A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors

Le design sensoriel

The roasting of coffee beans generates stable radicals within melanoidins produced by non-enzymatic browning. Roasting coffee beans has further been suggested to increase the antioxidant (AO) capacity of coffee brews. Herein, we have characterized the radical content and AO capacity of brews prepared from Coffea arabica beans sourced directly from an industrial roasting plant. In-tact beans exhibited electron paramagnetic resonance signals arising from Fe3+, Mn2+ and at least three distinct stable radicals as a function of roasting time, whose intensity changed upon grinding and ageing. In coffee brews, the roasting-induced radicals were harboured within the high molecular weight (> 3 kD) melanoidin-containing fraction at a concentration of 15 nM and was associated with aromatic groups within the melanoidins. The low molecular weight (< 3 kD) fraction exhibited the highest AO capacity using DPPH as an oxidant. The AO activity was not mediated by the stable radicals or by metal complexes within the brew. While other non-AO functions of the roasting-induced radical and metal complexes may be possible in vivo, we confirm that the in vitro antiradical activity of brewed coffee is dominated by low molecular weight phenolic compounds

Exploring the link between coffee matrix microstructure and flow properties using combined X-ray microtomography and smoothed particle hydrodynamics simulations

Abstract Coffee extraction involves many complex physical and transport processes extremely difficult to model. Among the many factors that will affect the final quality of coffee, the microstructure of the coffee matrix is one of the most critical ones. In this article, we use X-ray micro-computed (microCT) technique to capture the microscopic details of coffee matrices at particle-level and perform fluid dynamics simulation based on the smoothed particle hydrodynamics method (SPH) with the 3D reconstructured data. Information like flow permeability and tortuosity of the matrices can be therefore obtained from our simulation. We found that inertial effects can be quite significant at the normal pressure gradient conditions typical for espresso brewing, and can provide an explanation for the inconsistency of permeability measurements seen in the literature. Several types of coffee powder are further examined, revealing their distinct microscopic details and resulting flow features. By comparing the microCT images of pre- and post-extraction coffee matrices, it is found that a decreasing porosity profile (from the bottom-outlet to the top-inlet) always develops after extraction. This counterintuitive phenomenon can be explained using a pressure-dependent erosion model proposed in our prior work. Our results reveal not only some important hydrodynamic mechanisms of coffee extraction, but also show that microCT scan can provide useful microscopic details for coffee extraction modelling. MicroCT scan establishes the basis for a data-driven numerical framework to explore the link between coffee powder microstructure and extraction dynamics, which is the prerequisite to study the time evolution of both volatile and non-volatile organic compounds and then the flavour profile of coffee brews

Antiradical activity of brewed coffee does not consume or generate stable coffee radicals.

<p>Room-temperature CW-EPR spectra of 1:1 MeOH/water solutions containing (a) 50 μM DPPH^• alone, (b) brewed coffee added to an equal volume of 100 μM DPPH^• in MeOH, and (c) brewed coffee added to an equal volume of MeOH. Data represent results of assay performed on a single brew. For clarity, the vertical scale is an order of magnitude higher spectra in <i>b</i> and <i>c</i> as compared with <i>a</i>. Experimental conditions: microwave frequency, 9.860 GHz; microwave power, 10 mW; magnetic field modulation amplitude, 4 G; field modulation frequency, 100 kHz; receiver time constant, 82 ms; receiver gain, 70 dB; sweep rate, 4 G/s; averages, (<i>a</i>) 4, (<i>b</i>,<i>c</i>) 40.</p

Reduction of DPPH^• to its hydrazine form DPPH-H in the presence of brewed coffee.

<p>(a) Dose response curves; (b) EC50 values calculated from the curves. The brew was optionally pre-treated with PVPP, followed by filtration through a 3 kD MWCO membrane. Reactions contained MeOH/water (1:1) solutions of 50 μM DPPH and varying dilutions of coffee brew. Significant differences were calculated by two-way ANOVA using the Holm-Šídák multiple comparison test (<i>n</i> = 3): ****<i>P</i> < 0.0001, ***<i>P</i> < 0.001, **<i>P</i> < 0.01, *<i>P</i> < 0.05. Numerical EC50 data is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122834#pone.0122834.s013" target="_blank">S1 Table</a>.</p

(a) UV-vis spectra of coffee brew following various treatments; quantification at discrete wavelengths associated with (b) total protein and polyphenol content (280 nm, 320 nm) and (c) melanoidins (420 nm).

<p>Consistent with a reduction in chlorogenic acid content [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122834#pone.0122834.ref003" target="_blank">3</a>], a significant decrease in the relative absorbance at 320 nm versus 280 nm was observed following phenolic extraction with PVPP, (one-way ANOVA, <i>F</i> = 24.77, <i>P</i> < 0.0001, <i>n</i> = 3; Holm-Šídák test, ****<i>P</i> < 0.0001 vs. untreated, < 3 kD and > 3 kD). A significant increase in the relative absorbance at 420nm versus 280 nm was also observed in the HMW fraction following 3 kD filtration (one-way ANOVA, <i>F</i> = 57.91, <i>P</i> < 0.0001, <i>n</i> = 3; Holm-Šídák test, ****<i>P</i> < 0.0001 vs. untreated, < 3 kD, PVPP treated), in keeping with brown color intensity arising from HMW melanoidins.</p

Spin Hamiltonian parameters determined from numerical simulation of the experimental EPR spectra.

<p>Uncertainty in <i>g</i> estimated ±0.0001.</p><p>^<i>a</i> ⟨<i>g</i>⟩ = (<i>g</i>_|| + 2<i>g</i>_⊥)/3.</p><p>^<i>b</i> Lorentzian residual linewidth (×10^–4cm^–1).</p><p>^<i>c</i><i>σ</i> = width of gaussian distribution of <i>g</i> values (“<i>g</i> strain”).</p><p>^<i>d</i> This broad spectrum could also be simulated using an isotropic <i>g</i> factor of 2.0047 and a phenomenological isotropic linewidth of ≈80% Gaussian and 20% lorentzian character.</p><p>^<i>e</i> Solution spectrum of brew prepared from 12 min-roasted beans.</p><p>Spin Hamiltonian parameters determined from numerical simulation of the experimental EPR spectra.</p

Multiple radical species are identified during roasting.

<p><b>(a–c)</b> Experimental (―) and simulated (―) EPR spectra of three putative radicals present in whole and ground coffee beans, isolated as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122834#pone.0122834.s004" target="_blank">S4 Fig</a> Using the basis spectra in <i>a–c</i>, the total EPR signal intensity (determined by double integration) of the experimental spectra from <b>(d)</b> in-tact beans, <b>(e)</b> freshly ground and <b>(f)</b> same grounds aged 1 month, was decomposed into contributions from species I–III. Details of the decompositions are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122834#pone.0122834.s005" target="_blank">S5</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122834#pone.0122834.s007" target="_blank">S7</a> Figs The dashed vertical line in <i>a</i>–<i>d</i> is positioned at the line center of species I to aid comparison of the different spectra. Error bars in <i>d</i> represent the mean and standard error of the intensity of the EPR spectra from individual beans. Error bars in <i>e</i>-<i>f</i> depict an arbitrary ±10% error associated with EPR spectra from a single sample of ground beans. Note that the intensity in <i>e-f</i> is comparable, but the intensity in <i>d</i> is not directly comparable with <i>e-f</i>.</p