A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm.

In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid species Coffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species, Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.

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.

HS-SPME-MS-Enose Coupled with Chemometrics as an Analytical Decision Maker to Predict In-Cup Coffee Sensory Quality in Routine Controls: Possibilities and Limits.

The quality assessment of the green coffee that you will go to buy cannot be disregarded from a sensory evaluation, although this practice is time consuming and requires a trained professional panel. This study aims to investigate both the potential and the limits of the direct headspace solid phase microextraction, mass spectrometry electronic nose technique (HS-SPME-MS or MS-EN) combined with chemometrics for use as an objective, diagnostic and high-throughput technique to be used as an analytical decision maker to predict the in-cup coffee sensory quality of incoming raw beans. The challenge of this study lies in the ability of the analytical approach to predict the sensory qualities of very different coffee types, as is usual in industry for the qualification and selection of incoming coffees. Coffees have been analysed using HS-SPME-MS and sensory analyses. The mass spectral fingerprints (MS-EN data) obtained were elaborated using: (i) unsupervised principal component analysis (PCA); (ii) supervised partial least square discriminant analysis (PLS-DA) to select the ions that are most related to the sensory notes investigated; and (iii) cross-validated partial least square regression (PLS), to predict the sensory attribute in new samples. The regression models were built with a training set of 150 coffee samples and an external test set of 34. The most reliable results were obtained with acid, bitter, spicy and aromatic intensity attributes. The mean error in the sensory-score predictions on the test set with the available data always fell within a limit of ±2. The results show that the combination of HS-SPME-MS fingerprints and chemometrics is an effective approach that can be used as a Total Analysis System (TAS) for the high-throughput definition of in-cup coffee sensory quality. Limitations in the method are found in the compromises that are accepted when applying a screening method, as opposed to human evaluation, in the sensory assessment of incoming raw material. The cost-benefit relationship of this and other screening instrumental approaches must be considered and weighed against the advantages of the potency of human response which could thus be better exploited in modulating blends for sensory experiences outside routine.

New medium-to-high polarity twister coatings for liquid and vapour phase sorptive extraction of matrices of vegetable origin.

Stir Bar Sorptive Extraction (SBSE) is a solventless sampling technique first introduced to extract organic analytes from aqueous samples, in the following applied to headspace sampling (HeadSpace Sorptive Extraction - HSSE). In SBSE and HSSE, analytes are sorbed onto a thick film of polydimethylsiloxane (PDMS) coating a glass-coated magnet. However, PDMS is apolar and not highly effective in recovering polar analytes (i.e. with logK(o/w) below 2), making difficult their sampling in complex matrices. A new generation of medium-to-high polarity polymeric coatings for twisters i.e. polyethyleneglycol-modified silicone (EG) and polyacrylate/polyethyleneglycol (PA) has recently been introduced to overcome this limit. In this study, EG and PA twisters have been applied to SBSE and HSSE of a number of dedicated standard mixtures and real-world samples of vegetable origin to evaluate their capability to increase recovery of medium to highly polar analytes. The results obtained, expressed as percent concentration factor (CF%) versus PDMS twisters taken as reference, showed that analyte logK(o/w) is a key-factor driving the choice of the most effective coating. The new twisters showed to be successful for both SBSE and HSSE, although to a different extent. EG twisters gave high recoveries with analytes over a wide range of polarities and in particular with logK(o/w) below 2 and/or containing hydroxyl or carboxylic functional groups independently on their logK(o/w). On the other hand, PA twisters were selectively effective for highly polar compounds with logK(o/w) below 1.

Quantitative analysis of volatiles from solid matrices of vegetable origin by high concentration capacity headspace techniques: determination of furan in roasted coffee.

The study compares standard addition (SA), stable isotope dilution assay (SIDA) and multiple headspace extraction (MHE) as methods to quantify furan and 2-methyl-furan in roasted coffee with HS-SPME-GC-MS, using CAR-PDMS as fibre coating, d(4)-furan as internal standard and in-fibre internal standardization with n-undecane to check the fibre reliability. The results on about 150 samples calculated with the three quantitation approaches were all very satisfactory, with coefficient of variation (CV) versus the U.S. Food and Drug Administration (FDA) method, taken as reference, almost always below the arbitrarily-fixed limit of 15%. Furan was detected in the 1-5 ppm range, 2-methyl-furan in the 4-20 ppm range. Moreover, experimental exponential slopes (Q) and linearity (r) of both furan and 2-methyl-furan MHE regression equation on 50 samples were very similar thus making possible to use the same average Q value for all samples of the investigated set and their quantitation with a single determination. This makes this approach very rapid and competitive in-time with SA and SIDA. A non-separative method (HS-SPME-MS) was also developed in view of possible application on-line monitoring of furan and 2-methyl-furan in a pilot-plant with the aim of optimizing the roasting process to reduce these compounds to a minimum. Sampling times of 20 and 5 min were tested, the latter enabling total analysis time to be reduced to about 9 min. The results on 105 samples with both SIDA and MHE approaches were again highly satisfactory most of the samples giving a CV% versus the conventional methods below 20%. In this case too average Q values for both furan and 2-methyl-furan were used for MHE. The separative method presented very good repeatability (RSD% always below 10%) and intermediate precision over three months (RSD% always below 15%); performance were similar for the non-separative method, with repeatability (RSD%) always below 12% and intermediate precision over three months (RSD%) always below 15%. The sensitivity of both separative and non-separative methods was also very good, LOD and LOQ being in the ppb range for both furan and 2-methyl-furan, i.e. well below the amounts present in the roasted coffee samples.