Manuela Silva

Manuela Silva
University of Lisbon | UL · Linking Landscape, Environment, Agriculture and Food (LEAF) - Instituto Superior de Agronomia

PhD in Agriculture Engineering

About

81
Publications
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1,509
Citations
Citations since 2016
26 Research Items
520 Citations
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2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080

Publications

Publications (81)
Article
Full-text available
High temperature (HT) events have negative impact on wheat grains yield and quality. Transcriptome profiles of wheat developing grains of commercial genotypes (Antequera and Bancal) and landraces (Ardito and Magueija) submitted to heatwave-like treatments during grain filling were evaluated. Landraces showed significantly more differentially expres...
Article
Full-text available
Wheat is a dietary staple consumed worldwide strongly responsible for proteins and carbohydrate population intake. However, wheat production and quality will scarcely fulfill forward demands, which are compounded by high-temperature (HT) events as heatwaves, increasingly common in Portugal. Thus, landraces assume crucial importance as potential res...
Article
Full-text available
Wheat is one of the most important cereals for food and feed, and it is, therefore, necessary to determine the effects of short-term high temperature events (heatwaves) during grain filling. These heatwave events are increasingly common, especially in Portugal. In this work, seven commercial varieties recommended for production in Portugal were sub...
Article
Assessing durum wheat genomic diversity is crucial in a changing environmental particularly in the Mediterranean region where it is largely used to produce pasta. Durum wheat varieties cultivated in Portugal and previously assessed regarding thermotolerance ability were screened for the variability of coding sequences associated with technological...
Article
Full-text available
The predicted world population increase along with climate changes threatens sustainable agricultural supply in the coming decades. It is therefore vital to understand crops diversity associated to abiotic stress response. Heat stress is considered one of the major constrains on crops productivity thus it is essential to develop new approaches for...
Data
Accession numbers. Accession numbers of TdHSP101C coding sequence for the C-terminal region of the corresponding protein of distinct Portuguese durum wheat varieties. (PDF)
Data
TdHSP101C inter-varietal comparison. Inter-varietal comparison of TdHSP101C partial sequences and comparison between the two forms identified in Portuguese durum wheat varieties. (PDF)
Data
TdHSP101C intra-varietal comparison. Intra-varietal comparison of TdHSP101C partial sequences in Portuguese durum wheat varieties. (PDF)
Article
Full-text available
Faba bean (Vicia faba L.) is a facultative cross-pollinating legume crop with a great importance for food and feed due to its high protein content as well as the important role in soil fertility and nitrogen fixation. In this work we evaluated genetic diversity and population structure of faba bean accessions from the Western Mediterranean basin an...
Data
Isolation by distance test for all cultivated, and only Portuguese accessions. Testing Isolation-By-Distance (IBD) by plotting pairwise geographic distances against pairwise FST (left) and pairwise genetic distances (D) (right) for each pair of accessions genotyped in the cultivated panel only (A-B) and the Portugal only accessions (C-D). Regressio...
Data
PCA analysis of allele frequencies for the Portuguese faba bean accessions. Lettuce Plot of the 1st to 5th components of a PCA analysis based on the accession allele frequencies of polymorphic SSR markers for the Portuguese faba bean accessions. See Fig 2 for legend. (TIF)
Data
Consensus Neighbour-Joining tree for cultivated accessions. Consensus boot-strapped Neighbour-Joining tree between faba bean accessions based on the allele frequencies of polymorphic SSRs for cultivated accessions. The tree was constructed from Nei’s (D) genetic distances with 100 bootstrap replicates. The number of times the same node is retrieved...
Data
SSR markers used in this study, including primer sequences and expected sizes. (XLSX)
Data
Pairwise FST and pairwise genetic distance matrices for each pair of accessions. Each spreadsheet represents one of the three different levels of analysis: all cultivated and wild accessions; cultivated accessions; Portuguese accessions (XLSX)
Data
Evanno’s ΔK calculations for the STRUCTURE runs with different accession panels. (XLSX)
Data
Geographical distribution of population structure in Portuguese individual. Geographical distribution of population structure in Portuguese individual faba plants according to the models K = 2 (upper map) and K = 7 (lower map) produced by STRUCTURE. Each individual is depicted as a pie chart with the proportional membership of its alleles to each o...
Data
Correlations between inbreeding coefficient (F) for the cultivated accessions and four climatic variables. Clockwise from upper left: average daily temperature (°C), average yearly rainfall (mm), average highest temperature (°C) and average lowest temperature (°C). Regression line and r2 values are shown in blue. (TIF)
Data
PCA analysis of allele frequencies for the all wild and cultivated faba bean accessions. Lettuce Plot of the 1st to 4th components of a PCA analysis based on the accession allele frequencies of polymorphic SSR markers for the all wild and cultivated faba beanaccessions. See Fig 2 for legend. (TIF)
Data
PCA analysis of allele frequencies for the all cultivated faba bean accessions. Lettuce Plot of the 1st to 5th components of a PCA analysis based on the accession allele frequencies of polymorphic SSR markers for the cultivated faba bean accessions. See Fig 2 for legend. (TIF)
Data
Consensus Neighbour-Joining tree for Portuguese accessions. Consensus boot-strapped Neighbour-Joining tree between faba bean accessions based on the allele frequencies of polymorphic SSRs for Portuguese accessions. The tree was constructed from Nei’s (D) genetic distances with 100 bootstrap replicates. The number of times the same node is retrieved...
Data
List of individuals analysed and their alleles for each SSR. (XLSX)
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Genetic diversity measures for the SSR markers screened in the three different levels of analysis. (XLSX)
Data
Genetic diversity measures for the accessions genotyped in the three different levels of analysis. Included are information about accessions (species, geographic coordinates, country provenance, type, region of origin). (XLSX)
Article
Full-text available
Faba bean have been grown in Portugal for a long time and locally adapted populations are still maintained on farm. The genetic diversity of four Portuguese faba bean populations that are still cultivated in some regions of the country was evaluated using the Inter Retrotransposons Amplified Polymorphism (IRAP) technique. It was shown that molecula...
Article
Full-text available
Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, re...
Article
Full-text available
Polyploidization is a major genome modification that results in plant species with multiple chromosome sets. Parental genome adjustment to co-habit a new nuclear environment results in additional innovation outcomes. We intended to assess genomic changes in polyploid model species with small genomes using inter retrotransposons amplified polymorphi...
Article
Full-text available
Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a...
Article
Full-text available
The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploi...
Article
Full-text available
The plant stress response has been extensively characterized at the biochemical and physiological levels. However, knowledge concerning repetitive sequence genome fraction modulation during extreme temperature conditions is scarce. We studied high-temperature effects on subtelomeric repetitive sequences (pSc200) and 45S rDNA in rye seedlings submit...
Article
Full-text available
Abstract: Nucleolar dominance is an enigma. The puzzle of differential amphiplasty has remained unresolved since it was first recognised and described in Crepis hybrids by Navashin in 1934. Here we review the body of knowledge that has grown out of the many models that have tried to find the genetic basis for differential rRNA gene expression in hy...
Article
Full-text available
Polyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes i...
Article
Full-text available
Regulation of nondisjunction of the rye B chromosome was investigated using the cytidine analog 5-azacytidine, which affects DNA methylation. The B chromosome of rye normally undergoes nondisjunction at first pollen grain mitosis and is stable at all other mitotic nuclear divisions. Observations on mitosis in the control root cells showed normal ch...
Article
Full-text available
Genetic and epigenetic modifications resulting from different genomes adjusting to a common nuclear environment have been observed in polyploids. Sequence restructuring within genomes involving retrotransposon/microsatellite-rich regions has been reported in triticale. The present study uses inter-retrotransposon amplified polymorphisms (IRAP) and...
Article
Full-text available
Background: Chromatin organizational and topological plasticity, and its functions in gene expression regulation, have been strongly revealed by the analysis of nucleolar dominance in hybrids and polyploids where one parental set of ribosomal RNA (rDNA) genes that are clustered in nucleolar organizing regions (NORs), is rendered silent by epigenet...
Article
Full-text available
Polyploidization is a major evolutionary process in plants where hybridization and chromosome doubling induce enormous genomic stress and can generate genetic and epigenetic modifications. However, proper evaluation of DNA sequence restructuring events and the precise characterization of sequences involved are still sparse. Inter Retrotransposons A...
Data
IRAP banding profiles - wheat, rye, triticale and wheat+rye test tube. IRAP banding profile obtained with primer Nikita of wheat (W), rye (R), triticale (T), and wheat+rye test tube (W+R) showing triticale rearranged bands. Arrows indicate two rearranged band of rye genome origin absent in triticale but present in the wheat+rye test tube. (0.16 MB...
Data
IRAP banding profiles - individual plants of each genotype. IRAP banding profiles obtained with primer Nikita from three individuals of each genotype: (W) Wheat, (R) Rye, and (T) Triticale. (0.40 MB TIF)
Data
Frequencies (%) of DNA-FISH signals for A. thaliana-derived NORs in root tip interphase nuclei of A. suecica. Nuclei of wild-type (LC1), HDT1-RNAi and HDA6-RNAi plants were compared at 2, 4 and 15 days post-germination. (0.04 MB DOC)
Data
Frequencies (%) at which H3K9me2 and H3K4me3 colocalize with A. arenosa-derived NORs in root tip interphase nuclei of A. suecica. Nuclei of wild-type (LC1) plants were observed at 2, 4 and 15 days post-germination. (0.05 MB DOC)
Data
Frequencies (%) of root meristem nuclei observed with distinct HDT1 interphase localization patterns in A. suecica. Nuclei of wild-type (lab strain LC1), HDT1-RNAi and HDA6-RNAi plants were compared at 2, 4 and 15 days post-germination. (0.04 MB DOC)
Data
Frequencies (%) of DNA-FISH signals for A. arenosa-derived NORs in root tip interphase nuclei of A. suecica. Nuclei of wild-type (LC1), HDT1-RNAi and HDA6-RNAi plants were compared at 2, 4 and 15 days post-germination. (0.03 MB DOC)
Data
Frequencies (%) of DNA-FISH signals for A. thaliana-derived NORs in interphase nuclei of wild-type A. suecica (strain LC1) cotyledons and mature leaves (0.03 MB DOC)
Data
Frequencies (%) of H3K9me2 and H3K4me3 localization patterns, relative to A. thaliana-derived NORs, in root tip interphase nuclei of A. suecica. Nuclei of wild-type (LC1), HDT1-RNAi and HDA6-RNAi plants were compared at 2, 4 and 15 days post-germination. (0.05 MB DOC)
Data
Frequencies (%) of root meristem nuclei observed with distinct HDA6 interphase localization patterns in A. suecica. Nuclei of wild-type (lab strain LC1), HDT1-RNAi and HDA6-RNAi plants were compared at 2, 4 and 15 days post-germination. (0.04 MB DOC)
Data
DNA-FISH detection of A. thaliana-derived NORs (green signals) in meristematic zone nuclei of whole-mounted A. suecica lateral root tips, comparing wild-type (strain LC1) and HDA6-RNAi plants. DNA was counterstained with DAPI (grey/white signals). The nuclei enclosed by rectangles are shown enlarged in the insets. The upper inset shows the DNA-FISH...
Data
HDT1 immunolocalization patterns in meristematic zone nuclei of whole-mounted 2 and 15 day-old plant root tips. Anti-HDT1 antibody (α-HDT1) signals are in green; DNA counterstained with DAPI is in grey. Each panel shows a single confocal optical section that passes through the centers of the nucleoli (Nuc) in two or more neighboring cells. The nucl...
Data
Immunolocalization of HDA6 protein (green signals) in wild-type (Col-0 ecotype) and hda6 (allele axe1-5 allele) mutant A. thaliana. DNA was counterstained with DAPI (blue). The size bar correspond to 5 μm. The severely reduced HDA6 signal in the axe1-5 mutant indicates that the strong signals detected in wild-type nuclei are attributable to HDA6. M...
Data
HDT1-YFP localizes to the nucleolus. An intact root of a transgenic A. thaliana plant expressing an HDT1-YFP translational fusion protein was stained with DAPI and subjected to differential interference contrast (DIC) and fluorescence microscopy. The three panels show the nucleus of a single root cell. The nucleolus is readily apparent in the DIC i...
Data
Frequencies (%) at which H3K9me2 colocalizes with A. thaliana-derived NORs in interphase nuclei of wild-type A. suecica (strain LC1) cotyledons and mature leaves (0.03 MB DOC)
Data
Frequencies (%) of 5-methylcytosine (5-mC) localization patterns, relative to A. thaliana-derived NORs, in root tip interphase nuclei of A. suecica. Nuclei of wild-type (LC1), HDT1-RNAi and HDA6-RNAi plants were compared at 2, 4 and 15 days post-germination. (0.04 MB DOC)
Data
DNA-FISH detection of A. thaliana-derived NORs (green signals) in meristematic zone cell nuclei of whole-mounted A. suecica primary root tips. DNA was counterstained with DAPI (grey/white signals). The size bars correspond to 5 μm. (2.93 MB TIF)
Article
Full-text available
Nucleolar dominance is an epigenetic phenomenon in plant and animal genetic hybrids that describes the expression of 45S ribosomal RNA genes (rRNA genes) inherited from only one progenitor due to the silencing of the other progenitor's rRNA genes. rRNA genes are tandemly arrayed at nucleolus organizer regions (NORs) that span millions of basepairs,...
Chapter
Full-text available
The functional importance of Epigenetics arise from DNA sequencing programs that show the need for another code to explain the dynamics of gene expression patterns observed along cell differentiation and organism development. In this context, the study of ribosomal gene silencing is in fact an excellent model to better understand the relationships...
Article
Full-text available
Nucleolar dominance describes the silencing of one parental set of ribosomal RNA (rRNA) genes in a genetic hybrid, an epigenetic phenomenon that occurs on a scale second only to X-chromosome inactivation in mammals. An RNA interference (RNAi) knockdown screen revealed that the predicted Arabidopsis histone deacetylase, HDA6, is required for rRNA ge...
Article
Full-text available
The aim of this review is to integrate earlier results and recent findings to present the current state-of-the-art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene...