Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria

Abstract

The flavor and health benefits of coffee (Coffea spp.) are derived from the metabolites that accumulate in the mature bean. However, the chemical profiles of many C. canephora genotypes remain unknown, even as the production of these coffee types increases globally. Therefore, we used Gas Chromatography-Mass Spectrophotometry to determine the chemical composition of C. canephora genotypes in Nigeria—those conserved in germplasm repositories and those cultivated by farmers. GC-MS revealed 340 metabolites in the ripe beans, with 66 metabolites differing (p-value < 0.05) across the represented group. Univariate and multivariate approaches showed that the ‘Niaouli’ genotypes could be clearly distinguished from ‘Kouillou’ and ‘Java’ genotypes, while there was almost no distinction between ‘Kouillou’ and ‘Java,’. Varietal genotyping based on bean metabolite profiling was synchronous with that based on genome-wide Single Nucleotide Polymorphism analysis. Across genotypes, the sucrose-to-caffeine ratio was low, a characteristic indicative of low cup quality. The sucrose-to-caffeine ratio was also highly correlated, indicative of common mechanisms regulating the accumulation of these compounds. Nevertheless, this strong correlative link was broken within the ‘Niaouli’ group, as caffeine and sucrose content were highly variable among these genotypes. These ‘Niaouli’ genotypes could therefore serve as useful germplasm for starting a Nigerian C. canephora quality improvement breeding program.

Metabolomics-Based Approach for Coffee Beverage Improvement in the Context of Processing, Brewing Methods, and Quality Attributes

“…GC/MS was employed by Anagbogu et al [ 32 ] to study the different varieties of C. robusta in order to determine which genotype should be used in coffee breeding programs to improve its quality. GC–MS analysis revealed 340 metabolites, among which 66 showed differences between genotypes, mainly attributed to sugar derivatives, while the others were organic acids, amino acids and nitrogenous compounds.…”

Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in Southwestern Nigeria

“…Metabolomics and lipidomics are powerful strategies to qualitatively and quantitatively analyze a wide range of small molecules in a biological sample, which represent endpoints of genome expression [54]. The metabolomics data from our recent work [24] was subjected to PLS-DA analysis for both primary and secondary metabolites and compared to the lipidomics profile of these coffees. Our aim was to determine the diversity of metabolism across genotypes.…”

“…However, there have not been extensive studies of lipids of C. canephora genotypes, so the variability relative to C. arabica still remains largely undiscovered. This is important because although C. canephora is not as popular as C. arabica, its production and consumption is increasing, making it important to understand its organoleptic properties [24]. Further, genetic diversity among tetraploid C. arabica is not as high as diploid C. canephora [25] and this may be reflected in the metabolomic and lipid species diversity within these species.…”

Lipidomic and metabolomic profiles ofCoffea canephoraL. beans cultivated in South-western Nigeria

“…[49]. The metabolomics data from our recent work [21] was subjected to PLS-DA analysis for both primary and secondary metabolites and compared to the lipidomics profile of these coffees. Our aim was to determine the diversity of metabolism across genotypes.…”

“…However, there have not been extensive studies of lipids of C. canephora genotypes, so the variability relative to C. arabica still remains largely undiscovered. This is important because although C. canephora is not as popular as C. arabica, its production and consumption is increasing, making it important to understand its organoleptic properties [21]. Further, genetic diversity among tetraploid C. arabica is not as high as diploid C. canephora [22] and this may be reflected in the metabolomic and lipid species diversity within these species.…”