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A new set of quantitative trait loci linked to lipid content in Coffea arabica
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Muniz, Herison Victor Lima

; Ariyoshi, Caroline

; Ferreira, Rafaelle Vecchia

; Felicio, Mariane Silva

; Pereira, Luiz Filipe Protasio

Crop Breeding and Applied Biotechnology

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2024, Volume 24 N. 2 elocation e478824212

Abstract: En | Text: En | PDF: En

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. development quality Genomewide Genome wide (GWAS (QTNs (GBS 10 C cultivar var utilized Et Et03 genome singlelocus single locus multilocus multi employed matrix analysis 1 adjustments breeding Et0

https://doi.org/10.1590/1984-70332024v24n2a25

Assisted selection using molecular markers linked to rust resistance SH3 gene in Coffea arabica SH
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Silva, Angelita Garbossi

; Ariyoshi, Caroline

; Shigueoka, Luciana Harumi

; Pereira, Luiz Filipe Protasio

; Sera, Gustavo Hiroshi

Crop Breeding and Applied Biotechnology

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2023, Volume 23 N. 4 elocation e445323413

Abstract: En | Text: En | PDF: En

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. SH (CLR selection Initially Next conditions BA10, BA10 BA 10, 10 C liberica SPM16SH3, SPM16SH3 SPMSH SP M16 SH3, M (SP-M16-SH3 BA4821Of, BA4821Of BAOf 48 21O f, f O BA-48-21O-f BA12412Kf BAKf 124 12K K BA-124-12K-f Sat244 Sat (Sat244 DNA SP-M16-SH BA12412Kf, BA-1 evaluations codominant BA1 1 SPM SPM16SH M1 (SP-M16-SH Of 4 Kf 12 Sat24 (Sat24 BA- Sat2 (Sat2 (Sat

https://doi.org/10.1590/1984-70332023v23n4a48

Influence of Silver Nitrate on Somatic Embryogenesis Induction in Arabica Coffee (Coffea arabica L.)
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Rojas-Lorz, Laura

; Arrieta-Espinoza, Griselda

; Valdez-Melara, Marta

; Pereira, Luiz Filipe Protasio

; Gatica-Arias, Andrés

Brazilian Archives of Biology and Technology

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2019, Volume 62 elocation e19180228

Abstract: En | Text: En | PDF: En

Abstract The influence of silver nitrate (AgNO3), benzyladenine (BAP), and indole-3-acetic acid (IAA) on low frequency somatic embryogenesis (LFSE) induction in Caturra and Catuaí arabica coffee was evaluated. For the Caturra cultivar, the production of somatic embryos was significantly increased by adding AgNO3 to the semisolid culture medium. The highest average number of somatic embryos for this cultivar was obtained using 6.6 μM BAP, 2.85 μM IAA, and 40 μM AgNO3. In contrast, for the Catuaí cultivar, the highest average number of somatic embryos was obtained using semisolid medium supplemented with 8.8 μM BAP, and 2.85 μM IAA. Using these protocols, somatic embryos were directly induced using leaf sections of in vitro plants of both coffee cultivars within 8 weeks. The somatic embryos developed into rooted plants with a 100% survival rate upon transfer to the greenhouse.

https://doi.org/10.1590/1678-4324-2019180228 831 downloads

Galactinol synthase transcriptional profile in two genotypes of Coffea canephora with contrasting tolerance to drought
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Santos, Tiago Benedito Dos

; Lima, Rogério Barbosa de

; Nagashima, Getúlio Takashi

; Petkowicz, Carmen Lucia de Oliveira

; Carpentieri-Pípolo, Valéria

; Pereira, Luiz Filipe Protasio

; Domingues, Douglas Silva

; Vieira, Luiz Gonzaga Esteves

Genetics and Molecular Biology

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jun 2015, Volume 38 N. 2 Pages 182 - 190

Abstract: En | Text: En | PDF: En

Increased synthesis of galactinol and raffinose family oligosaccharides (RFOs) has been reported in vegetative tissues in response to a range of abiotic stresses. In this work, we evaluated the transcriptional profile of a Coffea canephora galactinol synthase gene (CcGolS1) in two clones that differed in tolerance to water deficit in order to assess the contribution of this gene to drought tolerance. The expression of CcGolS1 in leaves was differentially regulated by water deficit, depending on the intensity of stress and the genotype. In clone 109A (drought-susceptible), the abundance of CcGolS1 transcripts decreased upon exposure to drought, reaching minimum values during recovery from severe water deficit and stress. In contrast, CcGolS1 gene expression in clone 14 (drought-tolerant) was stimulated by water deficit. Changes in galactinol and RFO content did not correlate with variation in the steady-state transcript level. However, the magnitude of increase in RFO accumulation was higher in the tolerant cultivar, mainly under severe water deficit. The finding that the drought-tolerant coffee clone showed enhanced accumulation of CcGolS1 transcripts and RFOs under water deficit suggests the possibility of using this gene to improve drought tolerance in this important crop.

https://doi.org/10.1590/S1415-475738220140171 3449 downloads

Composição química de cafés árabica de cultivares tradicionais e modernas
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Kitzberger, Cíntia Sorane Good

; Scholz, Maria Brígida dos Santos

; Pereira, Luiz Filipe Protasio

; Benassi, Marta de Toledo

Pesquisa Agropecuária Brasileira

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nov 2013, Volume 48 N. 11 Pages 1498 - 1506

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

O objetivo deste trabalho foi avaliar a influência da diversidade genética sobre a composição química de cultivares modernas e tradicionais de café arábica brasileiro. Cultivares tradicionais (Bourbon, Catuaí e Icatu) e modernas (Iapar 59, IPR 98, IPR 99 e IPR 103) foram cultivadas nas mesmas condições edafoclimáticas e submetidas a tratamentos pós-colheita padronizados. Determinaram-se os teores de sacarose, açúcares redutores, ácidos orgânicos (quínico, málico e cítrico), compostos fenólicos totais, ácido 5-cafeoilquínico, compostos nitrogenados (proteína, trigonelina e cafeína), lipídeos totais, cafestol e caveol. A diversidade genética confere variabilidade à composição do café e permite a discriminação entre cultivares tradicionais e modernas. As cultivares modernas apresentam maior teor de ácidos málico e 5-cafeoilquínico, lipídeos totais, caveol e trigonelina. Os parâmetros caveol e a relação caveol/cafestol são propostos como discriminadores entre cultivares modernas e tradicionais, uma vez que a introgressão de genes de Coffea canephora aumenta os teores de caveol e os valores da relação caveol/cafestol.

The objective of this work was to evaluate the influence of genetic diversity on the chemical composition of traditional and modern cultivars of Brazilian arabica coffee. Traditional (Bourbon, Catuaí and Icatu) and modern cultivars (Iapar 59, IPR 98, IPR 99, and IPR 103) were subjected to the same edaphoclimatic conditions, and to standardized post-harvest treatments. Contents of sucrose, reducing sugars, organic acids (quinic, malic, and citric), total phenolic compounds, 5-caffeoylquinic acid, nitrogenous compounds (protein, caffeine, and trigonelline), total lipids, cafestol, and kahweol were determined. Genetic diversity provides variability in coffee composition, allowing the discrimination between traditional and modern cultivars. Modern cultivars have higher contents of malic and 5-caffeoylquinic acids, total lipids, kahweol and trigonelline. The parameters kahweol and the kahweol/cafestol ratio are proposed as discriminators between traditional and modern cultivars, since the introgression of genes from Coffea canephora increase the kahweol content and the values of kahweol/cafestol ratio.

https://doi.org/10.1590/S0100-204X2013001100011 4389 downloads Cited 1 time in SciELO

Produção de prolina e suscetibilidade ao glufosinato de amônio em plantas transgênicas de citrumelo Swingle
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Carneiro, Cristine Elizabeth Alvarenga

; Molinari, Hugo Bruno Correa

; Andrade, Giselly Aparecida

; Pereira, Luiz Filipe Protasio

; Vieira, Luiz Gonzaga Esteves

Pesquisa Agropecuária Brasileira

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may 2006, Volume 41 N. 5 Pages 747 - 753

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

O objetivo deste trabalho foi avaliar a sensibilidade de plantas transgênicas de citrumelo Swingle com elevada produção de prolina, ao herbicida glufosinato de amônio. As plantas utilizadas apresentavam a inserção do gene mutante da enzima delta1-pirrolina-5-carboxilato sintetase (P5CS), responsável pela biossíntese de prolina. A expressão do gene p5cs em plantas transgênicas causou aumento nas quantidades de prolina em tecidos foliares, em até cinco vezes, quando comparadas às plantas-controle tratadas com 200 µM de glufosinato de amônio. As plantas transgênicas acumularam maior quantidade de NH4+ nas folhas, em relação às plantas não-transgênicas. Os danos causados pelo herbicida foram avaliados in vitro, utilizando-se discos foliares cultivados em meio MS com diferentes concentrações de glufosinato de amônio. Observou-se maior clorose em discos foliares das plantas transgênicas, o que comprova a maior suscetibilidade de plantas de citrumelo Swingle com alta produção de prolina ao herbicida.

The objective of this work was to evaluate the susceptibility to glufosinate ammonium of transgenic plants of Swingle citrumelo with high proline production. The mutant gene of the enzyme delta1-pyrroline-5-carboxylate synthetase (P5CS), the rate-limiting enzyme in proline biosynthesis, was inserted into Swingle citrumelo plants. The expression of the gene p5cs caused up to 5-fold increase on the proline content in leaf tissues of transgenic plants treated with 200 µM glufosinate ammonium, when compared with control plants. Leaves of transgenic plants accumulated higher amounts of NH4+ than the nontransgenic control. The herbicide toxicity was evaluated using leaf disks cultivated in MS medium, containing different concentrations of glufosinate ammonium. The severity of the chlorosis, observed in leaf disks of transgenic plants, confirmed the higher susceptibility of Swingle citrumelo plants, with high proline production, to this herbicide.

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Genetic transformation of coffee
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Ribas, Alessandra Ferreira

; Pereira, Luiz Filipe Protasio

; Vieira, Luiz Gonzaga E.

Brazilian Journal of Plant Physiology

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mar 2006, Volume 18 N. 1 Pages 83 - 94

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

Nos últimos 15 anos, vários avanços foram obtidos na transformação genética de café. Diferentes grupos de pesquisa no mundo obtiveram plantas de café transformadas com genes para resistência a insetos, café descafeinado, resistência a herbicidas e controle da maturação de frutos. Apesar da maioria dos trabalhos ainda estar restrito a laboratórios e casas de vegetação, os primeiros dados de café em testes de campo começaram a surgir. Nesta revisão, os principais e mais recentes trabalhos em transformação do cafeeiro são apresentados, principalmente os aspectos técnicos de cultura de tecidos, estratégias de seleção e transformação via bombardeamento de partículas e via Agrobacterium tumefaciens. As aplicações potenciais desta tecnologia considerando possíveis riscos e benefícios assim como aspectos de mercado e consumo são também discutidos.

In the last 15 years, considerable advances were made in coffee genetic transformation. Different research groups in the world have been able to transform coffee with genes for insect resistance, decaffeinated coffee, herbicide resistance and control of fruit maturation. Although the majority of the research is still limited to laboratory and greenhouse studies, initial field tests with transformed coffee are beginning to appear in the literature. In this review we provide an update on the state of coffee genetic transformation, presenting technical aspects related to tissue culture systems, strategies for selection and transformation with particle bombardment, as well as the use of Agrobacterium tumefaciens. We also discuss the potential applications of this technology, taking into consideration the benefits, the possible environmental risks, as well as market and consumer issues.

10690 downloads Cited 2 times in SciELO

Brazilian coffee genome project: an EST-based genomic resource
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Vieira, Luiz Gonzaga Esteves

; Andrade, Alan Carvalho

; Colombo, Carlos Augusto

; Moraes, Ana Heloneida de Araújo

; Metha, Ângela

; Oliveira, Angélica Carvalho de

; Labate, Carlos Alberto

; Marino, Celso Luis

; Monteiro-Vitorello, Claúdia de Barros

; Monte, Damares de Castro

; Giglioti, Éder

; Kimura, Edna Teruko

; Romano, Eduardo

; Kuramae, Eiko Eurya

; Lemos, Eliana Gertrudes Macedo

; Almeida, Elionor Rita Pereira de

; Jorge, Érika C.

; Albuquerque, Érika V. S.

; Silva, Felipe Rodrigues da

; Vinecky, Felipe

; Sawazaki, Haiko Enok

; Dorry, Hamza Fahmi A.

; Carrer, Helaine

; Abreu, Ilka Nacif

; Batista, João A. N.

; Teixeira, João Batista

; Kitajima, João Paulo

; Xavier, Karem Guimarães

; Lima, Liziane Maria de

; Camargo, Luis Eduardo Aranha de

; Pereira, Luiz Filipe Protasio

; Coutinho, Luiz Lehmann

; Lemos, Manoel Victor Franco

; Romano, Marcelo Ribeiro

; Machado, Marcos Antonio

; Costa, Marcos Mota do Carmo

; Sá, Maria Fátima Grossi de

; Goldman, Maria Helena S.

; Ferro, Maria Inês T.

; Tinoco, Maria Laine Penha

; Oliveira, Mariana C.

; Van Sluys, Marie-Anne

; Shimizu, Milton Massao

; Maluf, Mirian Perez

; Eira, Mirian Therezinha Souza da

; Guerreiro Filho, Oliveiro

; Arruda, Paulo

; Mazzafera, Paulo

; Mariani, Pilar Drummond Sampaio Correa

; Oliveira, Regina L.B.C. de

; Harakava, Ricardo

; Balbao, Silvia Filippi

; Tsai, Siu Mui

; Mauro, Sonia Marli Zingaretti di

; Santos, Suzana Neiva

; Siqueira, Walter José

; Costa, Gustavo Gilson Lacerda

; Formighieri, Eduardo Fernandes

; Carazzolle, Marcelo Falsarella

; Pereira, Gonçalo Amarante Guimarães

Brazilian Journal of Plant Physiology

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mar 2006, Volume 18 N. 1 Pages 95 - 108

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

O café é um dos principais produtos agrícolas, sendo considerado o segundo item em importância do comércio internacional de "commodities". O gênero Coffea pertence à família Rubiaceae que também inclui outras plantas importantes. Este gênero contém aproximadamente 100 espécies, mas a produção comercial é baseada somente em duas espécies, Coffea arabica e Coffea canephora, que representam aproximadamente 70 % e 30 % do mercado total de café, respectivamente. O Projeto Genoma Café Brasileiro foi desenvolvido com o objetivo de disponibilizar os modernos recursos da genômica à comunidade científica e aos diferentes segmentos da cadeia produtiva do café. Para isso, foram seqüenciados 214.964 clones escolhidos aleatoriamente de 37 bibliotecas de cDNA de C. arabica, C. canephora e C. racemosa representando estádios específicos do desenvolvimento de células e de tecidos do cafeeiro, resultando em 130.792, 12.381 e 10.566 seqüências de cada espécie, respectivamente, após processo de trimagem. Os ESTs foram agrupados em 17.982 contigs e em 32.155 singletons. A comparação destas seqüências pelo programa BLAST revelou que 22 % não tiveram nenhuma similaridade significativa às seqüências no banco de dados do National Center for Biotechnology Information (de função conhecida ou desconhecida). A base de dados de ESTs do cafeeiro resultou na identificação de cerca de 33.000 unigenes diferentes. Os resultados de anotação das seqüências foram armazenados em base de dados "online" em <A HREF="http://www.lge.ibi.unicamp.br/cafe">http://www.lge.ibi.unicamp.br/cafe</A>. Os recursos desenvolvidos por este projeto disponibilizam ferramentas genéticas e genômicas que podem ser decisivas para a sustentabilidade, a competitividade e a futura viabilidade da agroindústria cafeeira nos mercados interno e externo.

Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa, representing specific stages of cells and plant development that after trimming resulted in 130,792, 12,381 and 10,566 sequences for each species, respectively. The ESTs clustered into 17,982 clusters and 32,155 singletons. Blast analysis of these sequences revealed that 22 % had no significant matches to sequences in the National Center for Biotechnology Information database (of known or unknown function). The generated coffee EST database resulted in the identification of close to 33,000 different unigenes. Annotated sequencing results have been stored in an online database at <A HREF="http://www.lge.ibi.unicamp.br/cafe">http://www.lge.ibi.unicamp.br/cafe</A>. Resources developed in this project provide genetic and genomic tools that may hold the key to the sustainability, competitiveness and future viability of the coffee industry in local and international markets.

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Production of herbicide-resistant coffee plants (Coffea canephora P.) via Agrobacterium tumefaciens-mediated transformation
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Ribas, Alessandra Ferreira

; Kobayashi, Adilson Kenji

; Pereira, Luiz Filipe Protasio

; Vieira, Luiz Gonzaga Esteves

Brazilian Archives of Biology and Technology

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jan 2006, Volume 49 N. 1 Pages 11 - 19

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

Plantas transgênicas de Coffea canephora P resistentes ao herbicida glufosinato de amônio foram regeneradas a partir de explantes foliares co-cultivados com Agrobacterium tumefaciens EHA105 contendo o plasmídio pCambia3301 que contém os genes bar e uidA ambos sob controle do promotor 35S. Embriogênese somática direta foi induzida no meio contendo ¼ da concentração de macro, metade da concentração de micronutrientes do meio MS, constituintes orgânicos do meio B5 e 30 g.L-1 de sacarose suplementado com 5µM N6 - (2-isopentenil)-adenina (2-iP) e 10 µM de glufosinato de amônio para seleção de embriões transgênicos putativos. A presença e a integração do gene bar foram confirmados pelas análises de PCR e Southern blot. As plantas transgênicas selecionadas de café, pulverizadas com 1600 mg.L-1 do herbicida FinaleTM que contém glufosinato como ingrediente ativo, mantiveram a coloração e continuaram crescendo normalmente na aclimatação ex vitro.

Transgenic plants of Coffea canephora P. resistant to the herbicide ammonium glufosinate were regenerated from leaf explants after co-culture with Agrobacterium tumefaciens strain EHA105 harboring pCambia3301, a plasmid that contains the bar and the uidA genes both under control of 35S promoter. Direct somatic embryogenesis was induced on basal medium contained ¼ strength macro salts and half strength micro salts of MS medium, organic constituents of B5 medium and 30 g.L-1 sucrose supplemented with 5µM N6 - (2-isopentenyl)-adenine (2-iP). Ten µM ammonium glufosinate was used for putative transgenic somatic embryos selection. Presence and integration of the bar gene were confirmed by PCR and Southern blot analysis. Selected transgenic coffee plants sprayed with up to 1600 mg.L-1 of FinaleTM, a herbicide containing glufosinate as the active ingredient, retained their pigmentation and continued to grow normally during ex vitro acclimation.

4740 downloads Cited 3 times in SciELO

10.

Ethylene production and acc oxidase gene expression during fruit ripening of Coffea arabica L.
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Pereira, Luiz Filipe Protasio

; Galvão, Rafaelo M.

; Kobayashi, Adilson K.

; Cação, Sandra Maria B.

; Vieira, Luiz Gonzaga Esteves

Brazilian Journal of Plant Physiology

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sep 2005, Volume 17 N. 3 Pages 283 - 289

Abstract: Pt En | Text: Pt En | PDF: Pt | PDF: En

O fitormônio etileno está associado a vários eventos fisiológicos e etapas de desenvolvimento da plantas. A enzima 1-aminociclopropano-1-carboxilato oxidase (ACO) catalisa o último passo da biossíntese desse fitormônio. Neste trabalho, estudou-se a produção de etileno durante a maturação de frutos de café, assim como a expressão do gene de ACC oxidase de cafeeiro durante a maturação e em diferentes órgãos da planta. Verificou-se rápido crescimento na produção de etileno em frutos verde-cana, após o final da formação do endosperma, com um decréscimo nos frutos-cereja, indicando uma fase climatérica na maturação. Usando oligonucleotídeos previamente descritos, efetuou-se a clonagem e caracterização de um gene de ACO de C. arabica (Ca-ACO). A seqüência de nucleotídeos, assim como a de aminoácidos, demonstrou alta similaridade com ACO de frutos climatéricos. O padrão de transcrição gênica de Ca-ACO em frutos em diferentes fases de maturação e em diferentes tecidos foi analisado em Northern Blots. Frutos verdes apresentaram a menor transcrição de Ca-ACO, com um aumento a partir dos frutos verde-cana, havendo pouca alteração nas etapas subseqüentes de maturação, sugerindo a atuação de mecanismos de controle pós-transcricionais. Os resultados indicam a natureza climatérica da maturação dos frutos de café.

The phytohormone ethylene is involved in several physiological and developmental processes in higher plants, including ripening of fruits, abscission of organs and tissues, senescence, wound response as well as in other abiotic stresses. The enzyme 1-aminocyclopropane-1-carboxylate oxidase (ACO) catalyzes the last step of ethylene biosynthesis. The production of ethylene and the expression of a Coffea arabica ACO gene during the last stages of fruit maturation were investigated. A rapid increase of ethylene production at the green-yellow stage of fruit ripening, after the end of endosperm formation, and a decrease of ethylene production at the cherry stage indicates a climacteric phase during ripening. An ACC oxidase (Ca-ACO) from coffee fruit cDNA was cloned and characterized using primers previously reported. The cDNA is homologous to previously described ACC oxidase cDNA in Coffea. The nucleotide and amino acid deduced sequences of the clone showed high homology with ACO from climacteric fruits. Northern blots were performed to determine the Ca-ACO transcription pattern from different tissues and from fruits at different ripening stages. Coffee fruits at an early ripening stage (green) showed the lowest level of Ca-ACO transcript accumulation. The transcript levels of Ca-ACO did not change significantly during the later stages, suggesting the presence of post- transcriptional control mechanisms. These results, taken together, strongly suggest a climacteric nature of coffee fruit ripening.

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