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 lowfrequency 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-toeast 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.

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This study describes a non-separative headspace solid phase microextraction-mass spectrometry (HS-SPME-MS) approach, in view of its application to online monitoring of a roasting process. The system can quickly provide representative and diagnostic fingerprints of the volatile fraction of samples and, in combination with appropriate chemometric pattern recognition and regression techniques, can successfully be applied to characterize, discriminate, and/or correlate patterns with the roasting process. Eighty coffee samples of different varieties, geographical origins, and blends were analyzed. The experimental HS-SPME-MS results show that the TIC fingerprint can be used to discriminate the degree of roasting; diagnostic ion abundance(s) or ratios were closely correlated with the roasting process; both could successfully be used as markers or analytical decision makers, to monitor roasting processes online, and to define quality and safety of roasted coffee.

Aroma is a primary hedonic aspect of a good coffee. Coffee aroma quality is generally defined by cup tasting, which however is time-consuming in terms of panel training and alignment and too subjective. It is challenging to define a relationship between chemical profile and aroma sensory impact, but it might provide an objective evaluation of industrial products. This study aimed to define the chemical signature of coffee sensory notes, to develop prediction models based on analytical measurements for use at the control level. In particular, the sensory profile was linked with the chemical composition defined by HS-SPME-GC-MS, using a chemometric-driven approach. The strategy was found to be discriminative and informative, identifying aroma compounds characteristic of the selected sensory notes. The predictive ability in defining the sensory scores of each aroma note was used as a validation tool for the chemical signatures characterized. The most reliable models were those obtained for woody, bitter, and acidic properties, whose selected volatiles reliably represented the sensory note fingerprints. Prediction models could be exploited in quality control, but compromises must be determined if they are to become complementary to panel tasting.