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• Background: Brief review of Peter W Barlows' contributions to research on gravity tide-related phenomena in plant biology, or 'selenonastic' effects as he called them, including his early research on root growth. Also, new results are presented here from long-term recordings of spontaneous ultra-weak light emission during germination, reinforcing the relationship between local lunisolar tidal acceleration and seedlings growth.• Scope: The main ideas and broad relevance of the work by Peter Barlow and his collaborators about the effects of gravity on plants are reviewed, highlighting the necessity of new models to explain the apparent synchronism betweenroot growth and microscale gravity changes 107 times lower than that exerted by the Earth's gravity. The new results, showing for the first time the germination of coffee beans in sequential tests over two months, confirm the covariation between the patterns in ultra-weak light emission and the lunisolar tidal gravity curves for the initial growth phase. For young sprouts (less than one month old), the rhythm of growth as well as variation in light emission exhibit the once a day and twice a day periodic variations, frequency components that are the hallmark of local lunisolargravimetric tides. Although present, this pattern is less pronounced in coffee beans older than a month.• Conclusions: The apparent co-variation between ultra-weak light emission and growth pattern in coffee seedlings and the lunisolar gravity cycles corroborate those previously found in seedlings from other species. It is proposed here that such patterns may attenuate with time for older sprouts with slow development. These data suggest that new models considering both intra- and intercellular interactions are needed to explain the putative sensing and reaction of seedlings to the variations in the gravimetric tide. Here, a possible model is presented based on supracellular matrixinterconnections.

Galactomannans act as storage reserves for the seeds in some plants, such as guar (Cyamopsis tetragonoloba) and coffee (Coffea arabica and Coffea canephora). In coffee, the galactomannans can represent up to 25 % of the mass of the mature green coffee grain, and they exert a significant influence on the production of different types of coffee products. The objective of the current work was to isolate and characterize cDNA encoding proteins responsible for galactomannan synthesis in coffee and to study the expression of the corresponding transcripts in the developing coffee grain from C. arabica and C. canephora, which potentially exhibit slight galactomannan variations. Comparative gene expression analysis was also carried out for several other tissues of C. arabica and C. canephora.cDNA banks, RACE-PCR and genome walking were used to generate full-length cDNA for two putative coffee mannan synthases (ManS) and two galactomannan galactosyl transferases (GMGT). Gene-specific probe-primer sets were then generated and used to carry out comparative expression analysis of the corresponding genes in different coffee tissues using quantitative RT-PCR.Two of the putative galactomannan biosynthetic genes, ManS1 and GMGT1, were demonstrated to have very high expression in the developing coffee grain of both Coffea species during endosperm development, consistent with our proposal that these two genes are responsible for the production of the majority of the galactomannans found in the grain. In contrast, the expression data presented indicates that the ManS2 gene product is probably involved in the synthesis of the galactomannans found in green tissue.The identification of genes implicated in galactomannan synthesis in coffee are presented. The data obtained will enable more detailed studies on the biosynthesis of this important component of coffee grain and contribute to a better understanding of some functional differences between grain from C. arabica and C. canephora.

Background Solanaceae seed morphology and physiology have been widely studied but mainly in domesticated crops. The present study aimed to compare the seed morphology and the physiology of germination of Solanum lycocarpum, an important species native to the Brazilian Cerrado, with two species with endospermic seeds, tomato and coffee. Methods Morphological parameters of fruits and seeds were determined by microscopy. Germination was monitored for 40 d under different temperature regimes. Endosperm digestion and resistance, with endo-beta-mannanase activity and required force to puncture the endosperm cap as respective markers, were measured during germination in water and in abscisic acid. Key Results Fruits of S. lycocarpum contain dormant seeds before natural dispersion. The best germination condition found was a 12-h alternating light/dark and high/low (20/30 degrees C) temperature cycle, which seemed to target properties of the endosperm cap. The endosperm cap contains 7-8 layers of elongated polygonal cells and is predestined to facilitate radicle protrusion. The force required to puncture the endosperm cap decreased in two stages during germination and showed a significant negative correlation with endo-beta-mannanase activity. As a result of the thick endosperm cap, the puncture force was significantly higher in S. lycocarpum than in tomato and coffee. Endo-beta-mannanase activity was detected in the endosperm cap prior to radicle protrusion. Abscisic acid inhibited germination, increase of embryo weight during imbibition, the second stage of weakening of the endosperm cap and of endo-beta-mannanase activity in the endosperm cap. Conclusions The germination mechanism of S. lycocarpum bears resemblance to that of tomato and coffee seeds. However, quantitative differences were observed in embryo pressure potential, endo-beta-mannanase activity and endosperm cap resistance that were related to germination rates across the three species.

• Background and Aims Dehydrins, or group 2 late embryogenic abundant proteins (LEA), are hydrophilic Gly-rich proteins that are induced in vegetative tissues in response to dehydration, elevated salt, and low temperature, in addition to being expressed during the late stages of seed maturation. With the aim of characterizing and studying genes involved in osmotic stress tolerance in coffee, several full-length cDNA-encoding dehydrins (CcDH1, CcDH2 and CcDH3) and an LEA protein (CcLEA1) from Coffea canephora (robusta) were isolated and characterized. • Methods The protein sequences deduced from the full-length cDNA were analysed to classify each dehydrin/LEA gene product and RT–PCR was used to determine the expression pattern of all four genes during pericarp and grain development, and in several other tissues of C. arabica and C. canephora. Primer-assisted genome walking was used to isolate the promoter region of the grain specific dehydrin gene (CcDH2). • Key Results The CcDH1 and CcDH2 genes encode Y3SK2 dehydrins and the CcDH3 gene encodes an SK3 dehydrin. CcDH1 and CcDH2 are expressed during the final stages of arabica and robusta grain development, but only the CcDH1 transcripts are clearly detected in other tissues such as pericarp, leaves and flowers. CcDH3 transcripts are also found in developing arabica and robusta grain, in addition to being detected in pericarp, stem, leaves and flowers. CcLEA1 transcripts were only detected during a brief period of grain development. Finally, over 1 kb of genomic sequence potentially encoding the entire grain-specific promoter region of the CcDH2 gene was isolated and characterized. • Conclusions cDNA sequences for three dehydrins and one LEA protein have been obtained and the expression of the associated genes has been determined in various tissues of arabica and robusta coffees. Because induction of dehydrin gene expression is associated with osmotic stress in other plants, the dehydrin sequences presented here will facilitate future studies on the induction and control of the osmotic stress response in coffee. The unique expression pattern observed for CcLEA1, and the expression of a related gene in other plants, suggests that this gene may play an important role in the development of grain endosperm tissue. Genomic DNA containing the grain-specific CcDH2 promoter region has been cloned. Sequence analysis indicates that this promoter contains several putative regulatory sites implicated in the control of both seed- and osmotic stress-specific gene expression. Thus, the CcDH2 promoter is likely to be a useful tool for basic studies on the control of gene expression during both grain maturation and osmotic stress in coffee.

Estimates of genome size using flow cytometry can be biased by the presence of cytosolic compounds, leading to pseudo‐intraspecific variation in genome size. Two important compounds present in coffee trees—caffeine and chlorogenic acid—modify accessibility of the dye propidium iodide to Petunia DNA, a species used as internal standard in our genome size evaluation. These compounds could be responsible for intraspecific variation in genome size since their contents vary between trees. They could also be implicated in environmental variations in genome size, such as those revealed when comparing the results of evaluations carried out on different dates on several genotypes.

Somatic embryos were developed from in vitro-grown leaf discs of Coffea arabusta in modified Murashige and Skoog medium under 30 micromol m(-2) s(-1) photosynthetic photon flux (PPF). Cotyledonary stage embryos were selected from the 14-week-old cultures and were placed under a high (100 micromol m(-2) s(-1) PPF for 14 d. These pretreated embryos were grown photoautotrophically in three different types of culture systems: Magenta vessel; RITA-bioreactor (modified to improve air exchange); and a specially designed temporary root zone immersion bioreactor system (TRI-bioreactor) with forced ventilation. The aims of the study were to achieve large-scale embryo-to-plantlet conversion, and to optimize growth of plantlets under photoautotrophic conditions. The plantlet conversion percentage was highest (84 %) in the TRI-bioreactor and lowest in the modified RITA-bioreactor (20 %). Growth and survival of converted plantlets following 45 d of photoautotrophic culture in each of the three culture systems were studied. Fresh and dry masses of leaves and roots of plantlets developed in the TRI-bioreactor were significantly greater than those of plantlets developed in the modified RITA-bioreactor or Magenta vessel. The net photosynthetic rate, chlorophyll fluorescence and chlorophyll contents were also highest in plantlets grown in the TRI-bioreactor. Normal stomata were observed in leaves of plantlets grown in the TRI-bioreactor, whereas they could be abnormal in plantlets from the modified RITA-bioreactor. Survival of the plants after transfer from culture followed a similar pattern and was highest in the group grown in the TRI-bioreactor, followed by plants grown in the modified RITA-bioreactor and Magenta vessel. In addition, ex vitro growth of plants transferred from the TRI-bioreactor was faster than that of plants from the other culture systems.

The genome size of coffee trees (Coffea sp.) was assessed using flow cytometry. Nuclear DNA was stained with two dyes [4¢,6-diamino-2-phenylindole dihydrochloride hydrate (DAPI) and propidium iodide (PI)]. Fluorescence in coffee tree nuclei (C-PI or C-DAPI) was compared with that of the standard, petunia (P-PI or P-DAPI). If there is no stoichiometric error, then the ratio between fluorescence of the target nuclei and that of the standard nuclei (R-PI or R-DAPI) is expected to be proportional to the genome size. Between-tree differences in target : standard fluorescence ratios were noted in Coffea liberica var. dewevrei using propidium iodide and DAPI. For both dyes, between-tree differences were due to a lack of proportionality when comparing locations of the coffee peak and the petunia peak. Intraspecific genome size variations clearly cannot explain variations in the target : standard fluorescence ratio. The origin of the lack of proportionality between target and standard fluorescences differed for the two dyes. With propidium iodide, there was a regression line convergence point, and no between-tree differences were noted in this respect, whereas there was no such convergence with DAPI. An accurate estimate of genome size can thus be obtained with PI. Implications with respect to accessibility and binding mode are discussed. a 2002 Annals of Botany Company

Using two parental clones of outcrossing Trifolium ambiguum as a potential model system, we examined how during seed development the maternal parent, number of seeds per pod, seed position within the pod, and pod position within the inflorescence influenced individual seed fresh weight, dry weight, water content, germinability, desiccation tolerance, hardseededness, and subsequent longevity of individual seeds.Near simultaneous, manual reciprocal crosses were carried out between clonal lines for two experiments. Infructescences were harvested at intervals during seed development. Each individual seed was weighed and then used to determine dry weight or one of the physiological behaviour traits.Whilst population mass maturity was reached at 33-36 days after pollination (DAP), seed-to-seed variation in maximum seed dry weight, when it was achieved, and when maturation drying commenced, was considerable. Individual seeds acquired germinability between 14 and 44 DAP, desiccation tolerance between 30 and 40 DAP, and the capability to become hardseeded between 30 and 47 DAP. The time for viability to fall to 50 % (p(50)) at 60 % relative humidity and 45 degrees C increased between 36 and 56 DAP, when the seed coats of most individuals had become dark orange, but declined thereafter. Individual seed f. wt at harvest did not correlate with air-dry storage survival period. Analysing survival data for cohorts of seeds reduced the standard deviation of the normal distribution of seed deaths in time, but no sub-population showed complete uniformity of survival period.Variation in individual seed behaviours within a developing population is inherent and inevitable. In this outbreeder, there is significant variation in seed longevity which appears dependent on embryo genotype with little effect of maternal genotype or architectural factors.

† Background and Aims When green coffee is stored for a prolonged time the coffee quality decreases distinctively. Apart from well-known ‘off-notes’ that arise from undesired oxidations of lipids, a typical ‘flattening’ of the cup quality is detectable. In order to elucidate the biological causes for this phenomenon, differentially processed coffees (wet, dry, semi-dry processing), were stored under standard conditions for 2 years and analysed comprehensively. † Methods Wet-processed coffee was stored either as parchment coffee, where the endocarp remained around the beans or as hulled beans. Viability of coffee seeds was estimated using the tetrazolium-test of seed viability. Changes in concentration of free amino acids and soluble carbohydrates were analysed by HPLC. † Key Results Whereas all other coffees lost viability within the first 6 months of storage, coffee beans stored within the parchment remained viable for .1 year. Glucose and fructose decreased slightly in the course of storage and glutamine content declined significantly. However, the changes observed in sugar and amino acid content were not correlated with the viability of the coffee beans. Consequently, neither typical metabolic reactions occurring within living cells nor characteristic post-mortem reactions could be responsible for the observed changes. As a result of post-mortem reactions in re-imbibed seeds, a characteristic bluish-green colour developed, putatively due to the oxidation of chlorogenic acids and subsequent reactions with primary amino compounds. This coloration might be an appropriate marker to substantiate if coffee seeds had been stored for an expanded time and putative quality losses were not relevant so far. † Conclusions It is suggested that loss of viability is relevant for the aroma flattening. As neither metabolic nor postmortem reactions were responsible for the observed changes, it is concluded that Maillard reactions that occur during storage might be the cause of the decrease in potential aroma precursors.

Background and Aims: The chemical composition of green coffee and thus the final coffee quality are specifically determined by the mode of post-harvest treatment, i.e. the wet and dry processing. Recently, it was shown that metabolic processes, i.e. germination and, a slightly delayed stress-related metabolism are executed during the course of processing. The specific ambient conditions of either post-harvest treatment may influence differentially the extent and time course of these metabolic reactions; therefore, the incidence and intensity of germination processes in coffee seeds were analysed during processing. Methods: Expression of the germination-specific isocitrate lyase was monitored using competitive RT-PCRs analyses. Resumption of cell cycle activity and cell division were determined by flow cytometry, as well as by the abundance of ß-tubulin quantified by Western blot analyses. Key Results: The extent and the time courses of germination processes in coffee seeds differed significantly between wet and dry processed beans. The highest germination activity occurred 2 d after the onset of wet processing, whereas the corresponding maximum in the course of dry processing appeared about 1 week after the start of post harvest treatment. Conclusions: As recently shown, there are specific differences in the chemical composition of differentially processed coffee beans. It is concluded that these substantial differences are the consequence of the differential expression of germination processes, i.e. they are the result of differences in the corresponding metabolic activities. The coherence of germination-related metabolism and of expression-specific coffee qualities establishes the basis for a novel approach in coffee research. Key words: Coffea arabica, coffee processing

� 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.

• Background and Aims In microdensitometry and flow cytometry, estimation of nuclear DNA content in a sample requires a standard with a known nuclear DNA content. It is assumed that dye accessibility to DNA is the same in the sample and standard nuclei. Stoichiometric error arises when dye accessibility is not proportional between the sample and standard. The aim of the present study was to compare the effects of standardization (external–internal) on nuclear fluorescence of two Coffea species and petunia when temperature increases, and the consequences on genome size estimation. • Methods Two coffee tree taxa, C. liberica subsp dewevrei (DEW) and C. pseudozanguebarieae (PSE), and Petunia hybrida were grown in a glasshouse in Montpellier, France. Nuclei were extracted by leaf chopping and at least 2 h after nuclei extraction they were stained with propidium iodide for approx. 3 min just before cytometer processing. In the first experiment, effects of heat treatment were observed in mixed (DEW + petunia) and unmixed extracts (petunia and DEW in separate extracts). Nine temperature treatments were carried out (21, 45, 55, 60, 65, 70, 75, 80 and 85 °C). In a second experiment, effects of heating on within-species genome size variations were investigated in DEW and PSE. Two temperatures (21 and 70 °C) were selected as representative of the maximal range of chromatin decondensation. • Key Results and Conclusions In coffee trees, sample and standard nuclei reacted differently to temperature according to the type of standardization (pseudo-internal vs. external). Cytosolic compounds released in the filtrate would modify chromatin sensitivity to decondensation. Consequently, the ‘genome size’ estimate depended on the temperature. Similarly, intraspecific variations in genome size changed between estimations at 21 °C and 70 °C. Consequences are discussed and stoichiometric error detection methods are proposed, along with proposals for minimizing them.

Flow cytometry was conducted to evaluate genome size diversity among African diploid species of the Coffea genus. The study included 15 species and six new taxa from Congolese and Cameroonian forest regions which have yet to be botanically characterized. Between‐population differences were also recorded in some cases. These evaluations using an internal standard were highly correlated with previous results obtained with an external standard, but differences of up to 18 % existed for some species, involving stoichiometric errors. Consequently, genome size variation between species and within species are discussed as true genome size differences or stoichiometric errors. Environmental and phenotypic correlations with genome size are also discussed.