alvarez, R}, year={2014} }
 @misc{rellan-alvarez_2014, place={Limburgerhof, Germany}, title={Symposium on Unlocking Yield Potential in Soil}, author={Rellan-Alvarez, R}, year={2014} }
 @inproceedings{rellan-alvarez_2014, place={Portland, USA}, title={Understanding Root Physiology in Soil Using a Novel Imaging Platform}, author={Rellan-Alvarez, R}, year={2014} }
 @misc{rellan-alvarez_2014, title={Understanding Root Physiology in Soil Using a Novel Imaging Platform}, author={Rellan-Alvarez, R}, year={2014} }
 @misc{rellan-alvarez_2013, title={Growth and Luminescence Observatory of Roots (GLO-Roots) A platform for the Analysis of Root Structure and Physiology in Soil}, author={Rellan-Alvarez, R}, year={2013} }
 @article{sudre_gutierrez-carbonell_lattanzio_rellan-alvarez_gaymard_wohlgemuth_fiehn_alvarez-fernandez_zamarreno_bacaicoa_et al._2013, title={Iron-dependent modifications of the flower transcriptome, proteome, metabolome, and hormonal content in an <}, volume={64}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84879937784&partnerID=MN8TOARS}, DOI={10.1093/jxb/ert112}, abstractNote={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.}, number={10}, journal={Journal of Experimental Botany}, publisher={Oxford University Press}, author={Sudre, D. and Gutierrez-Carbonell, E. and Lattanzio, G. and Rellan-Alvarez, R. and Gaymard, F. and Wohlgemuth, G. and Fiehn, O. and Alvarez-Fernandez, A. and Zamarreno, A. M. and Bacaicoa, E. and et al.}, year={2013}, pages={2665–2688} }
 @misc{rellan-alvarez_2013, title={Understanding Root Physiology in Soil Using a Novel Imaging Platform}, author={Rellan-Alvarez, R}, year={2013} }
 @article{schüler_rellán-álvarez_fink-straube_abadía_bauer_2012, title={Nicotianamine Functions in the Phloem-Based Transport of Iron to Sink Organs, in Pollen Development and Pollen Tube Growth in Arabidopsis}, volume={24}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84864426728&partnerID=MN8TOARS}, DOI={10.1105/tpc.112.099077}, abstractNote={This work analyzes the effect of the metal chelator nicotianamine on plant growth and development. It reveals that the transport of Fe from phloem to sink organs depends on nicotianamine and that this chelator has a role in pollen germination and transfer through the style. 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.}, number={6}, journal={Plant Cell}, author={Schüler, M and Rellán-Álvarez, R and Fink-Straube, C and Abadía, J and Bauer, P}, year={2012}, month={Jun}, pages={2380–2400} }
 @article{development of a new hplc-esi-tofms method for the determination of low molecular mass organic acids in plant tissue extracts_2011, volume={59}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79960057580&partnerID=MN8TOARS}, DOI={10.1021/jf200482a}, abstractNote={A liquid chromatography-electrospray ionization time-of-flight mass spectrometry method has been developed for the direct and simultaneous determination of 10 low molecular mass organic acids in different plant tissue extracts. The method does not include a derivatization step. Quantification was accomplished using (13)C-labeled malic and succinic acids as internal standards. Good limits of detection (0.05-1.27 pmol) were obtained for malic, 2-oxoglutaric, succinic, quinic, shikimic, cis-aconitic, and citric acids, whereas for oxalic, ascorbic, and fumaric acids limits of detection were 255, 25, and 11 pmol, respectively. Repeatability values for the retention time and peak area were <5%, with the exception of ascorbic acid. Analyte recovery was between 92% and 110% in most cases, with the exception of oxalic (39-108%), 2-oxoglutaric (44-69%), and ascorbic (22-86%) acids, which may require specific extraction procedures and use of the corresponding (13)C-labeled organic acid as internal standards to improve accuracy. The method was applied to three types of plant materials: sugar beet leaf extracts, tomato xylem sap, and commercial orange juice.}, number={13}, journal={Journal of Agricultural and Food Chemistry}, year={2011}, pages={6864–6870} }
 @misc{rellan-alvarez_2011, title={Iron xylem transport, the long and short of it}, author={Rellan-Alvarez, R}, year={2011} }
 @article{rellán-álvarez_el jendoubi_wohlgemuth_abadía_fiehn_abadía_álvarez fernández_2011, title={Metabolite profile changes in xylem sap and leaf extracts of strategy I plants in response to iron deficiency and resupply}, volume={2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84873746765&partnerID=MN8TOARS}, DOI={10.3389/fpls.2011.00066}, abstractNote={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.}, number={OCT}, journal={Frontiers Plant Science}, author={Rellán-Álvarez, R. and El Jendoubi, H. and Wohlgemuth, G. and Abadía, A. and Fiehn, O. and Abadía, J. and Álvarez Fernández, A.}, year={2011}, month={Oct}, pages={66} }
 @article{navascués_pérez-rontomé_sánchez_staudinger_wienkoop_rellán-álvarez_becana_2012, title={Oxidative stress is a consequence, not a cause, of aluminum toxicity in the forage legume Lotus corniculatus}, volume={193}, ISSN={0028-646X}, url={http://dx.doi.org/10.1111/j.1469-8137.2011.03978.x}, DOI={10.1111/j.1469-8137.2011.03978.x}, abstractNote={• 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.}, number={3}, journal={New Phytologist}, publisher={Wiley}, author={Navascués, Joaquín and Pérez-Rontomé, Carmen and Sánchez, Diego H. and Staudinger, Christiana and Wienkoop, Stefanie and Rellán-Álvarez, Rubén and Becana, Manuel}, year={2012}, month={Feb}, pages={625–636} }
 @article{abadía_vázquez_rellán-álvarez_el jendoubi_abadía_fernández_lópez-millán_2011, title={Towards a knowledge-based correction of iron chlorosis}, volume={49}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79955140827&partnerID=MN8TOARS}, DOI={10.1016/j.plaphy.2011.01.026}, abstractNote={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.}, number={5}, journal={Plant Physiology and Biochemistry}, author={Abadía, Javier and Vázquez, Saúl and Rellán-Álvarez, Rubén and El Jendoubi, Hamdi and Abadía, Anunciación and Fernández, Ana Álvarez and López-Millán, Ana Flor}, year={2011}, pages={471–482} }
 @article{carboxylate metabolism in sugar beet plants grown with excess zn_2011, volume={168}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79952624546&partnerID=MN8TOARS}, DOI={10.1016/j.jplph.2010.10.012}, abstractNote={The effects of Zn excess on carboxylate metabolism were investigated in sugar beet (Beta vulgaris L.) plants grown hydroponically in a growth chamber. Root extracts of plants grown with 50 or 100μM Zn in the nutrient solution showed increases in several enzymatic activities related to organic acid metabolism, including citrate synthase and phosphoenolpyruvate carboxylase, when compared to activities in control root extracts. Root citric and malic acid concentrations increased in plants grown with 100μM Zn, but not in plants grown with 50μM Zn. In the xylem sap, plants grown with 50 and 100μM Zn showed increases in the concentrations of citrate and malate compared to the controls. Leaves of plants grown with 50 or 100μM Zn showed increases in the concentrations of citric and malic acid and in the activities of citrate synthase and fumarase. Leaf isocitrate dehydrogenase increased only in plants grown with 50μM Zn when compared to the controls. In plants grown with 300μM Zn, the only enzyme showing activity increases in root extracts was citrate synthase, whereas the activities of other enzymes decreased compared to the controls, and root citrate concentrations increased. In the 300μM Zn-grown plants, the xylem concentrations of citric and malic acids were higher than those of controls, whereas in leaf extracts the activity of fumarase increased markedly, and the leaf citric acid concentration was higher than in the controls. Based on our data, a metabolic model of the carboxylate metabolism in sugar beet plants grown under Zn excess is proposed.}, number={7}, journal={Journal of Plant Physiology}, year={2011}, pages={730–733} }
 @article{rellan-alvarez_andaluz_rodriguez-celma_wohlgemuth_zocchi_alvarez-fernandez_fiehn_lopez-millan_abadia_2010, title={Changes in the proteomic and metabolic profiles of Beta vulgaris root tips in response to iron deficiency and resupply}, volume={10}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77953672453&partnerID=MN8TOARS}, DOI={10.1186/1471-2229-10-120}, abstractNote={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.
          }, journal={BMC Plant Biology}, author={Rellan-Alvarez, Ruben and Andaluz, Sofia and Rodriguez-Celma, Jorge and Wohlgemuth, Gert and Zocchi, Graziano and Alvarez-Fernandez, Ana and Fiehn, Oliver and Lopez-Millan, Ana and Abadia, Javier}, year={2010} }
 @article{rodríguez-celma_rellán-álvarez_abadía_abadía_lópez-millán_2010, title={Changes induced by two levels of cadmium toxicity in the 2-DE protein profile of tomato roots}, volume={73}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77954656356&partnerID=MN8TOARS}, DOI={10.1016/j.jprot.2010.05.001}, abstractNote={Tomato is an important crop from nutritional and economical points of view, and it is grown in greenhouses, where special substrates and the use of recycled water imply an increased risk of Cd accumulation. We investigated tomato root responses to low (10 microM) and high (100 microM) Cd concentrations at the root proteome level. Root extract proteome maps were obtained by 2-DE, and an average of 121, 145 and 93 spots were detected in the 0, 10 and 100 microM Cd treatments, respectively. The low Cd treatment (10 microM) resulted in significant and higher than 2-fold changes in the relative amounts of 36 polypeptides, with 27 of them identified by mass spectrometry, whereas the 100 microM Cd treatment resulted in changes in the relative amounts of 41 polypeptides, with 33 of them being identified. The 2-DE based proteomic approach allowed assessing the main metabolic pathways affected by Cd toxicity. Our results suggests that the 10 microM Cd treatment elicits proteomic responses similar to those observed in Fe deficiency, including activation of the glycolytic pathway, TCA cycle and respiration, whereas the 100 microM Cd treatment responses are more likely due to true Cd toxicity, with a general shutdown of carbon metabolism and increases in stress related and detoxification proteins.}, number={9}, journal={Journal of Proteomics}, author={Rodríguez-Celma, Jorge and Rellán-Álvarez, Rubén and Abadía, Anunciación and Abadía, Javier and López-Millán, Ana-Flor}, year={2010}, pages={1694–1706} }
 @misc{rellan-alvarez_2010, title={Delving into iron deficiency metabolomics}, author={Rellan-Alvarez, R}, year={2010} }
 @article{pascual_azcona_aguirreolea_morales fermı́n_corpas_palma_rellán-álvarez_sánchez-díaz_2010, title={Growth, Yield, and Fruit Quality of Pepper Plants Amended with Two Sanitized Sewage Sludges}, volume={58}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77953165133&partnerID=MN8TOARS}, DOI={10.1021/jf100282f}, abstractNote={Organic wastes such as sewage sludge have been successfully used to increase crop productivity of horticultural soils. Nevertheless, considerations of the impact of sludges on vegetable and fruit quality have received little attention. Therefore, the objective of the present work was to investigate the impact of two sanitized sewage sludges, autothermal thermophilic aerobic digestion (ATAD) and compost sludge, on the growth, yield, and fruit quality of pepper plants ( Capsicum annuum L. cv. Piquillo) grown in the greenhouse. Two doses of ATAD (15 and 30% v/v) and three of composted sludge (15, 30, and 45%) were applied to a peat-based potting mix. Unamended substrate was included as control. ATAD and composted sludge increased leaf, shoot, and root dry matter, as well as fruit yield, mainly due to a higher number of fruits per plant. There was no effect of sludge on fruit size (dry matter per fruit and diameter). The concentrations of Zn and Cu in fruit increased with the addition of sewage sludges. Nevertheless, the levels of these elements remained below toxic thresholds. Pepper fruits from sludge-amended plants maintained low concentrations of capsaicin and dihydrocapsaicin, thus indicating low pungency level, in accordance with the regulations prescribed by the Control Board of "Lodosa Piquillo peppers" Origin Denomination. The application of sludges did not modify the concentration of vitamin C (ASC) in fruit, whereas the highest doses of composted sludge tended to increase the content of reduced (GSH) and oxidized (GSSG) glutathione, without change in the GSH/GSSG ratio. There were no effects of sludge on the transcript levels of enzymes involved in the synthesis of vitamin C, l-galactono-1,4-lactone dehydrogenase (GLDH) or in the ascorbate-glutathione cycle, ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR), and glutathione reductase (GR). Results suggest that the synthesis and degradation of ASC and GSH were compensated for in most of the treatments assayed. The application of sanitized sludges to pepper plants can improve pepper yield without loss of food nutritional quality, in terms of fruit size and vitamin C, glutathione, and capsaicinoid contents.}, number={11}, journal={Journal of Agricultural and Food Chemistry}, author={Pascual, Immaculada and Azcona, Iñaki and Aguirreolea, Jone and Morales Fermı́n and Corpas, Francisco Javier and Palma, José Manuel and Rellán-Álvarez, Rubén and Sánchez-Díaz, Manuel}, year={2010}, pages={6951–6959} }
 @misc{rellan-alvarez_2010, title={Iron speciation in plant xylem sap using LC-ESI-TOFMS}, author={Rellan-Alvarez, R}, year={2010} }
 @article{metabolic response in roots of prunus rootstocks submitted to iron chlorosis_2011, volume={168}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79251595637&partnerID=MN8TOARS}, DOI={10.1016/j.jplph.2010.08.010}, abstractNote={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.}, number={5}, journal={Journal of Plant Physiology}, year={2011}, pages={415–423} }
 @misc{rellan-alvarez_2009, place={Sacramento, California, USA}, title={Changes in the proteomic and metabolic profiles of Beta vulgaris root tips in response to iron deficiency and resupply}, author={Rellan-Alvarez, R}, year={2009} }
 @article{martí_camejo_fernández-garcía_rellán-álvarez_marques_sevilla_jiménez_2009, title={Effect of oil refinery sludges on the growth and antioxidant system of alfalfa plants}, volume={171}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70349316752&partnerID=MN8TOARS}, DOI={10.1016/j.jhazmat.2009.06.083}, abstractNote={The refining process in the petrochemical industry generates oil refinery sludges, a potentially contaminating waste product, with a high content of hydrocarbons and heavy metals. Faster degradation of hydrocarbons has been reported in vegetated soils than in non-vegetated soils, but the impact of these contaminants on the plants physiology and on their antioxidant system is not well known. In this study, the effect of the addition of petroleum sludge to soil on the physiological parameters, nutrient contents, and oxidative and antioxidant status in alfalfa was investigated. An inhibition of alfalfa growth and an induction of oxidative stress, as indicated by an increase in protein oxidation, were found. Also, the superoxide dismutase isoenzymes, peroxidase, and those enzymes involved in the ascorbate–glutathione cycle showed significant activity increases, parallel to an enhancement of total homoglutathione, allowing plants being tolerant to this situation. This information is necessary to establish successful and sustainable plant-based remediation strategies.}, number={1-3}, journal={Journal of Hazardous Materials}, author={Martí, M. Carmen and Camejo, Daymi and Fernández-García, Nieves and Rellán-Álvarez, Rubén and Marques, Silvia and Sevilla, Francisca and Jiménez, Ana}, year={2009}, pages={879–885} }
 @article{rellan-alvarez_giner-martinez-sierra_orduna_orera_rodriguez-castrillon_garcia-alonso_abadia_alvarez-fernandez_2010, title={Identification of a Tri-Iron(III), Tri-Citrate Complex in the Xylem Sap of Iron-Deficient Tomato Resupplied with Iron: New Insights into Plant Iron Long-Distance Transport}, volume={51}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-74549203240&partnerID=MN8TOARS}, DOI={10.1093/pcp/pcp170}, abstractNote={The identification of Fe transport forms in plant xylem sap is crucial to the understanding of long-distance Fe transport processes in plants. Previous studies have proposed that Fe may be transported as an Fe-citrate complex in plant xylem sap, but such a complex has never been detected. In this study we report the first direct and unequivocal identification of a natural Fe complex in plant xylem sap. A tri-Fe(III), tri-citrate complex (Fe(3)Cit(3)) was found in the xylem sap of Fe-deficient tomato (Solanum lycopersicum Mill. cv. 'Tres Cantos') resupplied with Fe, by using an integrated mass spectrometry approach based on exact molecular mass, isotopic signature and Fe determination and retention time. This complex has been modeled as having an oxo-bridged tri-Fe core. A second complex, a di-Fe(III), di-citrate complex was also detected in Fe-citrate standards along with Fe(3)Cit(3), with the allocation of Fe between the two complexes depending on the Fe to citrate ratio. These results provide evidence for Fe-citrate complex xylem transport in plants. The consequences for the role of Fe to citrate ratio in long-distance transport of Fe in xylem are also discussed.}, number={1}, journal={Plant and Cell Physiology}, author={Rellan-Alvarez, R. and Giner-Martinez-Sierra, J. and Orduna, J. and Orera, I. and Rodriguez-Castrillon, J. A. and Garcia-Alonso, J. I. and Abadia, J. and Alvarez-Fernandez, A.}, year={2010}, pages={91–102} }
 @inproceedings{rellan-alvarez_2009, title={Iron is transported as a tri-Fe(III), tri-citrate complex in plant xylem sap}, author={Rellan-Alvarez, R}, year={2009} }
 @article{rellan-alvarez_abadia_alvarez-fernandez_2008, title={Formation of metal-nicotianamine complexes as affected by pH, ligand exchange with citrate and metal exchange. A study by electrospray ionization time-of-flight mass spectrometry}, volume={22}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-45149109934&partnerID=MN8TOARS}, DOI={10.1002/rcm.3523}, abstractNote={AbstractNicotianamine (NA) is considered as a key element in plant metal homeostasis. This non‐proteinogenic amino acid has an optimal structure for chelation of metal ions, with six functional groups that allow octahedral coordination. The ability to chelate metals by NA is largely dependent on the pK of the resulting complex and the pH of the solution, with most metals being chelated at neutral or basic pH values. In silico calculations using pKa and pK values have predicted the occurrence of metal‐NA complexes in plant fluids, but the use of soft ionization techniques (e.g. electrospray), together with high‐resolution mass spectrometers (e.g. time‐of‐flight mass detector), can offer direct and metal‐specific information on the speciation of NA in solution. We have used direct infusion electrospray ionization mass spectrometry (time‐of‐flight) ESI‐MS(TOF) to study the complexation of Mn, Fe(II), Fe(III), Ni, Cu by NA. The pH dependence of the metal‐NA complexes in ESI‐MS was compared to that predicted in silico. Possible exchange reactions that may occur between Fe‐NA and other metal micronutrients as Zn and Cu, as well as between Fe‐NA and citrate, another possible Fe ligand candidate in plants, were studied at pH 5.5 and 7.5, values typical of the plant xylem and phloem saps. Metal‐NA complexes were generally observed in the ESI‐MS experiments at a pH value approximately 1–2 units lower than that predicted in silico, and this difference could be only partially explained by the estimated error, approximately 0.3 pH units, associated with measuring pH in organic solvent‐containing solutions. Iron‐NA complexes are less likely to participate in ligand‐ and metal‐exchange reactions at pH 7.5 than at pH 5.5. Results support that NA may be the ligand chelating Fe at pH values usually found in phloem sap, whereas in the xylem sap NA is not likely to be involved in Fe transport, conversely to what occurs with other metals such as Cu and Ni. Some considerations that need to be addressed when studying metal complexes in plant compartments by ESI‐MS are also discussed. Copyright © 2008 John Wiley & Sons, Ltd.}, number={10}, journal={Rapid Communications in Mass Spectrometry}, author={Rellan-Alvarez, R. and Abadia, J. and Alvarez-Fernandez, A.}, year={2008}, pages={1553–1562} }
 @article{ortega-villasante_hernandez_rellan-alvarez_del campo_carpena-ruiz_2007, title={Rapid alteration of cellular redox homeostasis upon exposure to cadmium and mercury in alfalfa seedlings}, volume={176}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34548438158&partnerID=MN8TOARS}, DOI={10.1111/j.1469-8137.2007.02162.x}, abstractNote={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.}, number={1}, journal={New Phytologist}, author={Ortega-Villasante, C. and Hernandez, L. E. and Rellan-Alvarez, R. and Del Campo, F. F. and Carpena-Ruiz, R. O.}, year={2007}, pages={96–107} }
 @article{rellan-alvarez_hernandez_abadia_alvarez-fernandez_2006, title={Direct and simultaneous determination of reduced and oxidized glutathione and homoglutathione by liquid chromatographyelectrospray/mass spectrometry in plant tissue extracts}, volume={356}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33747878198&partnerID=MN8TOARS}, DOI={10.1016/j.ab.2006.05.032}, abstractNote={A simple, highly selective, sensitive, and reproducible liquid chromatography–electrospray ionization/mass spectrometry (time of flight) method has been developed for the direct and simultaneous determination of glutathione and related compounds such as homoglutathione in different plant tissues. These compounds are low-molecular mass antioxidants involved in cellular redox homeostasis in plants, and efforts are being made to develop methods to determine the concentrations of oxidized and reduced forms of these compounds and their ratio. Many of the methodologies developed so far, however, are time-consuming and complex; therefore, analytes can decompose and their redox status can change during the analysis process. The method we have developed allows the simultaneous determination of reduced forms (glutathione [GSH] and homoglutathione [hGSH]) and oxidized forms (glutathione disulfide [GSSG]) of these compounds and is also suitable for the determination of ascorbic acid (ASA) and S-nitrosoglutathione (GSNO). Quantification was done using isotopically labeled GSH and ASA as internal standards. All compounds were base peak resolved in less than 6 min, and limits of detection were 60 pmol for GSH, 30 pmol for hGSH, 20 pmol for GSSG, 100 pmol for ASA, and 30 pmol for GSNO. The intraday repeatability values were approximately 0.4 and 7% for retention time and peak area, respectively, whereas the interday repeatability values were approximately 0.6 and 9% for retention time and peak area, respectively. Analyte recoveries found were between 92 and 105%. The method was used to determine the concentrations of GSH, GSSG, hGSH, and ASA in extracts from several plant tissues.}, number={2}, journal={Analytical Biochemistry}, author={Rellan-Alvarez, R. and Hernandez, L. E. and Abadia, J. and Alvarez-Fernandez, A.}, year={2006}, pages={254–264} }
 @article{rellan-alvarez_ortega-villasante_alvarez-fernandez_campo_hernandez_2006, title={Stress responses of Zea mays to cadmium and mercury}, volume={279}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-32544431929&partnerID=MN8TOARS}, DOI={10.1007/s11104-005-3900-1}, number={1-2}, journal={Plant and Soil}, author={Rellan-Alvarez, R. and Ortega-Villasante, C. and Alvarez-Fernandez, A. and Campo, F. F. and Hernandez, L. E.}, year={2006}, pages={41–50} }
 @article{ortega-villasante_rellan-alvarez_del campo_carpena-ruiz_hernandez_2005, title={Cellular damage induced by cadmium and mercury in Medicago sativa}, volume={56}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-24944536376&partnerID=MN8TOARS}, DOI={10.1093/jxb/eri223}, abstractNote={Alfalfa (Medicago sativa) plantlets were exposed to Cd or Hg to study the kinetics of diverse stress indexes. In the so-called beaker-size hydroponic system, plantlets were grown in 30 microM of Cd or Hg for 7 d. Oxidative stress took place and increased over time, a linear response being observed with Cd but not with Hg. To improve the sensitivity of the stress assays used, a micro-assay system, in which seedlings were exposed for 24 h, was developed. Phytotoxicity of metals, quantified as growth inhibition, was observed well before there was any change in the non-protein thiol tissue concentration. When measured with conventional techniques, oxidative stress indexes did not show significant variation. To trace early and small plant responses to Cd and Hg, a microscopic analysis with novel fluorescent dyes, which had not yet been exploited to any significant extent for use in plants, was conducted. These fluorescent probes, which allowed minute cellular responses to 0, 3, 10, and 30 microM of both metals to be visualized in the roots of the alfalfa seedlings, were: (i) 2',7'-dichlorofluorescin diacetate that labels peroxides; (ii) monochlorobimane that stains reduced glutathione/homoglutathione (GSH/hGSH); and (iii) propidium iodide that marks nuclei of dead cells. Oxidative stress and cell death increased after exposure for 6-24 h to Cd and Hg, but labelling of GSH/hGSH decreased acutely. This diminution might be the result of direct interaction of GSH/hGSH with both Cd and Hg, as inferred from an in vitro conjugation assay. Therefore, both Cd and Hg not only compromised severely the cellular redox homeostasis, but also caused cell necrosis. In plants treated with 1 mM L-buthionine sulphoximine, a potent inhibitor of GSH/hGSH synthesis, only the oxidative stress symptoms appeared, indicating that the depletion of the GSH/hGSH pool was not sufficient to promote cell death, and that other phytotoxic mechanisms might be involved.}, number={418}, journal={Journal of Experimental Botany}, author={Ortega-Villasante, C. and Rellan-Alvarez, R. and Del Campo, F. F. and Carpena-Ruiz, R. O. and Hernandez, L. E.}, year={2005}, pages={2239–2251} }
 @misc{rellan-alvarez, title={Convergent phospholipid metabolism in highland adapted maize?}, author={Rellan-Alvarez, R} }