Coffee (<i>Coffea arabica</i> L.) genes early expressed during infection by the rust fungus (<i>Hemileia vastatrix</i>)

Fernandez, Diana; Santos, Patrícia da Conceição Ferreira dos; Agostini, Caroline; Bon, Marie‐Claude; Petitot, Anne‐Sophie; Silva, Maria do Céu; Guerra‐Guimarães, Leonor; Ribeiro, Ana Isabel; Argout, Xavier; Nicole, Michel

doi:10.1111/j.1364-3703.2004.00250.x

Cited by 76 publications

(77 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…A partir das sequências publicadas (Chen et al, 2003;Fernandez et al, 2004;Lin et al, 2005;Ganesh et al, 2006), foram identificadas 66 sequências do CafEST relacionadas à resistência do cafeeiro a doenças.…”

Section: Resultsunclassified

“…Vários estudos relatam a identificação de genes de cafeeiros relacionados à resistência a patógenos com uso de técnicas moleculares (Chen et al, 2003;Fernandez et al, 2004;Lin et al, 2005;Ganesh et al, 2006;Guzzo et al, 2009 Em relação aos 26 pares de iniciadores que não apresentaram polimorfismo, como o CARF 028 (Figura 1), os fragmentos podem ter apresentado polimorfismos de um único nucleotídeo ao longo da sequência e, por isso, não puderam ser observados por eletroforese em gel de agarose ou poliacrilamida. Essa diferença, provavelmente é resultado do padrão de expressão diferente desses genes entre indivíduos resistentes e susceptíveis, pode ser verificada por meio de análises de enzima de restrição e por meio de sequenciamento para detecção de SNPs ("single nucleotide polymorphisms").…”

Section: Resultsunclassified

“…Sequências publicadas, já disponíveis em bancos de dados públicos, que codificam genes de cafeeiros relacionados à resistência a patógenos (Chen et al, 2003;Fernandez et al, 2004;Lin et al, 2005;Ganesh et al, 2006), também foram usadas na mineração. Foi utilizada a ferramenta "search Blast local" do CafEST, para realizar uma busca por similaridade entre as sequências publicadas e as do CafEST.…”

Section: Methodsunclassified

See 2 more Smart Citations

Marcadores moleculares derivados de sequências expressas do genoma café potencialmente envolvidas na resistência à ferrugem

Alvarenga

Caixeta

Hufnagel

et al. 2011

Pesq. agropec. bras.

View full text Add to dashboard Cite

Resumo -O objetivo deste trabalho foi identificar marcadores moleculares relacionados à resistência do cafeeiro (Coffea arabica) à ferrugem (Hemileia vastatrix). Foram identificadas sequências de DNA potencialmente envolvidas na resistência do cafeeiro a doenças, por meio de análise "in silico", a partir das informações geradas pelo Projeto Brasileiro do Genoma Café. A partir das sequências mineradas, foram desenhados 59 pares de iniciadores para amplificá-las. Os 59 iniciadores foram testados em 12 cafeeiros resistentes e 12 susceptíveis a H. vastatrix. Vinte e sete iniciadores resultaram em bandas únicas e bem definidas, enquanto um deles amplificou fragmento de DNA em todos os cafeeiros resistentes, mas não nos suscetíveis. Esse marcador molecular polimórfico amplificou uma região do DNA que corresponde a uma janela aberta de leitura parcial do genoma de C. arabica que codifica uma proteína de resistência a doenças. O marcador CARF 005 é capaz de diferenciar os cafeeiros analisados em resistentes e susceptíveis a H. vastatrix.Termos para indexação: Coffea arabica, Hemileia vastatrix, bioinformática, EST-PCR, genes de resistência, mineração de dados. Molecular markers from coffee genome expressed sequences potentially involved in resistance to rustAbstract -The objective of this work was to identify molecular markers related to the resistance of coffee (Coffea arabica) to rust (Hemileia vastatrix). DNA sequences potentially involved in coffee disease resistance were identified, using "in silico" analysis, from data obtained by the Brazilian coffee genome project. After data mining, 59 primer pairs were designed to amplify the sequences identified. The 59 primers were tested on 12 resistant and 12 susceptible coffee plants to H. vastatrix. Twenty-seven primers resulted in unique and well-defined bands, while one of these amplified a DNA fragment in all resistant plants, but not in the susceptible ones. This polymorphic molecular marker amplified a region of DNA that corresponds to a partial open reading frame of C. arabica genome that encodes a disease resistance protein. The marker CARF 005 can be used to differentiate between resistant and susceptible coffee plants to H. vastatrix.

show abstract

Section: Resultsunclassified

Section: Methodsunclassified

See 1 more Smart Citation

Marcadores moleculares derivados de sequências expressas do genoma café potencialmente envolvidas na resistência à ferrugem

Alvarenga

Caixeta

Hufnagel

et al. 2011

Pesq. agropec. bras.

View full text Add to dashboard Cite

show abstract

“…In the past few years, several projects of sequencing coffee ESTs have been initiated in the USA (Mueller et al 2004), Brazil (http://www.cenargen.embrapa.br/ genomacafe/), and Europe (Fernandez et al 2004;Pallavicini et al 2004). Libraries were constructed from various organs and tissues sampled at different developmental stages.…”

Section: Genomicsmentioning

confidence: 99%

Coffee

Lebailly¹,

Anthony²

Technical Crops

View full text Add to dashboard Cite

“…The EST resources available in coffee have been reviewed by Kochko et al (2010) and are summarised in Table 2.5. A total of 246,500 ESTs have been reported with 69,801 for C. canephora, 166,133 for C. arabica and 10,566 for C. racemosa using different organs of the plant (leaves, flower, fruits and roots) at different stages of development and maturation (De Nardi et al, 2006;Fernandez et al, 2004;Lin et al, 2005;Montoya et al, 2006;Poncet et al, 2006;Salmona et al, 2008;Vieira et al, 2006). However, not all these resources are published or available, which limits their use.…”

Section: Bacterial Artificial Chromosome (Bac) Librarymentioning

confidence: 99%

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

Tran¹

View full text Add to dashboard Cite

Coffee is an important crop globally. Improving coffee quality is a primary breeding target that would benefit from understanding of trait inheritance and ancestral genetic information. However, comparatively little information exists on the genetics of quality and the relationships between wild and cultivated coffee genotypes, especially arabica coffee (Coffea arabica L.) which accounts for almost 60% of coffee production globally. The complex polyploidy genome and limited genomic information for C. arabica have impeded the progress of genetic studies. Arabica coffee is among the major organisms that do not have a reference genome. This project aimed to develop and utilise genomic resources in genetic studies of arabica coffee quality. The relationship between coffee species and the position of arabica within the Coffeeae tribe were investigated using complete chloroplast genome sequences to determine the value of these genetic resources in breeding. A draft genome sequence of arabica coffee was developed. Marker-trait associations were studied for caffeine and trigonelline, the two principal compounds known to be related to coffee quality, paving the way for developing new improved varieties with preferred levels of these compounds in the coffee beans.Chloroplast genomes of 16 coffee species were sequenced and their phylogeny constructed. Results support distinct Psilanthus and Coffea clades. It is likely that C. canephora is a hybrid that has a Psilanthus maternal genome but received much of its nuclear genome from Coffea. The maternal genomes of C. arabica and C. canephora are divergent. This result is in agreement with the fact that the chloroplast genome of arabica should be that of the maternal parent i.e. C. eugenioides. There were two species (C. humblotiana and C. tetragona) close to C. arabica and one species (P. ebracteolatus) close to C. canephora containing almost no caffeine. They could serve as important materials in arabica quality breeding and research.For the association study, 232 diverse arabica coffee accessions originating from 27 countries were harvested from the germplasm collection at CATIE (Tropical Agricultural Research and Higher Education Centre), Costa Rica. Substantial variation between genotypes was observed for bean morphology attributes. Non-volatiles including caffeine and trigonelline showed larger variation in range than was previously reported. Results of targeted analysis of 18 volatiles from 35 accessions also showed significant variation. No strong correlation was found between bean morphology and the levels of non-volatile or volatile compounds, implying that it is difficult to select for low or high non-volatile and volatile compounds based on bean physical characteristics. However, it also indicates that breeding for desirable combinations of traits (i.e. large bean size, low caffeine, high trigonelline, and favourable volatiles) is possible.ii The genome of the most popular arabica variety (K7) in Australia was sequenced. Genome assembly was performed using b...

show abstract

Coffee (Coffea arabica L.) genes early expressed during infection by the rust fungus (Hemileia vastatrix)

Cited by 76 publications

References 46 publications

Marcadores moleculares derivados de sequências expressas do genoma café potencialmente envolvidas na resistência à ferrugem

Marcadores moleculares derivados de sequências expressas do genoma café potencialmente envolvidas na resistência à ferrugem

Coffee

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

Contact Info

Product

Resources

About