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Open AccessArticle

Metabolomic Markers for the Early Selection of Coffea canephora Plants with Desirable Cup Quality Traits

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Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato, Km 9.6 Libramiento Norte Carr. Irapuato-León, Guanajuato 36824, Mexico
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Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Xalapa, Veracruz 91070, Mexico
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Laboratorio de Tecnología del Café, Unidad de Investigación y Desarrollo en Alimentos, TNM/Instituto Tecnológico de Veracruz, Veracruz 91897, Mexico
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Agroindustrias Unidas de México S.A. de C.V. (AMSA), Bosque de Alisos 45-A 2do Piso, Bosques de las Lomas, Ciudad de México 05120, Mexico
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Laboratorio de Metabolómica y Espectrometría de Masas, Unidad de Genómica Avanzada, CINVESTAV-IPN, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico
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Authors to whom correspondence should be addressed.
Metabolites 2019, 9(10), 214; https://doi.org/10.3390/metabo9100214
Received: 23 August 2019 / Revised: 19 September 2019 / Accepted: 20 September 2019 / Published: 4 October 2019
Genetic improvement of coffee plants represents a great challenge for breeders. Conventional breeding takes a too long time for responding timely to market demands, climatic variations and new biological threads. The correlation of genetic markers with the plant phenotype and final product quality is usually poor. Additionally, the creation and use of genetically modified organisms (GMOs) are often legally restricted and rejected by customers that demand natural products. Therefore, we developed a non-targeted metabolomics approach to accelerate conventional breeding. Our main idea was to identify highly heritable metabolites in Coffea canephora seedlings, which are linked to coffee cup quality. We employed a maternal half-sibs approach to estimate the metabolites heritability in open-pollinated plants in both leaves and fruits at an early plant development stage. We evaluated the cup quality of roasted beans and correlated highly heritable metabolites with sensory quality traits of the coffee beverage. Our results provide new insights about the heritability of metabolites of C. canephora plants. Furthermore, we found strong correlations between highly heritable metabolites and sensory traits of coffee beverage. We revealed metabolites that serve as predictive metabolite markers at an early development stage of coffee plants. Informed decisions can be made on plants of six months old, compared to 3.5 to 5 years using conventional selection methods. The metabolome-wide association study (MWAS) drastically accelerates the selection of C. canephora plants with desirable characteristics and represents a novel approach for the focused breeding of crops. View Full-Text
Keywords: plant metabolomics; early selection; cup quality; metabolic marker; Coffea canephora; metabolome-wide association study (MWAS) plant metabolomics; early selection; cup quality; metabolic marker; Coffea canephora; metabolome-wide association study (MWAS)
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Gamboa-Becerra, R.; Hernández-Hernández, M.C.; González-Ríos, Ó.; Suárez-Quiroz, M.L.; Gálvez-Ponce, E.; Ordaz-Ortiz, J.J.; Winkler, R. Metabolomic Markers for the Early Selection of Coffea canephora Plants with Desirable Cup Quality Traits. Metabolites 2019, 9, 214.

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