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

Gamboa-Becerra Gamboa-Becerra,Ordaz-Ortiz Ordaz-Ortiz,Suárez-Quiroz Suárez-Quiroz,González-Ríos González-Ríos,Gálvez-Ponce Gálvez-Ponce,Winkler Winkler,Hernández-Hernández Hernández-Hernández

doi:10.3390/metabo9100214

Gamboa-Becerra Gamboa-Becerra, Ordaz-Ortiz Ordaz-Ortiz + Show 5 more

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https://doi.org/10.3390/metabo9100214

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Abstract

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.

Highlights

Coffee is one of the most important crops in agriculture around the world since coffee beverages prepared from roasted and ground beans are the second most popular beverage only after tea [1,2].More than 100 species have been reported belonging to Coffea genus, but Coffea arabica and Coffea canephora are the most commercialized
Forty families of C. canephora were included in this study, comprising a total of 120 coffee plants
The identity of one of the parental was unknown since the coffee plants sibs were reproduced by open-pollinated seeds

Summary

Introduction

More than 100 species have been reported belonging to Coffea genus, but Coffea arabica and Coffea canephora are the most commercialized. Because of their economic importance, these two species. Traditional genetic breeding strategies for coffee mainly include traditional clones selection, generational selection, selection of pure lines following generational selection, generation of F1 hybrids, interspecific and intraspecific hybridization and selection by backcrossing. The best strategy is chosen according to the behavior of the coffee species, the aim of breeding (disease resistance, quality, yield) and the kind of variety (clone, pure line or variety, hybrid) [5,6,7]. The selection and breeding of new coffee varieties require at least 25 years, with vast investments of research and development resources

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