Genetic analysis of metabolome–phenotype interactions: from model to crop species

Carreño-Quintero, Natalia; Bouwmeester, Harro J.; Keurentjes, Joost J. B.

doi:10.1016/j.tig.2012.09.006

Cited by 111 publications

(69 citation statements)

References 90 publications

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“…With the currently available high-throughput genotyping technologies, genome-wide association studies (GWAS) have been developed as a powerful approach to characterize the genetic basis of complex traits and locus-locus interactions in plants (Nordborg and Weigel, 2008). More recent studies combining GWAS with metabolomics (mGWAS) demonstrate a powerful forward genetics strategy that can be used to dissect the genetic and biochemical basis of plant metabolism, including that in model species, such as Arabidopsis thaliana, tomato, rice (Oryza sativa), and Medicago truncatula, and other crop species, such as barley, perilla (Perilla ocymoides), and pepper (Capsicum annuum) (Achnine et al, 2005;Yamazaki et al, 2008;Widodo et al, 2009;Wahyuni et al, 2011;Carreno-Quintero et al, 2013;Luo, 2015). Moreover, recent studies have revealed that linkage disequilibrium mapping in combination with linkage mapping improves the ability to identify important loci.…”

Section: Introductionmentioning

confidence: 99%

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

et al. 2017

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Section: Introductionmentioning

confidence: 99%

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

et al. 2017

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“…Procedures such as liquid chromatography-mass spectrometry (LC-MS) and NMR have notably been used with both model and crop species to identify the genetic architecture of metabolic traits using quantitative trait locus mapping approaches (reviewed in ref. 13). Such approaches have been very successful in addressing genomic regions responsible for glucosinolate accumulation in Arabidopsis and related species (10,(14)(15)(16).…”

mentioning

confidence: 99%

Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

Baldwin

Gaquerel

2015

Proc. Natl. Acad. Sci. U.S.A.

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Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United Statesincluding the well-characterized Utah 30th generation inbred accession-and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis.plant-insect interactions | metabolomics | mass spectrometry | natural variation E lucidating the structure of metabolites underlying complex traits and the factors that maintain their variation in natural populations are important challenges in plant ecological studies (1). Many studies have notably shown that stress-responsive pathways that produce secondary metabolites are sporadically found across different plant taxa with extensive diversification (2). This important diversification suggests that particular metabolic systems have been recruited through natural selection when the set of compounds that they produce address specific ecological needs. Interactions with insects are important selection pressures that have sculpted plant metabolism, and many plant metabolites protect against herbivore attack and physical damage (3-5). The timely production of particular secondary metabolites in response to insect attack benefits plants by decreasing the costs of constitutive metabolite production. Trade-offs between defense metabolite productions and the intrinsic growth-related functions of central metabolic pathways likely prov...

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“…With this technique, it is easy to analyse essential oils and faty acids as well as terpenoids, alkaloids, monosaccharides and steroids, among others. Capillary electrophoresis, for its part, helps in the detection of oligosaccharides, hydrophobic vitamins, coenzymes, prosthetic groups, nitrogenous bases, nucleotides and nucleosides, among others [21].…”

Section: Applications Of Metabolomics In Agriculturementioning

confidence: 99%

“…Generate metabolic proiles to determine the impact of geographic location and season, study the phenotype of natural variations of certain plant species, evaluate transgenic varieties, study metabolic variations of diferent cultivars and carry out functional characterizations (functional genomics). Analyse metabolic changes during growth, development and diferentiation, elucidate biosynthetic pathways, analyse population diferentiation, carry out chemotaxonomic analyses, carry out nontargeted studies and characterize cultivars [21].…”

Section: Metabolomics -Fundamentals and Applicationsmentioning

confidence: 99%

Metabolomics as a Tool in Agriculture

Ibarra-Estrada¹,

Soto-Hernández²,

Palma-Tenango³

2016

Metabolomics - Fundamentals and Applications

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Metabolomics is a study through can be obtain a beter understanding of the complexity of the biological systems, through the chemical composition and relations with the physiology of the plant. The literature describes a lot of information on this support in areas of medicinal plants, chemosystematics, adulteration of plants, etc., but it is scarce in agriculture. At present, agriculture plays a crucial role in human beings. The demand of foods has increased due to the continuous increase in the population, and this requires an increase in the production of crops, besides the crops being afected by the climatic change, atack of pest and diseases and resistance to a conventional agrochemicals. At present, scientists are doing some practices or studies of genetic improvement of crops to increase their production and avoid the problems pointed out. It is an important part of the genomic studies; the results could be the basis for a genetic improvement based on the chemical composition of the crops, and in the metabolomics studies represent a crucial role in their quality for human consumption. The aim of the chapter is to review the literature from 10 years behind emphasizing the importance of metabolomics in crops of economic and feed value.

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Genetic analysis of metabolome–phenotype interactions: from model to crop species

Cited by 111 publications

References 90 publications

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

Metabolomics as a Tool in Agriculture

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