The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

Privat, Isabelle; Bardil, Amélie; Bombarely, Aureliano; Séverac, Dany; Dantec, Christelle Le; Fuentes, Ivanna; Mueller, Lukas A.; Joët, Thierry; Pot, David; Foucrier, Séverine; Dussert, Stéphane; Leroy, Thierry; Journot, Laurent; Kochko, Alexandre de; Campa, Claudine; Combes, Marie‐Christine; Lebailly, Philippe; Bertrand, Benoît

doi:10.1186/1471-2164-12-5

Cited by 30 publications

(33 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This will offer opportunities for enhancing breeding progress to increase crop quality and yield, as well as to protect the coffee crop from major losses caused by diseases, insect pests and abiotic stresses related to climatic changes. Genes and their arrangement are currently being deciphered and their role is explored by studying the genome's expression at the transcriptome, proteome and metabolome levels (Andrade 2015; Gongora et al 2015;Lashermes et al 2015;Moncada et al 2015;Mueller et al 2015;Privat et al 2011;Fig. 3).…”

Section: Development and Release Of Improved Varietiesmentioning

confidence: 99%

Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review

Vossen¹,

Bertrand

Charrier³

2015

Euphytica

166

View full text Add to dashboard Cite

Arabica coffees (60 % of current world coffee production) are generally sold at considerably better prices than robustas on account of superior beverage quality. However, costs of production are much higher, mainly due to more stringent demands for soil and climatic conditions, crop management, primary processing and control of several pests and diseases including the potentially very destructive coffee leaf rust (CLR) and berry disease (CBD). Breeding for disease resistance in combination with vigour, productivity and quality started in the early 1920s in India, but especially in the second half of the 20th century comprehensive breeding programmes have been implemented in several other coffee producing countries. Many of the resulting CLR-and CBD ? CLR-resistant cultivars (true-breeding lines and F1 hybrids) meet the required standards of profitable and sustainable crop production. Challenges of more recent date include limited access to additional genetic resources of Coffea arabica, breakdown of host resistance to CLR, aggravating insect pest problems and the increasingly negative impact of climate change on arabica coffee production worldwide. This review discusses prospects of breeding and disseminating next generation (hybrid) cultivars of arabica coffee for sustainable coffee production under changing conditions of diseases, pests and climate. International networking on coffee breeding will facilitate sharing of resources (financial, genetic) and scientific information, application of genomics-assisted selection technologies, and pre-breeding for specific characters. Breeding and multiplication of new cultivars well adapted to the local environment will continue to be carried out at national or regional levels. A tree crop like arabica coffee does not lend itself to centralized variety development and dissemination on a global scale.

show abstract

Section: Development and Release Of Improved Varietiesmentioning

confidence: 99%

Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review

Vossen¹,

Bertrand

Charrier³

2015

Euphytica

166

View full text Add to dashboard Cite

show abstract

“…Molecular tools recently made available for coffee include CAFEST Project (an EST database and clone bank; Vieira et al 2006), the PUCE CAFE Project that produced a 15k microarray for gene expression analyses (Privat et al 2011), and the Coffee Genome Project (http://bioinfo04.ibi.unicamp. br/coffea: Vidal et al 2010;Mondego et al 2011) that enables searching for candidate genes related to traits of interest.…”

Section: Introductionmentioning

confidence: 99%

In Silico and Quantitative Analyses of the Putative FLC-like Homologue in Coffee (Coffea arabica L.)

et al. 2011

View full text Add to dashboard Cite

The sequential pattern of coffee flowering is a major constraint that directly affects productivity, increases harvest costs, and generates a final product of lower quality for mixing dry fruits with ripe and unripe ones. The objective of this work was to identify and analyze one of the main genes involved in flowering regulation, FLOWER-ING LOCUS C (FLC) in coffee (Coffea arabica L.). The identification of this gene was conducted in silico using a coffee EST database (CAFEST) and bioinformatics tools. Quantitative PCR results suggest that the identified CaFLClike homologue is directly involved in flowering regulation in coffee. This expands our knowledge on evolutionary conservation of flowering pathways in dicot species. The functional studies of CaFLC-like with mutants of a more tractable species will lead to a better understanding of the molecular regulation as well as the specific functions of each gene flowering during floral induction in coffee.

show abstract

“…However, not all these resources are published or available, which limits their use. A number of studies have used the available resource of ESTs for further research such as microsatellite marker discovery , analysis of transcriptome divergence and analysis of genes involved in the biosynthesis pathways of lipids and main storage proteins (Privat et al, 2011), gene structure prediction and functional annotation with the detection of a total of 345 pathways in C. arabica and 300 pathways in C.…”

Section: Bacterial Artificial Chromosome (Bac) Librarymentioning

confidence: 99%

“…These are candidate genes which may control the variability of coffee quality . Genes regulating the main chemical components that are thought to be involved in the flavour and sensory quality of coffee are listed in Table 2.8 (Campa et al, 2003;Denoeud et al, 2014;Geromel et al, 2006;Joët et al, 2009;Kato and Mizuno, 2004;Koshiro et al, 2006;Lepelley et al, 2012;Leroy et al, 2011;Leroy et al, 2005;Mahesh et al, 2006;Mizuno et al, 2014;Mizuno et al, 2003b;Ogawa et al, 2001;Ogita et al, 2004;Perrois et al, 2014;Privat et al, 2011;Privat et al, 2008;Simkin et al, 2006;Uefuji et al, 2003).…”

Section: Gene Identificationmentioning

confidence: 99%

See 1 more Smart Citation

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

The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

Cited by 30 publications

References 32 publications

Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review

Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): a review

In Silico and Quantitative Analyses of the Putative FLC-like Homologue in Coffee (Coffea arabica L.)

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

Contact Info

Product

Resources

About