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.     

Photoinhibition and recovery of photosynthesis in Coffea arabica and C. canephora

Photosynthetic parameters were determined in disks from leaves of C. arabica cv. Red Catuaí and C. canephora cv. Kouillou grown in the field. Kouillou showed a relatively higher irradiance requirement for saturating photosynthesis, lower chlorophyll (Chl) content, and higher Chl a/b ratio than Catuaí. Photoinhibition of photosynthesis under bright irradiance was manifested by decreases in maximum photochemical efficiency (evaluated by the variable to maximum fluorescence ratio, Fv/Fm), as a consequence of an increased initial and a quenched maximum fluorescence. Restoration of Fv/Fm following photoinhibition in low irradiance was faster in Kouillou than in Catuaí. Chloramphenicol both accelerated photoinhibition (mainly in Kouillou) and blocked its recovery for at least 190 min in either cultivar. Photosynthetic oxygen evolution under photoinhibitory conditions was decreased by chloramphenicol; in control leaf disks this decrease was only observed in C. arabica, but with a rapid recovery within 90 min of low irradiance exposure. In both coffee cultivars, the depressed photochemical efficiency of photosystem 2 was not accompanied by a concomitant lowering in oxygen evolution during reversal from photoinhibition.     

Photoinhibition and recovery of photosynthesis in Coffea arabica and C. canephora

Photosynthetic parameters were determined in disks from leaves of C. arabica cv. Red Catuaí and C. canephora cv. Kouillou grown in the field. Kouillou showed a relatively higher irradiance requirement for saturating photosynthesis, lower chlorophyll (Chl) content, and higher Chl a/b ratio than Catuaí. Photoinhibition of photosynthesis under bright irradiance was manifested by decreases in maximum photochemical efficiency (evaluated by the variable to maximum fluorescence ratio, Fv/Fm), as a consequence of an increased initial and a quenched maximum fluorescence. Restoration of Fv/Fm following photoinhibition in low irradiance was faster in Kouillou than in Catuaí. Chloramphenicol both accelerated photoinhibition (mainly in Kouillou) and blocked its recovery for at least 190 min in either cultivar. Photosynthetic oxygen evolution under photoinhibitory conditions was decreased by chloramphenicol; in control leaf disks this decrease was only observed in C. arabica, but with a rapid recovery within 90 min of low irradiance exposure. In both coffee cultivars, the depressed photochemical efficiency of photosystem 2 was not accompanied by a concomitant lowering in oxygen evolution during reversal from photoinhibition.     

Allometric models for non-destructive leaf area estimation in coffee (Coffea arabica and Coffea canephora)

We aimed to evaluate the currently used allometric models, as well as to propose a reliable and accurate model using non-destructive measurements of leaf length (L) and/or width (W), for estimating the area of leaves of eight field-grown coffee cultivars. For model construction, a total of 1563 leaves were randomly selected from different levels of the tree canopies and encompassed the full spectrum of measurable leaf sizes (0.3–263 cm²) for each genotype. Power models better fit coffee leaf area (LA) than linear models. To validate the model, an independent data set of 388 leaves was used. We demonstrated that the currently used allometric models are biased, underestimating the area of a coffee leaf. We developed a single power model     based on two leaf dimensions [LA = 0.6626 (LW)^1.0116; standard errors: β₀ = 0.0064, β₁ = 0.0019; R² = 0.996] with high precision and accuracy, random dispersion pattern of residuals and also unbiased, irrespective of cultivar and leaf size and shape. Even when the L (but not width) alone was used as the single leaf dimension, the power model developed still predicted with good accuracy the LA but at the expense of some loss of precision, as particularly found for 8% of the leaves sampled with length-to-width ratios below 2.0 or above 3.0.     

Brevipalpus mites associated with coffee plants (Coffea arabica and C. canephora) in Chiapas,Mexico

Experimental and Applied Acarology - Tenuipalpid mites of the genus Brevipalpus are of significant economic and quarantine importance in agriculture. They can damage and vector phytopathogenic...     

Chicoric and chlorogenic acids in various plants growing in Georgia

Chicoric acid was isolated from dandelion (Taraxacum officinale Wigg.) leaves by column chromatography. Conditions for HPLC analysis of chicoric and chlorogenic acids were optimized. These acids were assayed in some plants growing in Georgia. The optimum conservation temperature for the preservation of chicoric and chlorogenic acids in leaves of dandelion and bilberry (Vaccinium arctostaphylos L.) was determined.     

Single-locus inheritance in the allotetraploid Coffea arabica L. and interspecific hybrid C. arabica x C. canephora

Molecular cytogenetic analysis has indicated that Coffea arabica is an amphidiploid formed from the hybridization between two closely related diploid progenitor species, C. canephora and C. eugenioides. Our aim was to determine the mode of inheritance in C. arabica and in a tetraploid interspecific hybrid (called arabusta) between C. arabica and C. canephora as revealed by segregation analyses of restriction fragment length polymorphism (RFLP) loci markers. The observed RFLP allele segregations in an F(2) progeny of C. arabica conform to disomic inheritance as expected, with regular bivalent pairing of homologous chromosomes in the F1 hybrid. In contrast, RFLP loci followed tetrasomic inheritance in the arabusta interspecific hybrid, although bivalents have been reported to predominate greatly at meiosis in its hybrid. These results suggest that homologous chromosomes do not pair in C. arabica, not as a consequence of structural differentiation, but because of the functioning of pairing regulating factors. Moreover, the arabusta hybrid seems to offer the possibility of gene exchange between the homologous genomes.     

Bee pollination and fruit set of Coffea arabica and C. canephora (Rubiaceae)

Self-sterile Coffea canephora and self-fertile C. arabica are important cash crops in many tropical countries. We examined the relative importance of insect, wind, and spontaneous self-pollination and the degree of self-fertility of these two coffee species in 24 agroforestry coffee fields in Indonesia. In both species, open pollination and cross pollination by hand led to the highest fruit set. Wind pollination (including self-pollination) led to 16% lower fruit set than open pollination in C. canephora and to 12.3% lower fruit set in C. arabica. Self-pollinated flowers and unmanipulated controls achieved an extremely low fruit set of 10% or less in the self-sterile species, and of 60% and 48%, respectively in the self-fertile species. These results constitute experimental evidence that cross pollination by bees causes a significant increase in fruit set of not only the self-sterile, but also the self-fertile coffee species. The practical implication is that coffee yield may be improved by managing fields for increased flower visitation by bees.     

Gene introgression into Coffea arabica by way of triploid hybrids (C. arabica x C. canephora)

Interspecific triploid hybrid plants between the tetraploid species Coffea arabica L. and the diploid species C. canephora P. were backcrossed to C. arabica. Although characterised by a low production and an important fruit dropping, all attempted crosses (ie, 6) generated BC(1) progenies. Flow cytometric analysis of the nuclear DNA content revealed that most of the BC1 individuals were nearly tetraploid. Among the male gametes produced by the interspecific triploid hybrids, those presenting a high number of chromosomes appeared strongly favoured. Only pollen mother cells having nearly 22 chromosomes were effective, the others leading to deficient endosperm and fruit dropping. Molecular markers (ie, microsatellite and AFLP) combined with evaluations of morphological characteristics and resistance to leaf rust were applied to verify the occurrence of gene transfer from C. canephora into C. arabica, and to estimate the amount of introgression present in BC(1) individuals. The results reveal a strong deficiency in the C. canephroa alleles indicating a severe counter-selection against the introgression of genetic material from C. canephora into C. arabica by way of triploid hybrids. However, introgressants displaying desirable traits such as a high resistance to leaf rust were obtained. The low level of introgression could be an advantage by facilitating the recovery of the recurrent parent and possibly reducing the number of required backcrosses. On the other hand, this could be a limitation when attempting the transfer of a complex trait or several simply inherited traits.     

Introgressive hybridization between the allotetraploid Coffea arabica and one of its diploid ancestors, Coffea canephora, in an exceptional sympatric zone in New Caledonia.

The importance of introgressive hybridization in plant evolution has long been recognized. Nevertheless, information on gene flow between allopolyploids and their diploid relatives is very limited, even though gene flow could play a major role in polyploid establishment and evolution. Here, we investigated the processes governing hybrid formation and introgression between the allotetraploid Coffea arabica and one of its ancestral diploid progenitors, C. canephora, in a sympatric zone of New Caledonia. The occurrence of a large assortment of hybridization events between the 2 coffee species is clearly established. First-generation hybrids (F1) and post-F1 hybrids were characterized. The involvement of unreduced gametes of C. canephora is suggested, because tetraploid F1 hybrid plants were detected. Moreover, although bidirectional mating was observed, only unidirectional gene flow from C. canephora to C. arabica was noted in post-F1 hybrids. Most of the collected post-F1 hybrid plants exhibited a high level of introgression, and the frequency of introgression observed among the different analyzed loci was homogeneous, suggesting no significant counterselection against introgressions from C. canephora. Overall, the New Caledonian central mountains appear to be a highly favourable environment for introgressive hybridization and a genetic diversity center for C. arabica.     

Transgenic plants of coffee Coffea canephora from embryogenic callus via Agrobacterium tumefaciens-mediated transformation

 Embryogenic calli were induced from leaf explants of coffee (Coffea canephora) on McCown's woody plant medium (WPM) supplemented with 5 μM N⁶–(2-isopentenyl)-adenosine (2-iP). These calli were co-cultured with Agrobacterium tumefaciens EHA101 harboring pIG121-Hm, containing β-glucuronidase (GUS), hygromycin phosphotransferase (HPT), and neomycin phosphotransferase II genes. Selection of putative transgenic callus was performed by gradual increase in hygromycin concentration (5, 50, 100 mg/l). The embryogenic calli surviving on medium containing 100 mg/l hygromycin showed a strong GUS-positive reaction with X-Gluc solution. Somatic embryos were formed from these putative transgenic calli and germinated on WPM medium with 5 μM 2-iP. Regenerated small plantlets with shoots and roots were transferred to medium containing both 100 mg/l hygromycin and 100 mg/l kanamycin for final selection of transgenic plants. The selected plantlets exhibited strong GUS activity in leaves and roots as indicated by a deep blue color. GUS and HPT genes were confirmed to be stably integrated into the genome of the coffee plants by the polymerase chain reaction. Received: 14 December 1998 / Revision received: 12 March 1999 / Accepted: 24 March 1999     

High frequency somatic embryogenesis in Coffea canephora

Leaf explants of Coffea canephora (P. ex Fr.) produced a friable yellow callus when they were cultured on a conditioning basal medium with 2.2 M 2,4-D, 2.4 M IBA and 9.8 M 2iP for 4 weeks then on an induction basal medium with 4.4 M 2,4-D and 17.8 M BA for 10 weeks. This calus could be maintained by means of regular subcultures or it could give rise to somatic embryos depending on the culture medium. Cytological studies documented somatic embryogenesis and embryo development.Abbreviations BA 6-benzyladenine - 2,4-D 2,4-dichlorophenoxyacetic acid - IBA indole-3-butyric acid - 2iP 2-isopentenyladenine - MS Murashige & Skoog medium - NAA -naphthaleneacetic acid - NPR nucleoplasmic ratio - PGR plant growth regulator     

Direct sowing of Coffea arabica somatic embryos mass-produced in a bioreactor and regeneration of plants

The effect of germination conditions on the morphology of Coffea arabica L. somatic embryos mass-produced in a 1-l temporary immersion bioreactor (RITA®) was studied with emphasis on direct sowing in soil. Using germinated embryos, direct sowing resulted in a highly successful conversion of embryos into plants. A culture density above 1600 embryos per 1-l bioreactor positively affected embryo morphology by causing higher embryonic axis elongation (+4–5?mm). At this density, the addition of a high concentration of sucrose (234?mM) 2 weeks before sowing promoted an increase in effective plant conversion in soil (78%) and a vigorous vegetative growth of the resulting plants. Furthermore, direct sowing reduced handling time to 13% and shelving area requirements to 6.3% of the values obtained by conventional acclimatization of plants developed on gel media.     

Differential regulation of grain sucrose accumulation and metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta) revealed through gene expression and enzyme activity analysis

* Coffea arabica (Arabica) and Coffea canephora (Robusta) are the two main cultivated species used for coffee bean production. Arabica genotypes generally produce a higher coffee quality than Robusta genotypes. Understanding the genetic basis for sucrose accumulation during coffee grain maturation is an important goal because sucrose is an important coffee flavor precursor. * Nine new Coffea genes encoding sucrose metabolism enzymes have been identified: sucrose phosphate synthase (CcSPS1, CcSPS2), sucrose phosphate phosphatase (CcSP1), cytoplasmic (CaInv3) and cell wall (CcInv4) invertases and four invertase inhibitors (CcInvI1, 2, 3, 4). * Activities and mRNA abundance of the sucrose metabolism enzymes were compared at different developmental stages in Arabica and Robusta grains, characterized by different sucrose contents in mature grain. * It is concluded that Robusta accumulates less sucrose than Arabica for two reasons: Robusta has higher sucrose synthase and acid invertase activities early in grain development - the expression of CcSS1 and CcInv2 appears to be crucial at this stage and Robusta has a lower SPS activity and low CcSPS1 expression at the final stages of grain development and hence has less capacity for sucrose re-synthesis. Regulation of vacuolar invertase CcInv2 activity by invertase inhibitors CcInvI2 and/or CcInvI3 during Arabica grain development is considered.     

Shade adaptation of photosynthesis in Coffea arabica

The effect of irradiance on the rate of net photosynthesis was measured for mature leaves of coffee grown under five levels of radiation from 100% to 5% daylight. The rate of light-saturated photosynthesis per unit leaf area (P_Nmax) increased from 2 mol CO₂ m^-2 s^-1 under 5% daylight to 4.4 mol CO₂ m^-2 s^-1 under 100% daylight. The photon flux density (PAR, photosynthetically active radiation) needed for 50% saturation of photosynthesis, as well as the light compensation point, also increased with increasing levels of irradiation during growth. The quantum efficiency of photosynthesis (), measured by the initial slope of the photosynthetic response to increasing irradiance, was greater under shaded growth conditions. The rate of dark respiration was greatest for plants grown in full daylight. On the basis of the increase in the quantal efficiency of photosynthesis and the low light compensation point when grown under shaded conditions, coffee shows high shade adaptation. Plants adjusted to shade by an increased ability to utilize short-term increases in irradiance above the level of the growth irradiance (measured by the difference between photosynthesis at the growth irradiance, P_Ng, and P_Nmax).     

Physiological and molecular analyses of early and late Coffea arabica cultivars at different stages of fruit ripening

Coffee quality is strongly influenced by a great number of factors, among which the fruit ripening stage at harvest time has a major influence on this feature. Studies comprising ethylene production and the regulation of ethylene biosynthesis genes during the ripening process indicate that ethylene plays an important role on coffee fruit ripening. Coffee early cultivars usually show a more uniform ripening process although little is known about the genetic factors that promote the earliness of ripening. Thus, in order to better understand the physiological and genetic factors involved in the regulation of ripening time, and consequently ripening uniformity, this study aimed to analyze ethylene and respiration patterns during coffee ripening, as well as to analyze ACC oxidase, an ethylene biosynthesis enzyme, gene expression, in fruits of early (Catucaí 785-15) and late (Acauã) coffee cultivars. Coffee fruits were harvested monthly from 124 days after flowering (end of February), until complete maturation (end of June). Dry matter, moisture content, color, respiratory rate and ethylene production analysis were performed. In silico analysis identified a coffee ACC oxidase gene (CaACO-like) and its expression was analyzed by real-time PCR. Dry matter and relative water content constantly increased and gradually decreased, respectively, during fruit ripening, and the color analysis enabled the observation of the earliness in the ripening process displayed by Catucaí 785-15 and its higher fruit ripening uniformity. The results obtained from the CaACO-like expression analysis and respiration and ethylene analysis suggest that the differences in ripening behavior between the two coffee cultivars analyzed in this study may be related to the differences in their capacity to produce ethylene, with fruits of Catucaí 785-15 and Acauã showing a typical and an attenuated climacteric phase, respectively, which may have lead to differences in their ripening time and uniformity.