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Linkage disequilibrium (LD) measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-growing, perennial crops such as Theobroma cacao, where experimental crosses are inherently time-consuming and logistically expensive. While LD has(More)
Saccharum species are autopolyploids with ploidy level ranging from 5× to 16x, and are considered the most complex genomes among crop plants. In present study, the genome sizes of 28 Saccharum spontaneum accessions, 15 Saccharum officinarum accessions, 28 Saccharum robustum accessions, and 12 Saccharum hybrids spp. were analyzed using flow cytometry. The(More)
Penicillium coffeae is described as a novel endophyte isolated from a Coffea arabica L. plant in Hawaii. The species is slow growing with short, vesiculate, monoverticillate conidiophores. Phylogenetic analysis using three loci shows that P. coffeae forms a strongly supported clade with P. fellutanum, P. charlesii, P. chermesinum, P. indicum, P. phoeniceum(More)
Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species(More)
Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C.(More)
Chlorogenic acids are major secondary metabolites found in coffee seeds. The accumulation of chlorogenic acids and free quinic acids was studied in Coffea arabica cv. Tall Mokka and Coffea canephora seeds. Growth stages are specified from I to V, corresponding to rapid expansion and pericarp growth (I), endosperm formation (II), mature (green) (III),(More)
The quality of coffee green beans is generally evaluated by the sensory cupping test, rather than by chemical compound-based criteria. In this study, we examined the relationship between metabolites and cupping scores for 36 varieties of beans, using a nontargeted LC-MS-based metabolic profiling technique. The cupping score was precisely predicted with the(More)
Changes occurring in phenolic compounds and purine alkaloids, during the growth of seeds of cacao (Theobroma cacao) cv. Trinitario, were investigated using HPLC-MS/MS. Extracts of seeds with a fresh weight of 125, 700, 1550, and 2050 mg (stages 1-4, respectively) were analyzed. The phenolic compounds present in highest concentrations in developing and(More)
The maturity of green coffee beans is the most influential determinant of the quality and flavor of the resultant coffee beverage. However, the chemical compounds that can be used to discriminate the maturity of the beans remain uncharacterized. We herein analyzed four distinct stages of maturity (immature, semi-mature, mature and overripe) of nine(More)