<sup>13</sup>C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research

Giavalisco, Patrick; Köhl, Karin; Hummel, Jan; Seiwert, Bettina; Willmitzer, Lothar

doi:10.1021/ac900979e

Cited by 175 publications

(164 citation statements)

References 27 publications

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“…Specific, individual saponins were identified in quinoa using a preparation of 20 mg of seeds performed according a modified protocol from Giavalisco et al 75 . Samples were measured with a Waters ACQUITY Reversed Phase Ultra Performance Liquid Chromatography (RP-UPLC) coupled to a Thermo-Fisher Exactive mass spectrometer, which consists of an electrospray ionisation source and an Orbitrap mass analyser.…”

Section: Article Researchmentioning

confidence: 99%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

590

706

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Quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. It was presumably first domesticated more than 7,000 years ago by pre-Columbian cultures and was known as the 'mother grain' of the Incan Empire 1 . Quinoa has adapted to the high plains of the Andean Altiplano (> 3,500 m above sea level), where it has developed tolerance to several abiotic stresses [2][3][4] . Quinoa has gained international attention because of the nutritional value of its seeds, which are gluten-free, have a low glycaemic index 5 , and contain an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals 6 . Quinoa has the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. This potential was recognized when the United Nations declared 2013 as the International Year of Quinoa, this being one of only three times a plant has received such a designation.Despite its agronomic potential, quinoa is still an underutilized crop 7 , with relatively few active breeding programs 8 . Breeding efforts to improve the crop for important agronomic traits are needed to expand quinoa production worldwide. To accelerate the improvement of quinoa, we present here the allotetraploid quinoa genome. We demonstrate the utility of the genome sequence by identifying a gene that probably regulates the presence of seed triterpenoid saponin content. Moreover, we sequenced the genomes of additional diploid and tetraploid Chenopodium species to characterize genetic diversity within the primary germplasm pool for quinoa and to understand sub-genome evolution in quinoa. Together, these resources provide the foundation for accelerating the genetic improvement of the crop, with the objective of enhancing global food security for a growing world population. Sequencing, assembly and annotationWe sequenced and assembled the genome of the coastal Chilean quinoa accession PI 614886 (BioSample accession code SAMN04338310) using single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) and optical and chromosome-contact maps from BioNano Genomics 9 and Dovetail Genomics 10 . The assembly contains 3,486 scaffolds, with a scaffold N50 of 3.84 Mb and 90% of the assembled genome contained in 439 scaffolds (Table 1). The total assembly size of 1.39 gigabases (Gb) is similar to the reported size estimates of the quinoa genome (1.45-1.50 Gb (refs 11,12)). To combine scaffolds into pseudomolecules, an existing linkage map from quinoa 13 was integrated with two new linkage maps. The resulting map (Extended Data Fig. 1) of 6,403 unique markers spans a total length of 2,034 centimorgans (cM) and consists of 18 linkage groups (Supplementary Table 7), corresponding to the haploid chromosome number of quinoa. Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage ...

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Section: Article Researchmentioning

confidence: 99%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

590

706

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“…Secondary metabolites were profiled by the Waters Acquity UPLC system coupled to the Exactive Orbitrap mass detector according to the previously published protocol (Giavalisco et al, 2009). The UPLC system was equipped with a HSS T3 C 18 reversed phase column (100 3 2.1 mm i.d., 1.8-µm particle size; Waters) that was operated at a temperature of 40°C.…”

Section: Secondary Metabolite Profilingmentioning

confidence: 99%

Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato

et al. 2015

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A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism.

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“…Secondary metabolites were profiled using the Waters Acquity UPLC system coupled to an Exactive Orbitrap mass detector according to the previously published protocol (Giavalisco et al, 2009). UPLC was equipped with a HSS T3 C18 reversed phase column (100 3 2.1-mm i.d.…”

Section: Secondary Metabolite Profilingmentioning

confidence: 99%

Canalization of Tomato Fruit Metabolism

et al. 2017

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To explore the genetic robustness (canalization) of metabolism, we examined the levels of fruit metabolites in multiple harvests of a tomato introgression line (IL) population. The IL partitions the whole genome of the wild species Solanum pennellii in the background of the cultivated tomato (Solanum lycopersicum). We identified several metabolite quantitative trait loci that reduce variability for both primary and secondary metabolites, which we named canalization metabolite quantitative trait loci (cmQTL). We validated nine cmQTL using an independent population of backcross inbred lines, derived from the same parents, which allows increased resolution in mapping the QTL previously identified in the ILs. These cmQTL showed little overlap with QTL for the metabolite levels themselves. Moreover, the intervals they mapped to harbored few metabolism-associated genes, suggesting that the canalization of metabolism is largely controlled by regulatory genes.

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¹³C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research

Cited by 175 publications

References 27 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato

Canalization of Tomato Fruit Metabolism

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13C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research

Cited by 175 publications

References 27 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato

Canalization of Tomato Fruit Metabolism

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Product

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¹³C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research