Botanical Classification of Coffee

Charrier, André; Berthaud, Julien

doi:10.1007/978-1-4615-6657-1_2

Cited by 106 publications

(70 citation statements)

References 17 publications

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“…Within the genus Coffea (which includes more than 100 different species), C. arabica is the only tetraploid species (2n = 4x = 44) and it is characterized by self-fertilization. In contrast, C. canephora and all other species are diploid and predominantly self-incompatible (Charrier and Berthaud 1985). Furthermore, molecular analyses support the hypothesis that C. arabica is an amphidiploid resulting from the association of 2 genomes, namely E a and C a , related to C. eugenioides (E genome) and C. canephora (C genome), respectively (Lashermes et al 1999).…”

Section: Introductionsupporting

confidence: 52%

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Herrera

D’Hont

Lebailly

2007

Genome

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Fluorescence in situ hybridization (FISH) was used to study the presence of alien chromatin in interspecific hybrids and one introgressed line (S.288) derived from crosses between the cultivated species Coffea arabica and the diploid relatives C. canephora and C. liberica. In situ hybridization using genomic DNA from C. canephora and C. arabica as probes showed elevated cross hybridization along the hybrid genome, confirming the weak differentiation between parental genomes. According to our genomic in situ hybridization (GISH) data, the observed genomic resemblance between the modern C. canephora genome (C) and the C. canephora-derived subgenome of C. arabica (C a ) appears rather considerable. Poor discrimination between C and C a chromosomes supports the idea of low structural modifications of both genomes since the C. arabica speciation, at least in the frequency and distribution of repetitive sequences. GISH was also used to identify alien chromatin segments on chromosome spreads of a C. liberica-introgressed line of C. arabica. Further, use of GISH together with BAC-FISH analysis gave us additional valuable information about the physical localization of the C. liberica fragments carrying the SH3 factor involved in resistance to the coffee leaf rust. Overall, our results illustrate that FISH analysis is a complementary tool for molecular cytogenetic studies in coffee, providing rapid localization of either specific chromosomes or alien chromatin in introgressed genotypes derived from diploid species displaying substantial genomic differentiation from C. arabica.Key words: coffee, BAC-FISH, interspecific hybridization, GISH, introgression, genome evolution.Résumé : L'hybridation in situ fluorescente (« FISH ») a été utilisée pour étudier la présence de chromatine introgressée chez des hybrides interspécifiques mais aussi chez une lignée cultivée, issues du croissement entre l'espèce cultivée Coffea arabica et ses proches diploïdes C. canephora et C. liberica, respectivement. L'hybridation in situ en utilisant l'ADN gé-nomique des espèces C. canephora et C. arabica comme sondes, a montré une hybridation croisée importante chez les gé-nomes hybrides, ce qui confirme une étroite différentiation génomique entre les parents. Cette ressemblance entre le génome actuel de C. canephora et le sous-génome de C. arabica dérivant de l'espèce C. canephora (C a ), semble très éle-vée. De plus, la faible discrimination entre les chromosomes du type C et ceux du type C a , suggère des modifications structurales mineures dès l'origine même de l'espèce C. arabica, au moins dans ce qui concerne la fréquence et distribution des séquences répétées. L'hybridation génomique in situ (« GISH ») a permis aussi l'identification de différents fragments d'introgression chez une lignée de C. arabica introgressée par C. liberica, ce qui a conduit à l'identification de quatre fragments d'introgression. De plus, l'analyse combiné GISH plus BAC-FISH a donné des informations importantes sur la localisation physique du fragment issu d...

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Section: Introductionsupporting

confidence: 52%

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Herrera

D’Hont

Lebailly

2007

Genome

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“…The Coffea genus includes the sections Eucoffea and Mascarocoffea (Charrier and Berthaud, 1985). The Eucoffea section includes 12 species, which were divided into five subsections: Erythrocoffea (4 species), Pachycoffea (2 species), Melanocoffea (1 species), Mozambicoffea (3 species), and Nanocoffea with two species (Charrier, 1978).…”

Section: Genetic Variation Among Coffea Species and Parentage Identifmentioning

confidence: 99%

Genetic relationship in Coffea species and parentage determination of interspecific hybrids using ISSR (Inter- Simple Sequence Repeat) markers

Ruas

Rampim

et al. 2003

Genet. Mol. Biol.

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Inter-simple sequence repeat (ISSR) markers were used to evaluate genetic divergence among eight Coffea species and to identify the parentage of six interspecific hybrids. A total of 14 primers which contained different simple sequence repeats (SSR) were used as single primers or combined in pairs and tested for PCR amplifications. Two hundred and thirty highly reproducible fragments were amplified, which were then used to estimate the genetic similarity and to cluster the Coffea species and hybrids. High levels of interspecific genetic variation were revealed. The dinucleotide motif (GA) 9 T combined with other di-tri-and tetra-nucleotides produced a greater number of DNA fragments, mostly polymorphics, suggesting a high frequency of the poly GA microsatellite motifs in the Coffea genomes. The genetic similarity ranged from 0.25 between C. racemosa and C. liberica var. dewevrei to 0.86 between C. arabica var. arabica and Hybrid N. 2. The C. arabica species shared most of its markers with five of the six hybrids suggesting that it is the most likely candidate as one of the progenitors of those hybrids. These results revealed that ISSR markers could be efficiently used for genetic differentiation of the Coffea species and to identify the parentage of Coffea interspecific hybrids.

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“…F 1 hybrids and beverage quality: Since the 1980s, several researchers have proposed the creation of hybrid varieties to help in increasing genetic diversity, notably by crossing wild Ethiopian origins with introgressed or non introgressed varieties (Charrier, 1978) and to exploit heterosis between genetic groups (Walyaro, 1983;Van der Vossen, 1985;Charrier and Berthaud, 1985). Ethiopian origins provide resistance to nematodes (Anzueto et al, 2001), partial resistance to leaf rust (Gil et al, 1990) and resistance to CBD (Van der Vossen, 2001) and likely a better beverage quality.…”

Section: Introgression and Qualitymentioning

confidence: 99%

Genetics of coffee quality

Leroy

Ribeyre

Bertrand

et al. 2006

Braz. J. Plant Physiol.

187

157

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Coffee quality, in the present context of overproduction worldwide, has to be considered as a main selection criterion for coffee improvement. After a definition of quality, and an overview of the non genetic factors affecting its variation, this review focuses on the genetic factors involved in the control of coffee quality variation. Regarding the complexity of this trait, the different types of quality are first presented. Then, the great variation within and between coffee species is underlined, mainly for biochemical compounds related to quality (caffeine, sugars, chlorogenic acids, lipids). The ways for breeding quality traits for cultivated species, Coffea arabica and Coffea canephora are discussed, with specific challenges for each species. For C. arabica, maintaining a good quality in F 1 intraspecific hybrids, introgressed lines from Timor hybrid, and grafted varieties are the main challenges. For C. canephora, the improvement is mainly based on intraspecific and interspecific hybrids, using the whole genetic variability available within this species. An improvement is obtained for bean size, with significant genetic gains in current breeding programmes. The content in biochemical compounds related to cup quality is another way to improve Robusta quality. Finally, ongoing programmes towards the understanding of the molecular determinism of coffee quality, particularly using coffee ESTs, are presented. Key words: Coffea spp., biochemical compounds, candidate genes, ESTs, genetic breeding, marker-assisted selection, quality. Genética da qualidade do café:No contexto do excedente de produção mundial, a qualidade do café tem sido considerada o principal critério de seleção no melhoramento dessa cultura. Após definir qualidade e fazer considerações sobre os fatores não genéticos afetando sua variação, esta revisão se concentra sobre os fatores genéticos envolvidos no controle da variação da qualidade do café. Em relação à complexidade desta característica, os diferentes tipos de qualidade são apresentados. Então, a grande variação dentro e entre as espécies de café é discutida, principalmente em relação aos caracteres bioquímicos relacionados com qualidade (cafeína, açúcares, ácidos clorogênicos, lipídeos). As maneiras para melhorar estes caracteres relacionados à qualidade nas espécies cultivadas Coffea arabica e Coffea canephora são discutidas, assim como os desafios específicos a cada espécie. Para C. arabica, manutenção da boa qualidade em híbridos interespecíficos F 1 , linhagens geradas por introgressão a partir do Híbrido do Timor, e enxertia de variedades são os principais desafios. Para C. canephora, o melhoramento é principalmente baseado em híbridos intra e interespecíficos, usando a variabilidade genética disponível nesta espécie. Um avanço é obtido com o tamanho da semente, com significante ganho genético em programas de melhoramento. O conteúdo de compostos bioquímicos relacionados com a qualidade da bebida é uma outra maneira de melhorar a qualidade do café Robusta. Finalmente, são comentados...

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Botanical Classification of Coffee

Cited by 106 publications

References 17 publications

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Use of fluorescence in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.)

Genetic relationship in Coffea species and parentage determination of interspecific hybrids using ISSR (Inter- Simple Sequence Repeat) markers

Genetics of coffee quality

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