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.     

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     

Definition of architectural ideotypes for good yield capacity in Coffea canephora

BACKGROUND: Yield capacity is a target trait for selection of agronomically desirable lines; it is preferred to simple yields recorded over different harvests. Yield capacity is derived using certain architectural parameters used to measure the components of yield capacity. METHODS: Observation protocols for describing architecture and yield capacity were applied to six clones of coffee trees (Coffea canephora) in a comparative trial. The observations were used to establish architectural databases, which were explored using AMAPmod, a software dedicated to the analyses of plant architecture data. The traits extracted from the database were used to identify architectural parameters for predicting the yield of the plant material studied. CONCLUSIONS: Architectural traits are highly heritable and some display strong genetic correlations with cumulated yield. In particular, the proportion of fruiting nodes at plagiotropic level 15 counting from the top of the tree proved to be a good predictor of yield over two fruiting cycles.     

Intraspecific variation in growth response to drought stress across geographic locations and genetic groups in Coffea canephora

Uganda lies within the drier end of the natural distribution range of Coffea canephora and contains unexplored genetic material that could be drought-adapted and useful for developing climate-resilient varieties. Using water treatment: (i) ample and (ii) restricted-water, the response of 148 genotypes were studied comprising wild, feral and cultivated C. canephora. Biomass allocation, standing leaf area and leaf area growth data were collected. Linear mixed effect models and PCA were used to the analyze effect of water treatment on genotypes from different: (i) cultivation status, (ii) genetic groups and (iii) locations. We also assessed the relationship between drought tolerance for relative growth rate in leaf area (RGRA), total number of leaves (TNL), total leaf area (TLA) and total leaf dry weight (TLDW) of genotypes at final harvest. Restricted-water reduced RGRA across genetic groups (3.2–32.5%) and locations (7.1–36.7%) but not cultivation status. For TNL, TLA and TLDW, genotypes that performed well in ample-water performed worse under restricted-water, indicating growth-tolerance trade-off. Drought tolerance in RGRA and TNL were negatively correlated with wetness index suggesting some degree of adaptation to local climate. Findings indicate a growth-tolerance trade-off within this tropical tree species and drought tolerance of Uganda's C. canephora is somewhat associated with local climate.     

Evolution in caffeoylquinic acid content and histolocalization during Coffea canephora leaf development

BACKGROUND AND AIMS: Caffeoylquinic acids are cinnamate conjugates derived from the phenylpropanoid pathway. They are generally involved in plant responses to biotic and abiotic stress and one of them, chlorogenic acid (5-O-caffeoylquinic acid, 5-CQA), is an intermediate in the lignin biosynthesis pathway. Caffeoylquinic acids, and particularly 5-CQA, are accumulated in coffee beans, where they can form vacuolar complexes with caffeine. Coffea canephora beans are known to have high caffeoylquinic acid content, but little is known about the content and diversity of these compounds in other plant parts. To gain new insights into the caffeoylquinic acid metabolism of C. canephora, caffeoylquinic acid content and in situ localization were assessed in leaves at different growth stages. METHODS: HPLC analyses of caffeoylquinic acid content of leaves was conducted in conjunction with detailed histochemical and microspectrofluorometrical analysis. KEY RESULTS AND CONCLUSIONS: HPLC analyses revealed that caffeoylquinic acid content was 10-fold lower in adult than in juvenile leaves. The most abundant cinnamate conjugate was 5-CQA, but dicaffeoylquinic acids (particularly in juvenile leaves) and feruloylquinic acids were also present. Using specific reagents, histochemical and microspectrofluorometrical analysis showed that caffeoylquinic acids (mono- and di-esters) were closely associated with chloroplasts in very young leaves. During leaf ageing, they were found to first accumulate intensively in specific chlorenchymatous bundle sheath cells and then in phloem sclerenchyma cells. The association with chloroplasts suggests that caffeoylquinic acids have a protective role against light damage. In older tissues, their presence in the leaf vascular system indicates that they are transported via phloem and confirms their involvement in lignification processes. In accordance with the hypothesis of a complex formation with caffeine, similar tissue distribution was observed for alkaloids and this is further discussed.     

Caffeine biosynthesis and adenine metabolism in transgenic Coffea canephora plants with reduced expression of N-methyltransferase genes

In anti-sense and RNA interference transgenic plants of Coffea canephora in which the expression of CaMXMT1 was suppressed, caffeine biosynthesis from [8-(14)C]adenine was investigated, together with the overall metabolism of [8-(14)C]adenine. Compared with wild type control plants, total purine alkaloid biosynthesis from adenine and conversion of theobromine to caffeine were both reduced in the transgenic plants. As found previously, [8-(14)C]adenine was metabolised to salvage products (nucleotides and RNA), to degradation products (ureides and CO(2)) and to purine alkaloids (theobromine and caffeine). In the transgenic plants, metabolism of [8-(14)C]adenine shifted from purine alkaloid synthesis to purine catabolism or salvage for nucleotides. HPLC analysis revealed a significantly reduced caffeine content in the transgenic plants. A small quantity (less than 20 nmol g(-1) fresh weight) of xanthosine had accumulated in at least one of the transgenic plants.     

Inheritance and genetic mapping of self-incompatibility in Coffea canephora Pierre

Cross-compatibility behaviour of doubled haploid (DH) and hybrid genotypes of Coffea camphora was established using both phenotypic bioassay and in situ seed-set examination. The availability of DHs provided the opportunity of working with genetically homogenous pollen and female parents. The aniline blue fluorescence (ABF) method was applied to detect callose accumulation in pollen and pistil. Clear cross-compatibility/incompatibility situations were observed and confirmed by in situ seed-set analysis. Cross-compatibility analysis of hybrid combinations involving different DHs corroborated the crossing behaviour observed at the DH level. Expression of the self-incompatibility system did not appear to be affected by the low vigour of the DH. The crossing-behaviour distribution observed within DHs derived from clone IF200 confirmed that self-incompatibility in C. canephora is a gametophytic self-incompatibility system controlled by a single locus (S-locus). Reduced seed-set developments following incompatible crosses may indicate the occurrence of pseudo-incompatibility. Molecular marker linkage analysis showed that the S-locus is associated with an RFLP marker on linkage group 9. The availability of a linked DNA marker should facilitate the genetic analysis of self-incompatibility in relation to coffee breeding programmes.     

Influence of functional traits on foraging behaviour and pollination efficiency of wild social and solitary bees visiting coffee (Coffea canephora) flowers in Uganda

An on-farm pollination experiment was conducted during the June–August and November–February blooming seasons of 2007 to 2008, in 30 small-scale coffee fields characterised by different habitat and vegetation types. The study was conducted in order to determine the best pollinator groups for coffee in Uganda and to collect relevant field information and determine the pollination efficiency of different bee species. Results indicate that across blooming seasons, coffee flowers were visited by 24–36 bee species. Hypotrigona gribodoi was the most frequent flower visitor, comprising over 60% of 5941 bee-visits recorded. Foraging rate and pollination speed varied among bee species. Solitary bees foraged on more flowers than social bees, but they spent less time per flower visited. Solitary bees visited more coffee trees and fields, but deposited less pollen, whereas social bees visited less trees and coffee fields in the landscape, but deposited more pollen on flowers. Fruit set was of 87%, 64% and 0.9%, respectively, in hand-cross pollination, open pollination and controlled-pollination treatments. Fruit abortion due to self-pollination was insignificant in this study. There was variability in pollination efficiency of different bee species. Pollination efficiency varied more significantly with sociality than with other bee functional traits and was not significantly influenced by tongue length and bee body size. Single-flower visits by social and solitary bees resulted in 89.7% and 68.14% fruit set, respectively. The most efficient bee species was Meliponula ferruginea (98.3%) followed by Meliponula nebulata (97.1%). Thus, very good pollinator species were wild social bees (mainly stingless bees) as opposed to honeybees and solitary bees that were previously reported to be the best pollinators of coffee in Panama and Indonesia. Morphological and anatomical characteristics of the bee pollen storage features may explain the difference in foraging behaviour activities and in pollination efficiency of social and solitary afrotropical bee species visiting lowland coffee in Uganda. In addition, pollination efficiency was influenced by land-use intensity, field management systems and habitat types found in the immediate surroundings of coffee fields, but not by coffee field size, coffee genotypes and mass blooming wild vegetation. It is recommended to farmers to adopt pollinator-friendly conservation and farming practices such as keeping an uncultivated portion (25%–30%) of their farms as pollinator reservoirs, protecting semi-natural habitats found in the vicinity of coffee fields, as well as promoting high on-farm tree cover to benefit a functionally diverse pollinator community.     

Evolutionary rate variation among genes involved in galactomannan biosynthesis in Coffea canephora

The endosperm cell walls of mature coffee seeds accumulate large amounts of mannan storage polysaccharides, which serve as nutrient reserve for embryo and contribute to beverage quality. Our study investigated the evolutionary patterns of key galactomannan (GM) biosynthesis genes using d_N/d_S ratio, synteny, and phylogenetic analysis and detected heterogeneity in rate of evolution among gene copies. Selection ratio index revealed evidence of positive selection in the branch editing gene Coffea canephora alpha (α) galactosidase (Cc‐alpha Gal) at Cc11_g15950 copy (ω = 1.12), whereas strong purifying selection on deleterious mutations was observed in the Coffea canephora uridine diphosphate (UDP)‐glucose 4′‐epimerase (Cc‐UG4E) and Coffea canephora mannose‐1P guanylytransferase (Cc‐MGT) genes controlling the crucial nucleotide carbon sugar building blocks flux in the pathway. Relatively low sequence diversity and strong syntenic linkages were detected in all GM pathway genes except in Cc‐alpha Gal, which suggests a correlation between selection pressure and nucleotide diversity or synteny analysis. In addition, phylogenetic analysis revealed independent evolution or expansion of GM pathway genes in different plant species, with no obvious inferable clustering patterns according to either gene family or congruent with evolutionary plants lineages tested due to high dynamic nature and specific biochemical cell wall modification requirements. Altogether, our study shows a significant high rate of evolutionary variation among GM pathway genes in the diploid C. canephora and demonstrates the inherent variation in evolution of gene copies and their potential role in understanding selection rates in a homogenously connected metabolic pathway.     

Genetic transformation of Coffea canephora by vacuum infiltration

Agrobacterium-mediated plant transformation protocol was evaluated as a fast method to obtain genetically modified Coffea canephora plantlets. Leaf explants were used as source material for Agrobacterium tumefaciens-mediated transformation involving a vacuum infiltration protocol, followed by a step of somatic embryogenesis induction and a final selection of the transformed plants. A. tumefaciens strain C58CI containing the binary vector pER10W-35SRed was used. PCR amplification of DsRFP gene and visual detection of the red fluorescent protein demonstrated 33% transformed embryos. The protocol presented here produces reliable transgenic coffee embryos in two months.     

Purification and characterization of adenine phosphoribosyltransferase from Arabidopsis thaliana

Adenine phosphoribosyltransferase (APRT; EC 2. 4,2. 7) from Arabidopsis thaliana was purified approximately 3800-fold, to apparent homogeneity. The purification procedure involved subjecting a leaf extract to heat denaturation, (NH₄)₂SO₄ precipitation, Sephadex G-25 salt separation, ultracentrifugation and liquid chromatography on Diethylaminoethyl Sephacel, Phenyl Sepharose CL-4B, Blue Sepharose CL-6B and adenosine 5'-monophosphate-Agarose. The purified APRT was a homodimer of approximately 54 kDa and it had a specific activity of approximately 300 μmol (mg total protein)^-1 min^-1. Under standard assay conditions, the temperature optimum for APRT activity was 65°C and the pH optimum was temperature dependent. High enzyme activity was dependent upon the presence of divalent cations (Mn²⁺ or Mg²⁺). In the presence of MnCl₂₊ other divalent cations (Mg²⁺, Ca²⁺, Ba²⁺, Hg²⁺ and Cd²⁺) inhibited the APRT reaction. Kinetic studies indicated that 5-phosphoribose-1-pyrophosphate (PRPP) caused substrate inhibition whereas adenine did not. The K_m for adenine was 4.5±1.5 μ M , the K_m for PRPP was 0.29±0.06 m M and the K_i for PRPP was 1.96±0.45 m M . Assays using radiolabelled cytokinins showed that purified APRT can also catalyze the phosphoribosylation of isopentenyladenine and benzyladenine. The K_m for benzyladenine was approximately 0.73±0.06 m M     

Possible Role of Light and Polyamines in the Onset of Somatic Embryogenesis of Coffea canephora

The concentration of free and bound polyamines was studied during the somatic embryogenesis induction process in Coffea canephora explants. In the present study we show that when the induction of somatic embryogenesis in C. canephora is carried out under light conditions and in the presence of the plant growth regulator, benzylaminopurine, a cytokinin, a faster response to induction is obtained. In the darkness, the response is delayed for more than 20 days, and the number of embryos is smaller. In the absence of benzylaminopurine no embryogenic response was observed. The pronounced changes in the levels of putrescine, spermidine, and spermine, both free and bound, found in C. canephora suggest that a close correlation exists between polyamine biosynthesis and somatic embryogenesis in C. canephora during a period of cellular differentiation associated with the induction of somatic embryogenesis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. We would like to dedicate this paper to Dra. Estela Sánchez, the pioneer of the Plant Biochemistry in Mexico, on occasion of her 75th anniversary.     

Inhibition of purine utilization by adenine in Alcaligenes eutrophus H16

With 0.5% substrate present in mineral medium, cells of Alcaligenes eutrophus H 16 were able to grow heterotrophically at the expense of guanine, hypoxanthine and xanthine, but not of adenine as sole sources of carbon and nitrogen. An increase in cell counts, however, was observed at lower adenine concentrations (0.1%). Similarly, adenine was only respired if present at low concentrations. Higher amounts of adenine were inhibitory to the utilization of adenine, guanine, hypoxanthine, xanthine, allantoin and glyoxylate, but not to that of fructose or glycerate. The adenine-dependent inhibition of adenine utilization was not overcome by the addition of thiamine, uridine or cytidine. The enzyme glyoxylate carboligase, usually formed in presence of metabolisable purines and of allantoin, was synthesized only at low adenine concentrations. Higher amounts were inhibitory even with allantoin present as additional substrate. According to these resutls, the utilization of purine derivatives and of allantoin as sources of carbon and energy is repressed by adenine in cells of A. eutrophus H 16.     

Genetic differentiation between Coffea liberica var. liberica and C. liberica var. Dewevrei and comparison with C. canephora

Coffea liberica Hiern includes C. liberica var. liberica (LIB) from western Africa and C. liberica var. dewevrei (DEW) from central Africa. This geographical distribution also includes cultivated C. canephora for which a within-species clustering in two interfertile groups is known. In this study, genetic differentiation between LIB and DEW was evaluated on the basis of morphological traits, molecular markers (AFLP) and male fertility of F1 hybrids. The results were also compared with the within-species differentiation in C. canephora. The morphological traits differed significantly but the distributions overlapped. By contrast, LIB and DEW constituted two distinct groups with high genetic differentiation (G_st=0.25) when using AFLP markers. In addition, the pollen viability of F1 hybrids between LIB and DEW was weak (44.2%) and similar to interspecific C. canephora x DEW F1 hybrids or C. canephora x LIB F1 hybrids, indicating that there are marked reproductive barriers between LIB and DEW.     

Kinetic properties of yeast lysine permeases coded by genes on multi-copy vectors

Abstract Amplification of the LYP1 transport system in the plasma membrane of Saccharomyces cerevisiae did not change the substrate specificity, the affinity and the pH optimum of the transport system for lysine, but significantly increased the uptake velocity and accumulation ratio. The dependence of active lysine uptake and accumulation on pH is probably given by the properties of the permease itself rather than by the value of available protonmotive force.     

Use of plasmid vectors to show that the uracil and cytosine permeases of the yeast Saccharomyces cerevisiae are electrogenic proton symports

Abstract Strains of Saccharomyces cerevisiae bearing the structural gene for either the uracil permease or the cytosine permease on a multicopy plasmid adsorbed uracil or cytosine at several times the rate exhibited by the wild-type. The basal rate of proton absorption by the yeast increased by at least a factor of 3 in the presence of uracil and a factor of 2 with cytosine. Assays with a voltage-sensitive carbocyanine dye showed that substrate uptake depolarized the plasma membrane. Amplification of the uracil permease activity led to uracil being concentrated about 2000-fold in comparison with 25-fold in the wild-type system. Enhanced cytosine permease activity produced a similar but smaller effect.     

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.