Sofia Alves

University of Lisbon

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João Neves-Martins

University of Lisbon

Leonor Morais–Cecílio

University of Lisbon

Agata Gulisano

Wageningen University & Research

Miguel Ramos

University of Lisbon

Luisa M. Trindade

Wageningen University & Research

Ana Teresa Alhinho

University of Minho

Pedro Talhinhas

University of Lisbon

Norberto Guilengue

University of Lisbon

Maria Manuela Ribeiro Costa

University of Minho

Margarida Rocheta

University of Lisbon

Cooperative Institutions

University of Lisbon

Universidade Estadual de Londrina

Wageningen University & Research

University of Minho

Universidade Nova de Lisboa

Universidade do Estado de Minas Gerais

Universidade Estadual de Maringá

Universidad San Francisco de Quito

Universidade do Porto

Graduate School Experimental Plant Sciences

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Genome‐wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae

Physiologia Plantarum (2022)

Sofia Alves Ângelo Braga Denise Parreira Ana Teresa Alhinho Helena Silva

Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.

10.1111/ppl.13788

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The Analysis of Partial Sequences of the Flavonone 3 Hydroxylase Gene in Lupinus mutabilis Reveals Differential Expression of Two Paralogues Potentially Related to Seed Coat Colour

Agronomy (2022)

Norberto Guilengue Helena G. Azinheira Sofia Alves João Neves-Martins Pedro Talhinhas

Flavonone 3 hydroxylases (EC 1.14.11.9) are key enzymes in the synthesis of anthocyanins and other flavonoids. Such compounds are involved in seed coat colour and stem pigmentation. Lupinus mutabilis (tarwi) is a legume crop domesticated in the Andean region, valued for the high protein and oil content of its seeds. Tarwi accessions are being selected for cultivation in Europe under defined breeding criteria. Seed coat colour patterns are relevant breeding traits in tarwi, and these are conditioned by anthocyanin content. We identified and isolated part of the tarwi flavonone 3-hydroxylase gene (LmF3h) from two accessions with distinct seed coat colour patterns. Two partial LmF3h paralogues, with predicted 20% amino-acid changes but little predicted tertiary structure alterations, were identified in the coloured seed genotype, while only one was present in the white seed genotype. Upon selection and validation of appropriate reference genes, a RT-qPCR analysis showed that these paralogues have different levels of expression during seed development in both genotypes, although they follow the same expression patterns. DNA and transcription analyses enabled to highlight potential F3H paralogues relatable to seed coat pigmentation in tarwi and, upon biochemical and genetic confirmation, prompt marker-assisted breeding for relevant phenotypic traits associated with flavonoid synthesis.

Coat

10.3390/agronomy12020450

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Citations (1)

Genomic organization and dynamics of repetitive DNA sequences in representatives of three Fagaceae genera

Genome (2012)

Sofia Alves Teresa Ribeiro Vera Inácio Margarida Rocheta Leonor Morais–Cecílio

Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology searches in available databases. Genomic polymorphisms involving some of these sequences were evaluated in two species of Quercus , one of Castanea , and one of Fagus with specific primers. Comparative FISH analysis with generated sequences was performed in interphase nuclei of the four species, and the co-immunolocalization of 5-methylcytosine was also studied. Some of the sequences isolated proved to be genus-specific, while others were present in all the genera. Retroelements, either gypsy-like of the Tat/Athila clade or copia-like, are well represented, and most are dispersed in euchromatic regions of these species with no DNA methylation associated, pointing to an interspersed arrangement of these retroelements with potential gene-rich regions. A particular gypsy-sequence is dispersed in oaks and chestnut nuclei, but its confinement to chromocenters in beech evidences genome restructuring events during evolution of Fagaceae. Several sequences generated in this study proved to be good tools to comparatively study Fagaceae genome organization.

Populus trichocarpa

Retrotransposon

Euchromatin

Subgenus

10.1139/g2012-020

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Citations (8)

The Dynamics of Flower Development in Castanea sativa Mill.

Plants (2021)

Ana Teresa Alhinho Miguel Ramos Sofia Alves Margarida Rocheta Leonor Morais–Cecílio

The sweet chestnut tree (Castanea sativa Mill.) is one of the most significant Mediterranean tree species, being an important natural resource for the wood and fruit industries. It is a monoecious species, presenting unisexual male catkins and bisexual catkins, with the latter having distinct male and female flowers. Despite the importance of the sweet chestnut tree, little is known regarding the molecular mechanisms involved in the determination of sexual organ identity. Thus, the study of how the different flowers of C. sativa develop is fundamental to understand the reproductive success of this species and the impact of flower phenology on its productivity. In this study, a C. sativa de novo transcriptome was assembled and the homologous genes to those of the ABCDE model for floral organ identity were identified. Expression analysis showed that the C. sativa B- and C-class genes are differentially expressed in the male flowers and female flowers. Yeast two-hybrid analysis also suggested that changes in the canonical ABCDE protein–protein interactions may underlie the mechanisms necessary to the development of separate male and female flowers, as reported for the monoecious Fagaceae Quercus suber. The results here depicted constitute a step towards the understanding of the molecular mechanisms involved in unisexual flower development in C. sativa, also suggesting that the ABCDE model for flower organ identity may be molecularly conserved in the predominantly monoecious Fagaceae family.

Plant reproductive morphology

Quercus suber

10.3390/plants10081538

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Citations (7)

Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions

Agronomy (2019)

Norberto Guilengue Sofia Alves Pedro Talhinhas João Neves-Martins

Lupinus mutabilis (tarwi) is a species of Andean origin with high protein and oil content and regarded as a potential crop in Europe. The success in the introduction of this crop depends in part on in depth knowledge of the intra-specific genetic variability of the collections, enabling the establishment of breeding and conservation programs. In this study, we used morphological traits, Inter-Simple Sequence Repeat markers and genome size to assess genetic and genomic diversity of 23 tarwi accessions under Mediterranean conditions. Phenotypic analyses and yield component studies point out accession LM268 as that achieving the highest seed production, producing large seeds and efficiently using primary branches as an important component of total yield, similar to the L. albus cultivars used as controls. By contrast, accession JKI-L295 presents high yield concentrated on the main stem, suggesting a semi-determinate development pattern. Genetic and genomic analyses revealed important levels of diversity, however not relatable to phenotypic diversity, reflecting the recent domestication of this crop. This is the first study of genome size diversity within L. mutabilis, revealing an average size of 2.05 pg/2C (2001 Mbp) with 9.2% variation (1897–2003 Mbp), prompting further studies for the exploitation of this diversity.

Germ plasm

Adaptability

Lupinus

Crop Diversity

10.3390/agronomy10010021

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Citations (41)

Research Article Genetic variability in food-type soybean accessions assessed by morphoagronomic traits

Genetics and Molecular Research (2019)

Douglas Mariani Zeffa Luiz Júnior Perini Gustavo Henrique Freiria Gustavo Matheus Silva Guilherme Renato Gomes

The estimation of genetic variability in germplasm banks is important not only for the conservation of genetic resources, but also for their use in plant breeding.However, a large number of traits from different categories (qualitative and quantitative) can make the analysis and interpretation of the results difficult, often resulting in an incomplete distinction among accessions.We characterized 45 accessions of food-type soybean (Glycine max) from the Soybean Germplasm Bank of Londrina State University based on morphoagronomic traits.The experiment was carried out in the university farm using a randomized block design with three replicates.Twelve traits were evaluated: flower color, pubescence color, tegument color, hilum color, days until flowering, days until maturation, plant height, height of insertion of the first pod, mass of 100 grains, grain yield per plot, agronomic value, and lodging index.The quantitative trait data were submitted to deviance analysis.The genetic divergence among the accessions was examined by Gower's distance and clustering of the accessions was made based on Ward's hierarchical method.Morphoagronomic descriptors proved efficient in detecting the levels of genetic variability among the accessions maintained in the germplasm collection.Gower's distance was efficient in the discrimination of accessions, showing that simultaneous analysis of quantitative and D.M. Zeffa et al. 2 qualitative traits is useful to evaluate the variability in a germoplasm bank.These results can be used as an additional source of information to be exploited in food-type soybean breeding programs.

10.4238/gmr18298

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Citations (0)

Diversity and Agronomic Performance of Lupinus mutabilis Germplasm in European and Andean Environments

Frontiers in Plant Science (2022)

Agata Gulisano Sofia Alves D. Rodríguez Ángel Murillo Bert-Jan van Dinter

The introduction of Lupinus mutabilis (Andean lupin) in Europe will provide a new source of protein and oil for plant-based diets and biomass for bio-based products, while contributing to the improvement of marginal soils. This study evaluates for the first time the phenotypic variability of a large panel of L. mutabilis accessions both in their native environment and over two cropping conditions in Europe (winter crop in the Mediterranean region and summer crop in North-Central Europe), paving the way for the selection of accessions adapted to specific environments. The panel of 225 accessions included both germplasm pools from the Andean region and breeding lines from Europe. Notably, we reported higher grain yield in Mediterranean winter-cropping conditions (18 g/plant) than in the native region (9 g/plant). Instead, North European summer-cropping conditions appear more suitable for biomass production (up to 2 kg/plant). The phenotypic evaluation of 16 agronomical traits revealed significant variation in the panel. Principal component analyses pointed out flowering time, yield, and architecture-related traits as the main factors explaining variation between accessions. The Peruvian material stands out among the top-yielding accessions in Europe, characterized by early lines with high grain yield (e.g., LIB065, LIB072, and LIB155). Bolivian and Ecuadorian materials appear more valuable for the selection of genotypes for Andean conditions and for biomass production in Europe. We also observed that flowering time in the different environments is influenced by temperature accumulation. Within the panel, it is possible to identify both early and late genotypes, characterized by different thermal thresholds (600°C-700°C and 1,000-1,200°C GDD, respectively). Indications on top-yielding and early/late accessions, heritability of morpho-physiological traits, and their associations with grain yield are reported and remain largely environmental specific, underlining the importance of selecting useful genetic resources for specific environments. Altogether, these results suggest that the studied panel holds the genetic potential for the adaptation of L. mutabilis to Europe and provide the basis for initiating a breeding program based on exploiting the variation described herein.

Germ plasm

Mediterranean Basin

Plant Breeding

Lupinus

10.3389/fpls.2022.903661

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Citations (13)

Genetics and Breeding of Lupinus mutabilis: An Emerging Protein Crop

Frontiers in Plant Science (2019)

Agata Gulisano Sofia Alves João Neves-Martins Luisa M. Trindade

Protein crops have gained increasing interest in recent years, as a transition towards plant-protein based diets appears pivotal to ensure global food security and preserve the environment. The Andean species Lupinus mutabilis emerges as an ideal protein crop with great potential for Europe and other regions with temperate climates. This species is characterized by an oil and protein content similar to soybean and is highly valued for its adaptability to colder climates and low input agriculture on marginal land. However, its introduction outside the Andes has yet to take off. To date, L. mutabilis remains an under-studied crop, lacking high yield, early maturity and a consistent breeding history. This review paper identifies L. mutabilis limitations and potential uses, and suggests the main breeding targets for further improvement of this crop. It also highlights the potential of new molecular tools and available germplasm resources that can now be used to establish L. mutabilis as a viable protein crop.

Germ plasm

Adaptability

10.3389/fpls.2019.01385

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Citations (66)