Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

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.

Background: A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan® e ArrayStar® platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach. Results: The microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars. Conclusions: Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response.

The effects of different calcium (Ca) concentrations in the nutrient solution and of air relative humidity (RH) on the Ca levels and on the incidence of blossom‐end rot in tomato fruit cv. Jumbo were studied. The experiment was conducted in a greenhouse under hydroponic conditions using a modified Hoagland solution containing different Ca concentrations (0.2, 2.5, 5.0, 10.0, 15.0, and 20.0 mm L^‐1) which represented the different treatments. The trial was conducted in a fully randomized design with three replications, with Ca doses representing the plots and environments with high and low RH the subplots. The fruits of the second and third clusters were used, with two fruits per cluster, one maintained at high (90±5%) and the other at low (40±5%) RH. The fruits were picked after full ripening. A greater Ca accumulation was observed in fruits submitted to low RH with this accumulation occurring at all Ca levels in the solution. In the treatment with 100 mg Ca L^‐1, the plants died and did not reach fructification. The fruits of plants treated with 100 mg Ca L^‐1 and submitted to low RH had blossom‐end rot although their Ca levels were higher than those detected in the fruits of this treatment submitted to high RH. At this Ca dose, the seeds were small, malformed, and black. Our results show that fruit kept at low RH had higher Ca accumulation although the excessive water loss from tissues may lead to blossom‐end rot when low Ca doses are supplied to the plants.

This study evaluated the transcriptional profile of genes related to nitrogen (N) assimilation in coffee plants susceptible and resistant to rust fungi under N sufficiency and N suppression. For this purpose, we inoculated young coffee leaves withHemileia vastatrixuredospores and collected them at 0, 12, 24 and 48 hours post-inoculation (HPI) to evaluate the relative expressions of genes encoding cytosolicglutamine synthetase(CaGS₁), plastidglutamine synthetase(CaGS₂),nitrate reductase(CaNR), andasparagine synthetase(CaAS). The genes exhibited distinct patterns of transcriptional modulation for the different genotypes and N nutritional regimes. The resistant genotype (I59) presented high levels of transcription in response to pathogen inoculation forCaNRandCaGS₁genes, evaluated under N sufficiency in the initial moments of infection (12 HPI). The geneCaGS₁also showed a peak at 48 HPI. The susceptible genotype (CV99) showed increased transcript rates ofCaNRat 12 and 24 HPI in response to rust inoculation. The transcriptional patterns observed for CV99, under N suppression, were high levels forCaASandCaGS₂at all post-inoculation times in response to coffee leaf rust disease. In addition,CaGS₁was up-regulated at 48 HPI for CV99. Cultivar I59 showed high transcript levels at 12 HPI forCaASand peaks at 24 and 48 HPI forCaGS₂in inoculated samples. Consequently, total chlorophyl concentration was influenced by N suppression and by rust infection. Regarding enzyme activities in vitro for glutamine synthetase andCaNR, there was an increase in infected coffee leaves (I59) and under N sufficiency. Moreover, CV99 was modulated in both N nutritional regimes for GS activity in response to rust. Our results indicate that N transport genes trigger a differential modulation between genotypes through the action of rust disease.