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

Gamboa-Becerra, Roberto; Hernández-Hernández, María Cecilia; González-Ríos, Óscar; Suárez-Quiroz, Mirna Leonor; Gálvez-Ponce, Eligio; Ordaz-Ortíz, José Juan; Winkler, Robert

doi:10.3390/metabo9100214

Cited by 30 publications

(21 citation statements)

References 59 publications

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“…in livestock and plant breeding where specific metabolites may be of interests. [53][54][55] Metabolite-wide association studies, which is the mapping of metabolite QTLs, seeks the same as genomewide and transcriptome-wide association studies, namely to identify genetic variants associated with variation in a functional character or an endophenotype. 56,57 Here we mapped the individual data points in the metabolome spectra with SNP genotypes and identified abundant metabolite feature -SNP associations ( Supplementary Table S1).…”

Section: Discussionmentioning

confidence: 99%

Prediction of complex phenotypes using theDrosophilametabolome

Rohde

Kristensen

Sarup

et al. 2020

Preprint

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Understanding the genotype -phenotype map and how variation at different levels of biological organization are associated are central topics in modern biology. Fast developments in sequencing technologies and other molecular omic tools enable researchers to obtain detailed information on variation at DNA level and on intermediate endophenotypes, such as RNA, proteins, metabolites. This facilitates our understanding of the link between genotypes and molecular and functional organismal phenotypes. Here, we use the Drosophila Genetic Reference Panel and nuclear magnetic resonance (NMR) metabolomics to investigate the ability of the metabolome to predict organismal phenotypes. We do this by performing NMR metabolomics on four replicate pools of male flies from each of 170 isogenic lines. We show first that metabolite profiles are variable among the investigated lines and that this variation is highly heritable. Second, we identify genes associated with metabolome variation. Third, we show that for four of five traits related to behaviour and stress resistance the metabolome predicts phenotypes more accurately than genomic data, and that the metabolites driving the increased accuracy was trait specific. Our comprehensive characterization of population-scale diversity of metabolomes and its genetic basis illustrates that metabolites have large potential as predictors of organismal phenotypes. This finding has strong applied importance e.g. in human medicine and animal and plant breeding.1 is a design matrix linking the genomic ( 1 ) and metabolomic ( 1 ) effects to the phenotypes. The random genomic effects are 1~( , [1,1] ! " ), and the metabolomic effects are 1~( , [1,1] 5 " ), where is the additive genomic relationship matrix as specified previously, and is the metabolomic relationship matrix.The metabolomic relationship matrix was computed as = ′ NMR ⁄ , where is a × NMR matrix of *77 18* T 6 , N 6 ), and was compared (using paired t-test corrected for multiple testing by a false discovery rate (FDR) of <0.05) within and across 9/ clusters to identify the NMR features resulting in the largest prediction accuracy. We only considered Drosophila melanogaster Genetic Reference Panel lines.

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Section: Discussionmentioning

confidence: 99%

Prediction of complex phenotypes using theDrosophilametabolome

Rohde

Kristensen

Sarup

et al. 2020

Preprint

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“…In coffee plants, SMs are well described in the economically valuable beans because of their contribution to coffee beverage quality and human health [ 20 , 21 , 22 ]. They include a variety of CGAs (esters of hydroxycinnamic acids—mainly 5-CQA), alkaloids such as caffeine and its derivatives [ 23 , 24 ], lipids [ 25 , 26 ] and volatile organic compounds [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

5-CQA and Mangiferin, Two Leaf Biomarkers of Adaptation to Full Sun or Shade Conditions in Coffea arabica L.

et al. 2020

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Phenolic compounds are involved in plant response to environmental conditions and are highly present in leaves of Coffea arabica L., originally an understory shrub. To increase knowledge of C. arabica leaf phenolic compounds and their patterns in adaptation to light intensity, mature leaves of Ethiopian wild accessions, American pure lines and their relative F1 hybrids were sampled in full sun or under 50% shade field plots in Mexico and at two contrasting elevations in Nicaragua and Colombia. Twenty-one phenolic compounds were identified by LC-DAD-MS2 and sixteen were quantified by HPLC-DAD. Four of them appeared to be involved in C. arabica response to light intensity. They were consistently more accumulated in full sun, presenting a stable ratio of leaf content in the sun vs. shade for all the studied genotypes: 1.6 for 5-CQA, F-dihex and mangiferin and 2.8 for rutin. Moreover, 5-CQA and mangiferin contents, in full sun and shade, allowed for differentiating the two genetic groups of Ethiopian wild accessions (higher contents) vs. cultivated American pure lines. They appear, therefore, to be potential biomarkers of adaptation of C. arabica to light intensity for breeding programs. We hypothesize that low 5-CQA and mangiferin leaf contents should be searched for adaptation to full-sun cropping systems and high contents used for agroforestry systems.

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“…In addition to dietary foods, humans consume many other plant-derived products such as wine, coffee, and tea. Today, metabolomics has been used to evaluate the quality of those typical plant-derived products, to correlate metabolites with taste and health properties in humans, and to promote the production of high-quality health-benefit plant-derived drinks [ 96 , 97 , 98 , 99 , 100 ]. Increasing studies begin to focus on metabolomics responses of humans to these plant-derived beverages as well.…”

Section: The Applications Of Plant Metabolomics In Crop Improvemenmentioning

confidence: 99%

“…Metabolomics has been mainly used for quality evaluation along the value chain in coffee [ 100 , 107 , 108 ], but with a higher focus on authenticity due to its high economic values [ 109 ]. Notably, because there are long-standing concerns about the association of coffee consumption with type-2 diabetes in humans [ 110 ], more metabolomics studies have been redirected to understanding the responses of humans to coffee consumption [ 111 , 112 ].…”

Section: The Applications Of Plant Metabolomics In Crop Improvemenmentioning

confidence: 99%

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

Sun

Chen

Hong

et al. 2020

Biology

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Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.

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

Cited by 30 publications

References 59 publications

Prediction of complex phenotypes using theDrosophilametabolome

Prediction of complex phenotypes using theDrosophilametabolome

5-CQA and Mangiferin, Two Leaf Biomarkers of Adaptation to Full Sun or Shade Conditions in Coffea arabica L.

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

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