21 results on '"Protasio Pereira, Luiz Filipe"'
Search Results
2. A Power Law Semantic Similarity from Gene Ontology
- Author
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Augusto Ito, Eric, primary, Rocha Vicente, Fábio Fernandes da, additional, Protasio Pereira, Luiz Filipe, additional, and Lopes, Fabricio Martins, additional
- Published
- 2023
- Full Text
- View/download PDF
3. Functional Characterization of ent-Copalyl Diphosphate Synthase and Kaurene Synthase Genes from Coffea arabica L
- Author
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Ivamoto-Suzuki, Suzana Tiemi, primary, Celedón, José Miguel, additional, Yuen, Macaire M. S., additional, Kitzberger, Cíntia Sorane Good, additional, Silva Domingues, Douglas, additional, Bohlmann, Jörg, additional, and Protasio Pereira, Luiz Filipe, additional
- Published
- 2023
- Full Text
- View/download PDF
4. Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica.
- Author
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Ariyoshi, Caroline, Sant'ana, Gustavo César, Silva Felicio, Mariane, Hiroshi Sera, Gustavo, Nogueira, Livia Maria, Rivero Rodrigues, Lucas Mateus, Vecchia Ferreira, Rafaelle, Rodrigues da Silva, Bruna Silvestre, Vilela de Resende, Mário Lúcio, Lanza Destéfano, Suzete Aparecida, Silva Domingues, Douglas, and Protasio Pereira, Luiz Filipe
- Subjects
GENOME-wide association studies ,COFFEE ,GENETIC variation ,PSEUDOMONAS syringae ,COFFEE growing ,KIWIFRUIT ,SINGLE nucleotide polymorphisms ,BINDING sites - Abstract
Bacteria halo blight (BHB), a coffee plant disease caused by Pseudomonas syringae pv. garcae, has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most Coffea arabica cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in C. arabica Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of C. arabica, we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C. arabica Ethiopian accessions from a historical FAO collection, 11 C. arabica cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to g000 (Chr_0_434_435) and g010741 genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a C. arabica susceptible cultivar and in a C. arabica cultivar with quantitative resistance, when infected with P. syringae pv. garcae. However, peaks of upregulation were observed in a C. arabica cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in C. arabica. In addition, the findings contribute to increasing understanding of the C. arabica domestication history. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
5. Flavor precursors and sensory attributes of coffee submitted to different post-harvest processing
- Author
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Good Kitzberger, Cíntia Sorane, Pot, David, Marraccini, Pierre, Protasio Pereira, Luiz Filipe, Dos Santos Scholz, Maria Brigida, Good Kitzberger, Cíntia Sorane, Pot, David, Marraccini, Pierre, Protasio Pereira, Luiz Filipe, and Dos Santos Scholz, Maria Brigida
- Abstract
Post-harvest processing (PHP) modifies the quality of the coffee and increases the value of coffee production. The choice of PHP to apply depends primarily on the available infrastructure, local climatic conditions and the desired end-value. The objective of this study was to evaluate the influence of PHP on the physico-chemical characteristics of green and roasted coffee beans and their sensory attributes. Coffee cherries from IAPAR 59 cultivar were processed as natural coffee (CN), semi-dry coffee (CD), de-pulped coffee (CP) and floating coffee (CF). Total and reducing sugars, phenolic compounds, chlorogenic acids, lipids, proteins, caffeine and water content were determined in coffee beans collected during (10thday) and at the end of each processing. The roasted beans and their sensory attributes were also analyzed. The greatest changes at the ending point of the processes were found in total and reducing sugars, phenolic compounds, chlorogenic acids and lipids contents. The PHP presented different weight loss to achieve the same visual brown color and luminosity. Beverage sensory attributes were influenced by the PHP: CN and CP coffees presented similar intensities of coffee aroma, but higher intensity of green grassy aroma, and taste were found in CF and CN coffees. Aroma and taste precursors were modified during the PHP and these were associated to husk removal of the coffee beans, suggesting an activation of the germination metabolism during the PHP. This study allowed the characterization of the effects of the different post-harvest processing on the roasted coffee beans and provides the foundations to monitor their efficiencies in the future.
- Published
- 2020
6. Transcriptome analysis of leaves, flowers and fruits perisperm of Coffea arabica L. reveals the differential expression of genes involved in raffinose biosynthesis
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Ivamoto, Suzana Tiemi, Reis Júnior, Osvaldo, Silva Domingues, Douglas, Dos Santos, Tiago Benedito, Freitas de Oliveira, Fernanda, Pot, David, Leroy, Thierry, Vieira, Luiz Gonzaga Esteves, Falsarella Carazzolle, Marcelo, Guimarães Pereira, Gonçalo Amarante, Protasio Pereira, Luiz Filipe, Ivamoto, Suzana Tiemi, Reis Júnior, Osvaldo, Silva Domingues, Douglas, Dos Santos, Tiago Benedito, Freitas de Oliveira, Fernanda, Pot, David, Leroy, Thierry, Vieira, Luiz Gonzaga Esteves, Falsarella Carazzolle, Marcelo, Guimarães Pereira, Gonçalo Amarante, and Protasio Pereira, Luiz Filipe
- Abstract
Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.
- Published
- 2017
7. Dihaploid Coffea arabica genome sequencing and assembly [W180]
- Author
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De Kochko, Alexandre, Crouzillat, Dominique, Rigoreau, Michel, Lepelley, Maud, Bellanger, Laurence, Merot l'Anthoene, Virginie, Vandecasteele, Céline, Guyot, Romain, Poncet, Valérie, Tranchant-Dubreuil, Christine, Hamon, Perla, Hamon, Serge, Couturon, Emmanuel, Descombes, Patrick, Moine, Deborah, Mueller, Lukas, Strickler, Susan R., Andrade, Alan A., Protasio Pereira, Luiz Filipe, Marraccini, Pierre, Giuliano, Giovanni, Fiore, Alessia, Pietrella, Marco, Aprea, Giuseppe, Ming, Ray, Wai, Jennifer, Domingues, Douglas S., Paschoal, Alexandre, Kuhn, Gerrit, Korlach, Jonas, Chin, Jason, Sankoff, David, Zheng, Chunfang, and Albert, Victor A.
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F30 - Génétique et amélioration des plantes - Abstract
Coffea arabica which accounts for 70% of world coffee production is an allotetraploid with a genome size of approximately 1.3 Gb and is derived from the hybridization of C. canephora (710 Mb) and C. eugenioides (670 Mb). To elucidate the evolutionary history of C. arabica, and generate critical information for breeding programs, a sequencing project is underway to finalize a reference genome using a dihaploid line and a set of 30 C. arabica accessions. For the reference genome, we have generated two assemblies, one from Illumina data (>150x coverage) and a second from PacBio sequences (>50x coverage). The present assemblies cover 1,031 and 1,042 Mb, respectively. After further refinement, using Illumina mate pairs and optical mapping, the genome assemblies will be annotated using RNA-Seq. Resequencing of C. eugenioides and C. canephora has been completed and is being used to better assess homeologs within the sub-genomes. Furthermore, 30 C. arabica accessions, representing wild and cultivated genotypes, are being resequenced (20x coverage) using Illumina. A C. arabica genetic map, currently including over 600 SSR markers, that differentiate between the two sub-genomes, is used to anchor the assemblies. Newly identified SNP markers are being added to the map. The final goals of the project are to produce a high quality reference genome, assess an eventual neo-diversification occurring in the cultivated varieties, have a better understanding of the species formation and evolution, and develop tools that will make the finished genome accessible and useful to breeders and researchers. (Texte intégral)
- Published
- 2015
8. Adaptação de acessos de Coffea arabica provenientes de Camarões em várias condições edafoclimáticas
- Author
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PIERRE CHARMETANT, Perthuis, Bernard, Mouen Bedimo, Joseph Aubert, Mbarga Manga, Amougou, Guerra, Antonio Fernando, Ferreira Bartholo, Gabriel, Cruz Rocha, Omar, Leroy, Thierry, Protasio Pereira, Luiz Filipe, Costa Rodrigues, Gustavo, Carvalho Andrade, Alan, and Pierre Marraccini
- Subjects
P40 - Météorologie et climatologie ,F70 - Taxonomie végétale et phytogéographie ,F30 - Génétique et amélioration des plantes - Abstract
O objetivo desse trabalho foi caracterizar recursos genéticos de Coffea arabica - acessos selvagens e cultivares - oriundo da África visando sua utilização no melhoramento. Os acessos provenientes de Camarões têm dados acumulados de mais de 30 anos. Oito acessos foram introduzidos em 2010 na Guiana Francesa e no Brasil para experimentação. No Brasil, depois de um período de quarentena, foram plantados ensaios no centro Cerrados da Embrapa e no IAPAR, além da Guiana Francesa Analisamos dados de crescimento, de ramificação secundária, de adaptação fisiológica à seca, para escolher genitores de cruzamentos com cultivares locais. Híbridos F1 estão sendo avaliados para selecionar os com melhor adaptação à evolução das condições climáticas.
- Published
- 2015
9. Identificação de novos acessos de Coffea arabica introduzidos na coleção da Etiópia do IAPAR
- Author
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Vecchia Ferreira, Rafaelle, Andrade, Giselly, PIERRE CHARMETANT, Leroy, Thierry, Silva Domingues, Douglas, and Protasio Pereira, Luiz Filipe
- Subjects
U30 - Méthodes de recherche ,F30 - Génétique et amélioration des plantes - Abstract
Marcadores microssatélites foram utilizados na discriminação de novos acessos de Coffea arabica que foram introduzidos na coleção da Etiópia do IAPAR, provenientes de uma coleção similar na República de Camarões. Inicialmente 46 acessos de Camarões foram repassados para a Embrapa CPAC (Embrapa Cerrados – Planaltina-DF), onde ficaram em quarentena. Em seguida, estes acessos foram transferidos para o IAPAR, porém durante os processos de quarentena e transferência, alguns dos acessos foram misturados. Visando identificar corretamente os acessos e também validar os SSRs previamente identificados, todos os 46 acessos foram analisados em géis de poliacrilamida. Os 8 locos microssatélites utilizados geraram um total de 19 alelos, com uma média de 2,3 alelos por loco. A variação alélica foi de 2 a 3 alelos por loco. Para realizar as análises de divergência genética uma matriz de distância foi computada e utilizada para obter uma árvore (dendograma) de diversidade global. Observou-se 3 diferentes agrupamentos entre os acessos ET34, Java e ET19. A análise genotípica dos diferentes locos microssatélites indicou quais acessos corresponderiam corretamente a ET34, Java ou ET19, já que este último teve o papel de controle positivo. Os marcadores microssatélites foram eficientes para discriminar os acessos de C. arabica provenientes de Camarões e o número de locos utilizado (8) também foi suficiente para a separação entre os acessos com seus respectivos genótipos.
- Published
- 2015
10. Chemical composition in wild Ethiopian Arabica coffee accessions
- Author
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Dos Santos Scholz, Maria Brigida, Good-Kitzberger, Cíntia Sorane, Pagiatto, Natalia Ferrarezi, Protasio Pereira, Luiz Filipe, Davrieux, Fabrice, Pot, David, Charmetant, Pierre, Leroy, Thierry, Dos Santos Scholz, Maria Brigida, Good-Kitzberger, Cíntia Sorane, Pagiatto, Natalia Ferrarezi, Protasio Pereira, Luiz Filipe, Davrieux, Fabrice, Pot, David, Charmetant, Pierre, and Leroy, Thierry
- Abstract
The exploration of accessions originating from Ethiopia is one option available to increase the genetic basis of new coffee cultivars. The aim of this study was to describe the chemical composition variability of Ethiopian coffee accessions maintained in Londrina and to evaluate the year effect on that. We observed no significant interaction between the years of cultivation and the amounts of caffeine, protein, lipids, chlorogenic acids, sucrose, cafestol and kahweol, thereby suggesting that evaluations of one year were reliable to describe this collection. All compounds showed variability, but the highest variability was found in cafestol and kahweol (32.81 and 34.45 %, respectively). Significant correlations among caffeine, chlorogenic acids and protein as well as between sucrose and lipids were observed. A significant negative correlation was found between kahweol and cafestol, and kahweol had positive and negative correlation with caffeine and chlorogenic acids, respectively. Hierarchical clustering analyses identified groups in the population, and the diversity found in one crop year was similar to that for 3 years. Greater diversity of composition was observed among the Western accessions compared to the ones from the East, but no clear separation was found between the accessions of these regions. These accessions are potential sources to increase the genetic diversity to obtain new coffee cultivars. (Résumé d'auteur)
- Published
- 2016
11. Identificação de polimorfismos em genótipos de Coffea arabica de uma coleção da Etiópia : [n.142]
- Author
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Yuyama, Priscilla Mary, Pot, David, Dereeper, Alexis, Pointet, Stéphanie, Gonçalves Dias da Silva, João Batista, Hiroshi Sera, Gustavo, Sera, Tumoru, Charmetant, Pierre, Silva Domingues, Douglas, Leroy, Thierry, and Protasio Pereira, Luiz Filipe
- Subjects
F30 - Génétique et amélioration des plantes - Abstract
Os marcadores moleculares são ferramentas importantes para acelerar os programas de melhoramento. Para o cafeeiro, uma espécie perene, o uso de marcadores é particularmente desejável devido ao tempo e recursos gastos para o lançamento de uma nova cultivar. Duas espécies do gênero Coffea são responsáveis por quase toda a produção de café: Coffea arabica e C. canephora. Contudo, para C. arabica, o número de marcadores polimórficos é relativamente baixo comparado a C. canephora e outras culturas, uma vez que a espécie apresenta baixa diversidade genética. Muitos estudos com marcadores genéticos foram feitos para analisar a diversidade da C. arabica, mas os resultados não foram eficientes para a discriminação genotípica detalhada e mapeamento genético. O Instituto Agronômico do Paraná (IAPAR) possui uma coleção de 132 acessos de C. arabica originários da Etiópia, que apresentam variabilidade fenotípica com potencial para serem utilizados para exploração da diversidade. Neste sentido, este estudo buscou analisar a diversidade nucleotídica pela identificação de polimorfismos, SNPs e INDELs, de uma população do centro de origem de C. arabica, associado com o sequenciamento de nova geração. O RNA-seq de dois tecidos, frutos e folhas, de quatro genótipos de C. arabica de uma população da Etiópia, C. arabica cv. Mundo Novo e de um dos seus ancestrais de C. arabica - C. eugenioides, foram sequenciados pela metodologia Illumina HiSeq2000. Os reads obtidos foram processados e posteriormente as sequências foram mapeadas em uma referência de C. canephora para identificação dos polimorfismos. Foram feitas duas estratégias: i) na primeira estratégia, foi utilizado uma ferramenta chamada SNiPloid com critérios de cobertura para o polimorfismo identificado e ii) uma segunda estratégia que considera os polimorfismos encontrados diretamente dos arquivos de detecção dos polimorfismos. Os resultados identificaram um número grande de polimorfismos. Na primeira estratégia, foram encontrados pelo menos 5.500 SNPs potenciais para a genotipagem e na segunda, 103.791 SNPs potenciais. Para essa última, ainda é necessário estabelecer critérios e filtros para escolher os polimorfismos que serão inicialmente genotipados. Os dados também mostraram a importância de utilizar um grupo mais diverso de genótipos associado com o sequenciamento de nova geração para detecção de SNPs. Este trabalho será importante para direcionar futuros trabalhos na caracterização da diversidade genética em C. arabica, além de estudos de mapeamento genético por associação.
- Published
- 2013
12. Phenotyping and genotyping genetic resources of Coffea Arabica at IAPAR. FAO collection
- Author
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Charmetant, Pierre, Ferreira, R., Andrade, Giselly, Dos Santos, M.A., Marraccini, Pierre, Leroy, Thierry, Pot, David, De Bellis, Fabien, Sera, T., and Protasio Pereira, Luiz Filipe
- Subjects
F70 - Taxonomie végétale et phytogéographie ,F30 - Génétique et amélioration des plantes - Abstract
The genetic diversity of C. arabica in Ethiopia, its region of origin, was explored. Its use for C. arabica breeding, though limited to a few F1 crosses with cultivars, proved to be efficient in terms of genetic gain regarding important coffee agronomic characteristics such as vigor, adaptability and quality. A collection derived from the 1964-65 FAO survey in Ethiopia was established at IAPAR in Londrina, PR, Brazil in 1976. Genotyping was undertaken using SSR markers that were polymorphic within these accessions. Preliminary results regarding the relation between genetic and phenotypic diversity are presented. Self pollinated progenies of 179 plants representing 115 Ethiopian accessions were established at IAPAR, from 2009 to 2012. 47 of them were also established at CPAC, DF. Various growth parameters were measured.
- Published
- 2013
13. A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W]
- Author
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Vidal, Ramon Oliveira, Mondego, Jorge M.C., Pot, David, Batista Ambrosio, Alinne, Carvalho Andrade, Alan, Protasio Pereira, Luiz Filipe, Colombo, Carlos Augusto, Vieira, Luiz Gonzaga Esteves, Carazzolle, Marcelo Falsarella, and Guimarães Pereira, Gonçalo Amarante
- Subjects
Séquence nucléotidique ,Génome ,Polymorphisme génétique ,Coffea eugenioides ,Coffea ,Coffea arabica ,F30 - Génétique et amélioration des plantes ,Coffea canephora ,Variation génétique ,PCR ,Gène ,Expression des gènes ,U30 - Méthodes de recherche - Abstract
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
- Published
- 2010
14. RNA-Seq analysis and de novo transcriptome assembly of Coffea arabica and Coffea eugenioides : P0068
- Author
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Yuyama, Priscilla Mary, Carazzolle, Marcelo Falsarella, Reis Júnior, Osvaldo, Mishima, Jaime Hikaru, Ivamoto, Suzana Tiemi, Domingues, Douglas S., Charmetant, Pierre, Leroy, Thierry, Protasio Pereira, Luiz Filipe, Yuyama, Priscilla Mary, Carazzolle, Marcelo Falsarella, Reis Júnior, Osvaldo, Mishima, Jaime Hikaru, Ivamoto, Suzana Tiemi, Domingues, Douglas S., Charmetant, Pierre, Leroy, Thierry, and Protasio Pereira, Luiz Filipe
- Abstract
Coffee is one of the most important agricultural commodites in the world. Coffea arabica, an allotetraploid from a recent hybridization of two diploid species (C.canephora and C.eugenioides) is responsible for 70% of world commercial production. Recent studies have been done to analyse transcriptome data of Coffea spp. in order to improve our knowledge in genetics and gene expression of those species. However, there is few data on coffee fruit transcriptome. In this work, RNA-Seq of two organs (whole fruit - cherry stage and mature leaves) from allotetraploid C. arabica cv. Mundo Novo and its diploid ancestor C.eugenioides, were done using Illumina HiSeq 2000 (100 bp single-end sequences). We report the generation of near 10 million reads for C.arabica (4,747,049 of fruits and 6,156,750 reads of leaves) and 7,5 million reads for C.eugenioides (3,688,364 of fruits and 3,835,373 reads of leaves). De novo assembly and digital gene expression analyses was performed to generate a collection of 35,462 contigs from C.arabica cv. Mundo Novo (average length of 691 bp) and 36,935 contigs of C.eugenioides (average length of 701 bp). Funnctional annotation were performed by sequence comparison with public databases (NCBI-nr, Swiss-prot and PlantCyc). Our results showed the presence of prevalent genes and species-specific either in C.arabica or C.eugenioides that could explain particular characteristics of these two species. Characterization of Coffea spp. transcriptome provides an effective tool for better understanding for differential gene expression in Coffea spp., providing important clues of C.arabica gene evolution, as well as valuable information for coffee breeding.
- Published
- 2013
15. Free choice profiling sensory analysis to discriminate coffees.
- Author
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Good Kitzberger, Cíntia Sorane, dos Santos Scholz, Maria Brígida, Gonçalves Dias da Silva, João Batista, de Toledo Benassi, Marta, and Protasio Pereira, Luiz Filipe
- Subjects
COFFEE ,SENSES ,BITTERNESS (Taste) ,PLANT genetics ,TURBIDITY - Abstract
Sensory attributes were evaluated from Arabica coffee genotypes growing in two places in Brazil, Mandaguari and Londrina. Post-harvest and roasted process was standardized. Free choice profiling sensory analysis was apply to investigate the influence of genetic variability and local cultivation (Londrina and Mandaguari, Brazil) on the sensory characteristics of coffee genotypes. A sensory panel evaluated coffees from Mandaguari in two groups: one (Sarchimor derived, IPR100, IPR102, IPR105, IPR106) characterized by transparency, coffee colour, green aroma, taste (green, bitter, fermented, astringent) and a watery texture, another group (Catuaí, Sarchimor derived, IPR101, IPR103) was characterized by coffee colour, brightness, aroma (coffee, acid, sweet, chocolate), acidity, bitterness, burnt aroma, sweetness and full-bodied. Coffees from Londrina presented brightness, coffee colour, sweet, green, burnt aroma, astringent, bitter, fermented, green taste; and watery texture (Catuaí, IPR97, IPR98, IPR100). Another group (Sarchimor derived, IPR101, IPR102, IPR103, IPR105, IPR106) were associated with turbidity, aroma (green, coffee, sweet), acidity, astringency, bitterness, sweetness and full-bodied. Catuaí, Iapar59, IPR99, IPR101, IPR103 and IPR108 exhibited positive attributes when grown in either locale. Edaphoclimatic conditions play a major role in the sensory profiles of coffee. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
16. Effects of shade on the development and sugar metabolism of coffee (Coffea arabica L.) fruits
- Author
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Geromel, Clara, primary, Ferreira, Lúcia Pires, additional, Davrieux, Fabrice, additional, Guyot, Bernard, additional, Ribeyre, Fabienne, additional, Brígida dos Santos Scholz, Maria, additional, Protasio Pereira, Luiz Filipe, additional, Vaast, Philippe, additional, Pot, David, additional, Leroy, Thierry, additional, Filho, Armando Androcioli, additional, Esteves Vieira, Luiz Gonzaga, additional, Mazzafera, Paulo, additional, and Marraccini, Pierre, additional
- Published
- 2008
- Full Text
- View/download PDF
17. A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica.
- Author
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Vidal, Ramon Oliveira, Costa Mondego, Jorge Maurício, Pot, David, Ambrósio, Alinne Batista, Andrade, Alan Carvalho, Protasio Pereira, Luiz Filipe, Colombo, Carlos Augusto, Esteves Vieira, Luiz Gonzaga, Carazzolle, Marcelo Falsarella, and Guimarães Pereira, Gonçalo Amarante
- Subjects
COFFEE ,FARM produce ,CROPS ,PESTS ,DROUGHTS ,GENES - Abstract
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
18. Evaluation of the stress-inducible production of proline in transgenic sugarcane (Saccharum spp.): osmotic adjustment, chlorophyll fluorescence and oxidative stress.
- Author
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Correa Molinari, Hugo Bruno, Marur, Celso Jamil, Daros, Edelclaiton, Freitas de Campos, Marília Kaphan, Portela de Carvalho, Jane Fiuza Rodrigues, Bespalhok Filho, João Carlos, Protasio Pereira, Luiz Filipe, and Esteves Vieira, Luiz Gonzaga
- Subjects
PROLINE ,SUGAR crops ,MALONDIALDEHYDE ,PLANT-water relationships ,TRANSGENIC plants ,WATER in agriculture ,PLANT species ,PLANT genetic engineering - Abstract
Proline accumulates in a variety of plant species in response to stresses such as drought, salinity and extreme temperatures. Although its role in plant osmotolerance remains controversial, proline is thought to contribute to osmotic adjustment, detoxification of reactive oxygen species and protection of membrane integrity. In the present study, we evaluated the effects of stress-inducible proline production on osmotic adjustment, chlorophyll fluorescence and oxidative stress protection in transgenic sugarcane transformed with a heterologous P5CS gene. In well-watered conditions, free proline, malondialdehyde (MDA) levels, Fv/Fm ratios and chlorophyll contents (Chls) in transgenic sugarcane were not statistically different from non-transformed control plants. After 9 days without irrigation, proline content in transgenic events was on the average 2.5-fold higher than in controls. However, no osmotic adjustment was observed in plants overproducing proline during the water-deficit period. The photochemical efficiency of PSII observed was higher (65%) in the transgenic events at the end of the water-deficit experiment. The effects of proline on lipid peroxidation as MDA levels and on the decline of Chl in paraquat-treated leaf discs along the drought period suggest that proline protected the plants against the oxidative stress caused by the water deficit. The overall capacity of transgenic plants to tolerate water-deficit stress could be assessed by the significantly higher biomass yields 12 days after withholding water. These results suggest that stress-inducible proline accumulation in transgenic sugarcane plants under water-deficit stress acts as a component of antioxidative defense system rather than as an osmotic adjustment mediator. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
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19. RNA-Seq analysis and de novo transcriptome assembly of #Coffea arabica# and #Coffea eugenioides# : P0068
- Author
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Yuyama, Priscilla Mary, Carazzolle, Marcelo Falsarella, Reis Júnior, Osvaldo, Mishima, Jaime Hikaru, Ivamoto, Suzana Tiemi, Domingues, Douglas S., PIERRE CHARMETANT, Leroy, Thierry, and Protasio Pereira, Luiz Filipe
- Subjects
F30 - Génétique et amélioration des plantes - Abstract
Coffee is one of the most important agricultural commodites in the world. Coffea arabica, an allotetraploid from a recent hybridization of two diploid species (C.canephora and C.eugenioides) is responsible for 70% of world commercial production. Recent studies have been done to analyse transcriptome data of Coffea spp. in order to improve our knowledge in genetics and gene expression of those species. However, there is few data on coffee fruit transcriptome. In this work, RNA-Seq of two organs (whole fruit - cherry stage and mature leaves) from allotetraploid C. arabica cv. Mundo Novo and its diploid ancestor C.eugenioides, were done using Illumina HiSeq 2000 (100 bp single-end sequences). We report the generation of near 10 million reads for C.arabica (4,747,049 of fruits and 6,156,750 reads of leaves) and 7,5 million reads for C.eugenioides (3,688,364 of fruits and 3,835,373 reads of leaves). De novo assembly and digital gene expression analyses was performed to generate a collection of 35,462 contigs from C.arabica cv. Mundo Novo (average length of 691 bp) and 36,935 contigs of C.eugenioides (average length of 701 bp). Funnctional annotation were performed by sequence comparison with public databases (NCBI-nr, Swiss-prot and PlantCyc). Our results showed the presence of prevalent genes and species-specific either in C.arabica or C.eugenioides that could explain particular characteristics of these two species. Characterization of Coffea spp. transcriptome provides an effective tool for better understanding for differential gene expression in Coffea spp., providing important clues of C.arabica gene evolution, as well as valuable information for coffee breeding.
20. A new set of quantitative trait loci linked to lipid content in Coffea arabica.
- Author
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Lima Muniz, Herison Victor, Ariyoshi, Caroline, Vecchia Ferreira, Rafaelle, Silva Felicio, Mariane, and Protasio Pereira, Luiz Filipe
- Subjects
- *
LOCUS (Genetics) , *COFFEE , *COFFEE beans , *GENOME-wide association studies , *LIPID metabolism , *PRINCIPAL components analysis , *LIPIDS - Abstract
Lipids are compounds that play an important role in coffee bean development, contributing to beverage quality. Genome-wide association studies (GWAS) were conducted to pinpoint quantitative trait nucleotides (QTNs) linked to lipid metabolism in Coffea arabica. Genotyping by sequencing (GBS) and phenotyping data from 104 wild C. arabica accessions, Mundo Novo cultivar, and C. arabica var. Typica were utilized. GBS data were aligned to C. arabica Et039 reference genome, and both single-locus and multi-locus GWAS methods were employed. Methods were adjusted for kinship matrix, population structure, and principal component analysis. Of the 19 QTNs identified, 5 showed consistency across different population structure adjustments. The multi-locus methods mrMLM and FarmCPU proved more effective in identifying QTNs associated with lipid content. Four QTNs were situated near seven genes potentially involved in lipid metabolism. Higher frequencies of identified QTNs in accessions with elevated lipid content suggest their utility as markers for coffee plant breeding. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
21. Assisted selection using molecular markers linked to rust resistance SH3 gene in Coffea arabica.
- Author
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Silva, Angelita Garbossi, Ariyoshi, Caroline, Harumi Shigueoka, Luciana, Protasio Pereira, Luiz Filipe, and Gustavo Hiroshi Sera
- Subjects
- *
COFFEE , *PLANT DNA , *GENES , *COFFEE growing , *GENOTYPES - Abstract
The aim of this work was to validate markers linked to the SH3 gene of coffee leaf rust (CLR) resistance and use them in assisted selection. Initially, we validated the markers in genotypes already known to carry SH3. Next, we performed phenotype and genotype evaluation for resistance to CLR in coffee plants growing under field conditions. We used Arabica coffee progenies derived from BA-10, which carries the SH3 gene due to introgression of C. liberica. Three SCAR markers (SP-M16-SH3, BA-48-21O-f, and BA-124-12K-f) and one SSR marker (Sat244) linked to SH3 gene were used to amplify the coffee plants' DNA. Our assessments of markers validation in resistant genotypes, SP-M16-SH3 and BA-124-12K-f, were efficient to identify the SH3 gene. These two markers were used to evaluate the progenies derived from BA-10 and were significantly linked to the phenotype evaluations. The SP-M16-SH3 marker was more efficient, with the advantage of being codominant. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
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