Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers.

Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard's coefficient and population structure in 33 genotypes of C. arabica and of three diploid Coffea species (C. canephora, C. eugenioides and C. racemosa) using 30 SSR markers. A total of 206 alleles were identified, with a mean of 6.9 over all loci. The set of SSR markers was able to discriminate all genotypes and revealed that Ethiopian accessions presented higher genetic diversity than commercial varieties. Population structure analysis indicated two genetic groups, one corresponding to Ethiopian accessions and another corresponding predominantly to commercial cultivars. Thirty-four private alleles were detected in the group of accessions collected from West side of Great Rift Valley. We observed a lower average genetic distance of the C. arabica genotypes in relation to C. eugenioides than C. canephora. Interestingly, commercial cultivars were genetically closer to C. eugenioides than C. canephora and C. racemosa. The great allelic richness observed in Ethiopian Arabica coffee, especially in Western group showed that these accessions can be potential source of new alleles to be explored by coffee breeding programs.

Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L.

Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley.

Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits.

Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffea eugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffea arabica together with Coffea canephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.

Comparison of bean biochemical composition and beverage quality of Arabica hybrids involving Sudanese-Ethiopian origins with traditional varieties at various elevations in Central America.

For buyers of Arabica coffee (Coffea arabica L.) in Central America, elevation and variety are important indicators of quality. We compared coffee produced by three types of varieties established in various trials at elevations ranging from 700-1600 m in three countries (El Salvador, Costa Rica and Honduras). Arabica hybrids resulting from crosses of Sudanese-Ethiopian origins with either traditional varieties or with introgressed lines derived from the hybrid of Timor (C. arabica x Coffea canephora Pierre ex Froehn) were compared with traditional cultivars (TC). Effects of elevation and variety on bean biochemical composition (caffeine, chlorogenic acid, trigonelline, fat and sucrose) were evaluated by predictive models based on calibration of near-infrared (NIR) spectra and by chemometric analysis of the global NIR spectrum. Beverage quality tests were performed by a panel of ten professional cup-tasters. Experiment 1 was carried out on the slopes of the Poas volcano (Costa Rica) with the traditional cultivar 'Caturra'. Experiment 2 compared the three varieties in a network of trials established in three countries of Central America. Significant linear regressions with elevation were observed in Experiment 1 with Caturra and in Experiment 2 for the traditional cultivars, and trends were established relating variation in biochemical compounds and cup quality to elevation. Convergence or divergence of the new hybrids in relation to these trends was observed. For the traditional cultivars, elevation had a significant effect on bean biochemical composition, with chlorogenic acid and fat concentrations increasing with increasing elevation. For the Arabica hybrids, elevation explained little of the variation in chlorogenic acid concentration and none of the variation in fat concentration. Nevertheless, Arabica hybrids had 10-20% higher fat concentrations than the traditional varieties at low elevations and similar fat concentrations at high elevations. The samples could be discriminated according to elevation based on NIR spectra; however, the spectra of the TC varieties were more strongly modified by elevation than the spectra of the hybrids. Nonetheless, this analysis confirmed homeostasis of the hybrids for which bean biochemical composition was less affected by elevation than that of the traditional varieties. The organoleptic evaluation, performed on samples originating from high elevations, showed no significant differences between Arabica hybrids and traditional cultivars. The new hybrid varieties with high beverage quality and productivity potential should act as a catalyst in increasing the economic viability of coffee agroforestry systems being developed in Central America.