Taxonomic significance of the distribution of constituents of leaf cuticular waxes of Croton species (Euphorbiaceae)

Foliar epicuticular waxes of specimens of 13 Croton species native in Brazil were extracted. The fractions containing alkanes and primary alcohols were isolated by preparative thin layer chromatography. Derivatized n-primary alcohols were identified by gas chromatography (GC) coupled with mass spectrometry and n-alkanes by GC and comparison with known standards. Relative abundances were estimated by GC coupled with flame ionization detector. The distribution of constituents of both classes was analyzed by cluster analysis, using the UPGMA method and Euclidean distances. The chemical affinities among species were compared with published data of molecular phylogenetic relationships. The distribution of n-alkanes and primary alcohols were shown to be useful markers of Croton species. Primary alcohols were more consistent than n-alkanes for species fingerprinting.     

Cytogenetic and flow cytometry data expand knowledge of genome evolution in three <Emphasis Type="Italic">Coffea</Emphasis> species

Karyotype and nuclear 2C-value data are considered important in taxonomic and evolutionary approaches in Coffea. Still, new methods are needed to further support such studies, especially to determine the progenitors of Coffea arabica. In this work, new cytogenetic and flow cytometry data were used to compare Coffea arabica, Coffea canephora and Coffea congensis. These data corroborate the hypothesis that C. canephora and C. congensis originated from a single ancestor, whose basic chromosome number was x = 11. In agreement with the observations of other authors, the karyotype and mean 2C-values confirm that C. arabica is a true allotetraploid originating from two diploid Coffea species with similar genomes. Although C. canephora and C. congensis have been considered potential progenitors of C. arabica, karyotype comparison revealed that only one of these species may be parental to C. arabica. These accurate cytogenetic and flow cytometry data contribute to expand our knowledge of the Coffea genome, as well as of possible progenitors of C. arabica.     

Development and evaluation of a genome‐wide Coffee 8.5K SNP array and its application for high‐density genetic mapping and for investigating the origin of Coffea arabica L.

Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single‐nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high‐density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora‐derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high‐density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.     

Introgression into the allotetraploid coffee ( Coffea arabica L.): segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid ( C. arabicax C. canephora)

Transfer of desired characters from the diploid relative species such as Coffea canephora into the cultivated allotetraploid coffee species (Coffea arabica L.) is essential to the continued improvement of varieties. Behaviour of the C. canephora genome and its interaction with the C. arabica genome were investigated in tetraploid interspecific hybrids (C. arabica×C. canephora 4x) resulting from a cross between an accession of C. arabica and a tetraploid plant of C. canephora obtained following colchicine treatment. Segregation and co-segregation of restriction fragment length polymorphism (RFLP) and microsatellite loci-markers were studied in two BC₁ populations. These two populations of 28 and 45 individuals, respectively, resulted from the backcross of two tetraploid F₁ plants to C. arabica. The presence in BC₁ plants of specific C. canephora markers was scored for 24 loci (11 RFLP and 13 microsatellites) distributed on at least 7 of the 11 linkage groups identified in C. canephora. At almost all loci analysed, the segregation of C. canephora alleles transmitted by the (C. arabica×C. canephora 4x) hybrids conformed to the expected ratio assuming random chromosome segregation and the absence of selection. The recombination fractions of C. canephora chromosome segments were estimated for seven marker intervals, and compared with the recombination fractions previously observed in C. canephora for the equivalent marker intervals. The recombination frequencies estimated in both plant materials were rather similar, suggesting that recombination in the (C. arabica×C. canephora 4x) hybrid is not significantly restricted by the genetic differentiation between chromosomes belonging to the different genomes. The hybrid (C. arabica×C. canephora 4x) therefore appeared particularly favourable to intergenomic recombination events and gene introgressions. Received: 26 March 2001 / Accepted: 29 June 2001     

Activities of Phosphoenolpyruvate Carboxylase and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase in Leaves and Fruit Pericarp Tissue of Different Coffee (Coffea sp.) Genotypes

In order to study photosynthetic characteristics, phosphoenolpyruvate carboxylase (PEPC) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activities as well as soluble protein and chlorophyll contents were determined in leaf and fruit pericarp samples from diverse coffee genotypes (Coffea arabica cv. Colombia, Caturra, Caturra Erecta, San Pacho, Tipica, C. stenophylla, C. eugenioides, C. congensis, C. canephora, C. canephora cv. Arabusta, C. arabica cv. Caturra×C. canephora and Hibrido de Timor. We found a slightly higher PEPC activity in fruit pericarp than in leaves, while RuBPCO activity was much lower in pericarp than leaf tissue. Partial purification of PEPC and RuBPCO was carried out from leaves of C. arabica cv. Caturra and Michaelis-Menten kinetics for RuBPCO (K_m CO₂ = 5.34 µM), (K_m RuBP = 9.09 µM) and PEPC (K_m PEP = 19.5 µM) were determined. Leaf tissues of Colombia, Hibrido de Timor, and Caturra consistently showed higher content of protein [55.4–64.4 g kg^–1 (f.m.)] than San Pacho, C. stenophylla, Tipica, Caturra Erecta, and Caturra×C. canephora [25.6–36.9 g kg^–1 (f.m.)] and C. canephora cv. Arabusta, Borbon, C. congensis, C. eugenioides, and C. canephora [16.1–21.1 g kg^–1 (f.m.)].     

Beitrag zur Cytologie des Genus Coffea

Zusammenfassung Fünf verschiedene Sorten vonCoffea arabica wurden vom Verfasser cytologisch untersucht; es handelt sich um 44 Chromosomen-Formen. Diese Ergebnisse stimmen nicht mitFabers Beobachtungen überein, der fürC. arabica 2n=16 fand; wohl aber wirdHomeyers Anschauung bestätigt, daß die Grundzahl auch fürCoffea n=11 ist. Drei andere Arten,Coffea Excelsa Pierre,Coffea canephora (Robusta-Kaffee) undCoffea congensis Froehner, haben nur2n=22 Chromosomen. An Hand dieser Chromosomenzahlen wird die Sterilität einiger interspezifischer Bastarde in Java erklärt.     

Biotechnological applications for the improvement of coffee (Coffea arabica L.)

Summary The important advances in coffee biotechnological techniques which have been made particularly during the last 10yr could benefit the coffee breeder in practice and open new perspectives for the development of new varieties. The molecular phylogeny of Coffea species has been established using DNA sequence data. The molecular markers have revealed an extremely reduced genetic diversity in Coffea arabica L. in comparison to C. canephora. However, wild accessions collected in the Ethiopian highlands appeared to constitute a valuable gene reservoir. A complete genetic linkage map of C. canephora was reported and additional ones are being constructed, particularly on C. arabica. The integration of Molecular Assisted Selection in coffee breeding promises to drastically increase the efficiency of breeding programs. Economically important genes of the caffeine biosynthetic pathway or genes encoding for seed storage proteins have been isolated. The high performance already achieved in the in vitro propagation process by somatic embryogenesis offers the possibility to mass propagate superior hybrids in different countries of both C. arabica (selected F₁ hybrids) and C. canephora (rootstock variety). Pilot productions by somatic embryogenesis currently permit preparation for commercial application. Somaclonal variation was observed. The percentage of the off-types can vary between 3 and 10% depending on the genotype. Seed cryopreservation enables a routine use for long-term conservation of coffee genetic resources. Transgenic plants have been obtained for the C. arabica and C. canephora cultivated species through Agrobacterium-mediated transformation which constitutes the technique now currently used to transfer directly genes in coffee plants.     

The impact of cold on photosynthesis in genotypes of Coffea spp.--photosystem sensitivity, photoprotective mechanisms and gene expression

Environmental constraints disturb plant metabolism and are often associated with photosynthetic impairments and yield reductions. Among them, low positive temperatures are of up most importance in tropical plant species, namely in Coffea spp. in which some acclimation ability has been reported. To further explain cold tolerance, the impacts on photosynthetic functioning and the expression of photosynthetic-related genes were analyzed. The experiments were carried out along a period of slow cold imposition (to allow acclimation), after chilling (4 °C) exposure and in the following rewarming period, using 1.5-year-old coffee seedlings of 5 genotypes with different cold sensitivity: Coffea canephora cv. Apoatã, Coffea arabica cv. Catuaí, Coffea dewevrei and 2 hybrids, Icatu (C. arabica × C. canephora) and Piatã (C. dewevrei × C. arabica). All genotypes suffered a significant leaf area loss only after chilling exposure, with Icatu showing the lowest impact, a first indication of a higher cold tolerance, contrasting with Apoatã and C. dewevrei. During cold exposure, net photosynthesis and Chl a fluorescence parameters were strongly affected in all genotypes, but stomatal limitations were not detected. However, the extent of mesophyll limitation, reflecting regulatory mechanisms and/or damage, was genotype dependent. Overnight retention of zeaxanthin was common to Coffea genotypes, but the accumulation of photoprotective pigments was highest in Icatu. That down-regulated photochemical events but efficiently protected the photosynthetic structures, as shown, e.g., by the lowest impacts on A_max and PSI activity and the strongest reinforcement of PSII activity, the latter possibly reflecting the presence of a photoprotective cycle around PSII in Icatu (and Catuaí). Concomitant to these protection mechanisms, Icatu was the sole genotype to present simultaneous upregulation of caCP22, caPI and caCytf, related to, respectively, PSII, PSI and to the complex Cytb₆/f, which could promote better repair ability, contributing to the maintenance of efficient thylakoid functioning. We conclude that Icatu showed the best acclimation ability among the studied genotypes, mostly due to a better upregulation of photoprotection and repair mechanisms. We confirmed the presence of important variability in Coffea spp. that could be exploited in breeding programs, which should be assisted by useful markers of cold tolerance, namely the upregulation of antioxidative molecules, the expression of selected genes and PSI sensitivity.     

Distribution of <Emphasis Type="Italic">Divo</Emphasis> in <Emphasis Type="Italic">Coffea</Emphasis> genomes,a poorly described family of angiosperm LTR-Retrotransposons

Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains. Reverse Trancriptase (RT) domain-based phylogeny demonstrated that Divo is a new and well-supported family in the Bianca lineage, but strictly restricted to dicotyledonous species. In C. canephora, Divo is expressed and showed a genomic distribution along gene rich and gene poor regions. The copy number, the molecular estimation of insertion time and the analysis at orthologous locations of insertions in diploid and allotetraploid coffee genomes suggest that Divo underwent a different and recent transposition activity in C. arabica and C. canephora when compared to C. eugenioides. The analysis of this novel LTR-RT family represents an important step toward uncovering the genome structure and evolution of C. arabica allotetraploid genome.     

植物角质层蜡质的化学组成研究综述

角质层是植物与外界的第一接触面,而角质层蜡质则是由位于角质层外的外层蜡质和深嵌在角质层中的内层蜡质两部分构成。植物角质层蜡质成分极其复杂,具有重要的生理功能。综述了有关植物角质层蜡质的化学组成信息,探讨了目前植物角质层蜡质化学成分研究中存在的一些问题,展望了角质层蜡质成分的研究前景。     

Developing Single Nucleotide Polymorphism (SNP) Markers for the Identification of Coffee Germplasm

Coffee is one of the most widely consumed beverages and represents a multibillion-dollar global industry. Accurate identification of coffee cultivars is essential for efficient management, exchange, and use of coffee genetic resources. To date, a universal platform that can allow data comparison across different laboratories and genotyping platforms has not been developed by the coffee research community. Using expressed sequence tags (EST) of Coffea arabica, C. canephora and C. racemosa from public databases, we developed 7538 single nucleotide polymorphism (SNP) markers and selected 180 for validation using 25 C. arabica and C. canephora accessions from Puerto Rico. Based on the validation result, we designated a panel of 55 SNP markers that are polymorphic across the two species. The average minor allele frequency and information index of this SNP panel are 0.281 and 0.690, respectively. This panel enabled the differentiation of all tested accessions of C. canephora, which accounts for 79.2 % of the total polymorphism in the samples. Only 21.8 % of the polymorphic SNPs were detected in the 12 C. arabica cultivars, which, nonetheless, were able to unambiguously differentiate the 12 Arabica cultivars into ten unique genotypes, including two synonymous groups. Several local Puerto Rican cultivars with partial Timor pedigree, including Limaní, Frontón, and TARS 18087, showed substantial genetic difference from the other common Arabica cultivars, such as Catuai, Borbón, and Mundo Nuevo. This coffee SNP panel provides robust and universally comparable DNA fingerprints, thus can serve as a genotyping tool to assist coffee germplasm management, propagation of planting material, and coffee cultivar authentication.     

Brewing trouble: coffee invasion in relation to edges and forest structure in tropical rainforest fragments of the Western Ghats, India

While the conservation impacts of invasive plant species on tropical biodiversity is widely recognised, little is known of the potential for cultivated crops turning invasive in tropical forest regions. In the Western Ghats biodiversity hotspot, India, fragmented rainforests often adjoin coffee plantations. This study in the Anamalai hills assessed the effects of distance from edges and forest structure on the occurrence and abundance of shade-tolerant coffee (Arabica Coffea arabica and Robusta C. canephora) in four fragments (32–200 ha) using replicate line transects laid from the edges into the interiors. The coffee species cultivated in adjoining plantations was more abundant than the other coffee species inside study fragments, showing a clear decline in stem density from edge (0 m) to interior (250 m), suggesting the influence of propagule pressure of adjoining plantations, coupled with edge effects and seed dispersal by animals. Significant positive correlations of coffee density with canopy cover indicate the potential threat of coffee invasion even in closed canopy rainforests. Stem density of Coffea arabica (150–1,825 stems/ha) was higher in more disturbed fragments, whereas Coffea canephora had spread in disturbed and undisturbed sites achieving much higher densities (6.3–11,486 stems/ha). In addition, a negative relationship between C. canephora and native shrub density indicates its potential detrimental effects on native plants.     

Identification and characterization of expressed sequence tags‐derived simple sequence repeats markers from robusta coffee variety ‘CxR’ (an interspecific hybrid of Coffea canephora × Coffea congensis)

SSR (simple sequence repeats) markers derived from ESTs (expressed sequence tags), commonly called EST‐SSRs or genic SSRs provide useful genetic markers for crop improvement. These are easy and economical to develop as by‐products of large‐scale EST resources that have become available as part of the functional genomic studies in many plant species. Here, we describe for the first time, nine genic‐SSRs of coffee that are developed from the microsatellite containing ESTs from a cDNA library of moisture‐stressed leaves of coffee variety, ‘CxR’ (a commercial interspecific hybrid between Coffea congensis and Coffea canephora). The markers show considerable allelic diversity with PIC values up to 0.70 and 0.75 for Coffea arabica and Coffea canephora, respectively, and robust cross‐species amplification in 16 other related taxa of coffee. The validation studies thus demonstrate the potential utility of the EST‐SSRs for genetic analysis of coffee germplasm.     

Effects of Pratylenchus brachyurus and P. coffeae on Seedlings of Coffea arabica

Two experiments were carried out to evaluate the effects of Pratylenchus brachyurus and P. coffeae on Coffea arabica. The first experiment was conducted in a greenhouse to determine the effects of Pratylenchus brachyurus and P. coffeae on seedlings of Coffea arabica cv. Mundo Novo. Both Pratylenchus spp. reduced the growth of coffee seedlings. Higher contents of soluble sugars were detected in the leaves of infected plants. The reproduction rate of P. brachyurus was very low on cv. Mundo Novo, indicating an intolerance to this nematode. In a second experiment, C. arabica cultivars Mundo Novo and Catuaf both were intolerant hosts of P. brachyurus.     

Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica

As microRNAs (miRNAs) are important regulators of many biological processes, a series of small RNAomes from plants have been produced in the last decade. However, miRNA data from several groups of plants are still lacking, including some economically important crops. Here microRNAs from Coffea canephora leaves were profiled and 58 unique sequences belonging to 33 families were found, including two novel microRNAs that have never been described before in plants. Some of the microRNA sequences were also identified in Coffea arabica that, together with C. canephora, correspond to the two major sources of coffee production in the world. The targets of almost all miRNAs were also predicted on coffee expressed sequences. This is the first report of novel miRNAs in the genus Coffea, and also the first in the plant order Gentianales. The data obtained establishes the basis for the understanding of the complex miRNA-target network on those two important crops.     

Variations in leaf epicuticular n-alkanes in some Broussonetia,Ficus and Humulus species

n-Alkanes are biosynthesized from very long-chain fatty acid wax precursors and its distribution grants the most useful taxonomic contribution for plant species. In current study, five species from three genera of Moraceae family were sampled separately from three areas (Mountain Jin-yun, Mountain Jin-fo and Bei-bei) in Chongqing, China, namely, Broussonetia papyrifera, Broussonetia kazinoki, Ficus virens, Ficus tikoua, and Humulus scandens. The amounts of n-alkanes in epicuticular wax enabled discrimination among areas, varying from 4.9 μg cm⁻² to 16.9 μg cm⁻² in Mountain Jin-yun, 6.9 μg cm⁻² to 20.5 μg cm⁻² in Bei–bei, and 4.7 μg cm⁻² to 61.7 μg cm⁻² in Mountain Jin-fo, respectively. Among the five species, the amount of n-alkanes was the highest in B. papyrifera and the lowest in F. tikoua for all areas, showing high species variation. The most abundant n-alkanes in all investigated species were two odd-numbered n-alkanes, i.e., C₂₉ and C₃₁. The epicuticular waxes of H. scandens from Bei-bei had a higher relative abundance of C₂₉ than other species from Mountain Jin-yun and Mountain Jin-fo. The chain length of n-alkanes from Bei-bei was longer than that from other areas. The even/odd predominance (EOP) or odd/even predominance (OEP) occurred in short-chain n-alkanes of plant epicuticular wax might be correlated with their growing environments. All Carbon Preference Index (CPIs) and Average Chain Length (ACLs) from Bei-bei were lower than those from other sampling areas, mainly attributing to the higher numbers of short- and mid-chain n-alkanes in plants from Bei-bei. Cluster analysis revealed that H. scandens from Bei-bei and F. virens from Mountain Jin-yun were different from other species. Based on these findings, it seems that environmental conditions contribute to the complex patterns and variation of n-alkanes and different plant species had different responses to environment changes. The distribution of n-alkanes could be a good indicator to distinguish plant species under different growing conditions before other obvious morphological changes could be observed.     

n-Alkanes and ω-hydroxyalkanoic acids from the needles of twenty-eight Picea species

The needle wax of twenty-eight species of Picea has been investigated. The quantitative patterns of the n-alkanes and ω-hydroxyalkanoic acids isolated from these waxes support the view that the genus should not be divided into sections.     

Lipid transfer proteins in coffee: isolation of Coffea orthologs,Coffea arabica homeologs,expression during coffee fruit development and promoter analysis in transgenic tobacco plants

The aim of the present study was to perform a genomic analysis of non-specific lipid-transfer proteins (nsLTPs) in coffee. Several nsLTPs-encoding cDNA and gene sequences were cloned from Coffea arabica and Coffea canephora species. In this work, their analyses revealed that coffee nsLTPs belong to Type II LTP characterized under their mature forms by a molecular weight of around 7.3 kDa, a basic isoelectric points of 8.5 and the presence of typical CXC pattern, with X being an hydrophobic residue facing towards the hydrophobic cavity. Even if several single nucleotide polymorphisms were identified in these nsLTP-coding sequences, 3D predictions showed that they do not have a significant impact on protein functions. Northern blot and RT-qPCR experiments revealed specific expression of Type II nsLTPs-encoding genes in coffee fruits, mainly during the early development of endosperm of both C. arabica and C. canephora. As part of our search for tissue-specific promoters in coffee, an nsLTP promoter region of around 1.2 kb was isolated. It contained several DNA repeats including boxes identified as essential for grain specific expression in other plants. The whole fragment, and a series of 5′ deletions, were fused to the reporter gene β-glucuronidase (uidA) and analyzed in transgenic Nicotiana tabacum plants. Histochemical and fluorimetric GUS assays showed that the shorter (345 bp) and medium (827 bp) fragments of nsLTP promoter function as grain-specific promoters in transgenic tobacco plants.