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Metabolomics provide valuable insight for the study of durum wheat: a review Sergio Saia, Mariagiovanna Fragasso, Pasquale De Vita, and Romina Beleggia J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.8b07097 • Publication Date (Web): 04 Mar 2019 Downloaded from http://pubs.acs.org on March 5, 2019
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Journal of Agricultural and Food Chemistry
Metabolomics provide valuable insight for the study of durum wheat: a review
Sergio Saia1,2,a, Mariagiovanna Fragasso1,a, Pasquale De Vita1, Romina Beleggia1,*
1
Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and
Industrial Crops (CREA-CI), S.S. 673, Km 25,200, 71122 Foggia, Italy [R.B. ORCID: 00000002-2880-5033; P.D.V. ORCID: 0000-0002-9573-0510] 2
Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and
Industrial Crops (CREA-CI), S.S. 11 per Torino, Km 2,5 - 13100, Vercelli, Italy [S.S. ORCID: 0000-0001-5465-8500]
a
These authors contributed equally to this review
* Correspondence: Dr Romina Beleggia Tel: +39 0881 742972 (425); Fax: +39 00881713150; Email:
[email protected] ACS Paragon Plus Environment
Journal of Agricultural and Food Chemistry
Abstract Metabolomics is increasingly being applied in various fields offering a highly informative tool for high-throughput diagnostics. However, in plant sciences, metabolomics is underused, even though plant studies are relatively easy and cheap when compared to those on humans and animals. Despite their importance for human nutrition, cereals, and especially wheat, remain understudied from a metabolomics point of view. The metabolomics of durum wheat has been essentially neglected, although its genetic structure allows the inference of common mechanisms that can be extended to other wheat and cereal species. This review covers the present achievements in durum wheat metabolomics highlighting the connections with the metabolomics of other cereal species (especially bread wheat). We discuss the metabolomics data from various studies and their relationships to other ‘-omics’ sciences, in terms of wheat genetics, abiotic and biotic stresses, beneficial microbes, and the characterization and use of durum wheat as feed, food, and food ingredient.
Keywords: agronomy; foodomics; omics technologies; plant metabolism; Triticum turgidum ssp. turgidum convar. Durum; Triticum aestivum.
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Introduction
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Metabolomics, one of the most recent of the ‘-omics’ technologies, was introduced at the
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beginning of third millennium, and it was rapidly realized to be a robust tool for biological/
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environmental/technological analyses, as it can be used to define the final products of the
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genetic, gene-expression and protein activities in a given moment and condition. At present,
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metabolomics provides a highly informative instrument for high-throughput diagnostics in
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various studies, and it is also an important complement to other approaches used in systems
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biology (e.g., genomics, transcriptomics, proteomics, phenomics)1.
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Oliver et al.2 defined the metabolome as the quantitative collection of all of the low
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molecular weight compounds present in a cell, tissue or organism, at a given moment. Thus,
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metabolomics allows comprehensive information about the composition of a metabolite pool,
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for functional screen of the state of a cell, tissue, or organ, or of their environment3.
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Metabolomics also allows direct measurement of biochemical activities through monitoring of
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substrates and their transformed products during metabolism, such that metabolomics studies
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are easier to relate to phenotypes4, as compared to genomics, transcriptomics and proteomics.
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This is because the functions of genomic regions and the expressed sequences and proteins
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can undergo epigenetic regulation, post-translational modifications5, and activity impairment,
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which depend on substrate and cofactors availability. In addition, it is important to underline
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that organism-specific genomic information is not necessary for metabolomics analyses.
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To draw meaningful conclusions of the functioning of a biological system, the
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metabolomics analyses consist of several steps, each of which is of equal importance in terms
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of the results thus, the scientific community established minimum sets of reporting standards6.
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Problems associated with metabolomics include the chemical diversity of metabolites, the
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relationship of each metabolite to the matrix, and the broad dynamic range of the abundance
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of a given metabolite. To date, there is no unique analytical technique that can cover the entire
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metabolome. As a consequence, a combination of different extraction techniques and
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analytical methods is needed to reach adequate ‘metabolite coverage7.
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Metabolomics and metabolite profiling have been defined for a large number of
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applications, to efficiently investigate plant responses to biotic and abiotic stress, and for
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phenotyping purposes1,5,8–12. Such profiling provides a valuable tool in the analysis of data
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relating to physiological responses of plants, as it has been shown that the whole metabolome,
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its structure, and its internal ebbs and flows, are also affected by the environment13, depend on
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the physiological status and vary by the phenological stage14. Metabolomics also have a role
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in food-related ‘nutrition and health’ studies (also defined as ‘foodomics’), and in the
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characterization of foodstuffs and food processing, to improve the quality of a product and/or
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its associated processes, and to ascertain the safety of an end product15.
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To perform the present review, we conducted a systematic map, i.e. a collection of
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relevant reports on metabolomics on Web of Science (WoS v. 5.31) and Scopus (dates of
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collection: 1st to 3rd December 2018). Systematic maps are unequivocal strategies to collect
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reports and implies the presentation of the collection terms and means. See Schillaci et al.16
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for further details and the guideline by the Social Care Institute for Excellence (SCIE, at
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http://www.scie.org.uk/research/maps.asp). Here we searched in title, abstract and keywords.
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In WoS, we searched by selecting “all databases”. An initial search was made with
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“metabolom*” as a research term, thus to include metabolomics, metabolomic (which is an
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unusual but seldom used term), and metabolome. Further searches implied the addition of
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“metabolom*” and a second research term (Supplementary Table 1 and 2). PubMed was also
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checked for amount of reports per search term, but not included.
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Metabolom*- related reports sharply increased over the past 20 years. As expected,
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these mainly related to human and animal studies. The number of reports (including journal
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articles conference contributions) that have included “metabolom*” AND “plant” are the 24%
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of the total number of articles included in the search term “metabolom*” only (Figure 1). On
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the one hand, this proportion confirms the relatively important role of this approach for new
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information on the plant kingdom. On the other hand, this proportion might be considered
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surprisingly low on the basis that studies on plants are often easier and cheaper than those on
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humans and animals, due to the ease of obtaining clones (and thus studying system responses
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in the absence of specific genotypic noise or using genotypes and genes as experimental
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variables); and to fewer ethical concerns.
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Most of the world food supply depends on cereals. Nonetheless, these crops have not
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been greatly studied from a metabolomics point of view: as shown in Figure 1, only the 17%
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of the metabolomics studies conducted on plants refer to cereals according to our search
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terms. In addition, although yield and quality of these crops are constantly jeopardized by
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abiotic/biotic stresses, which can lead to severe yield losses with a great economic and social
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impact, most metabolomics studies on cereals are designed to determine the chemical
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compositions of the kernel and/or the main cereal products. Few studies aimed to understand
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the physiological responses of the plants to internal or external factors. In the reports dealing
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with wheat, dealt with durum wheat. In addition, reports including wheat and another cereal
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species were 99 for corn, 103 for rice, 23 for oat, 103 for barley, 4 for triticale, 48 for rye, and
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11 for the sum of “Sorghum + Millet* + Panicum + Digitaria + Paspalum scrobiculatum +
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Brachiaria deflexa + Urochloa ramosa + Coix”. These reports may provide information for to
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compare wheat with species, at least corn, rice, and barley and to a lesser extent rye.
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Wheat is the third most important cereal species in terms of total world production. It
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is the most widely grown cereal and the major world livelihood. However, despite the great
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social and environmental implications of wheat cultivation, metabolomics reports on wheat
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represent
