TRI Genotyping and Chemotyping: A Balance of Power
Abstract
:1. Introduction
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- Identifying the source of mycotoxin contamination, i.e., fungus and toxin identification;
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- Toxicological profiling of mycotoxin residues in stored food/feed;
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- Assessing the current analytical methods to identify and quantify such residues;
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- Defining the relationship between mycotoxin levels and different types of food/feed;
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- Effects of mycotoxins on human and animal health.
2. Molecular Identification of Fusarium Species
3. Fusarium Species Known to Produce Trichothecenes
4. Chemotyping
Analytical Techniques for Chemotyping
5. Genotyping
5.1. Genotyping Platforms
5.1.1. Targeted Detection of TRI Genes by Conventional PCR: Single, Duplex, and Multiplex PCR Assays
5.1.2. Detection of TRI1 Gene Sequence Polymorphisms by PCR-RFLP
5.1.3. TRI5-TRI6 Intergenic Region Sequencing
5.1.4. Multi-locus Genotyping Assay (MLGT)
5.1.5. Quantitation of TRI Gene Products by Real-time qPCR
6. Advantages of TRI Genotyping
7. Incongruence between Chemotype and Genotype
8. Factors Affecting the Reliability of Genotype-chemotype Association
9. Future Prospects—Data Sharing and Quality Control
9.1. Data Repositories for Fusarium Genome Sequences
9.2. Fusarium MLST
9.3. A European Database of F. graminearum and F. culmorum Trichothecene Genotypes
9.4. Ensembl Fungi
9.5. FungiDB
9.6. MycoBank
Author Contributions
Funding
Conflicts of Interest
References
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Fusarium Species | Primer Name | Target Gene | Primer Sequence/5’ to 3’ | Amplicon/bp | Reference | |
---|---|---|---|---|---|---|
F. culmorum | FC01F (fwd) | SCAR | specific | ATGGTGAACTCGTCGTGGC | 570 | [17,18] |
FC01R (rev) | SCAR | CCCTTCTTACGCCAATCTCG | ||||
Fcg17F (fwd) | SCAR | F. culmorum + F. graminearum | TCGATATACCGTGCGATTTCC | 340 | ||
Fcg17R (rev) | SCAR | TACAGACACCGTCAGGGGG | ||||
Fcu-F (fwd) | IGS | specific | GACTATCATTATGCTTGCGAGAG | 200 | ||
Fgc-R (rev) | IGS | CTCTCATATACCCTCCG | ||||
F. graminearum + fungi belonging to FGSC - F. asiaticum; F. meridionale | Fg16F (fwd) | SCAR | FGSC members | CTCCGGATATGTTGCGTCAA | 400–500 | [18,19,20] |
Fg16R (rev) | SCAR | GGTAGGTATCCGACATGGCAA | ||||
Fgr-F (fwd) | IGS | specific | GTTGATGGGTAAAAGTGTG | 500 | [21] | |
Fgc-R (rev) | IGS | CTCTCATATACCCTCCG | ||||
GOFW (fwd) | gaoA gene | specific | ACCTCTGTTGTTCTTCCAGACGG | 472 | [22] | |
GORV (rev) | gaoA gene | CTGGTCAGTATTAACCGTGTGTG | ||||
F. poae | FP82F (fwd) | SCAR | specific | CAAGCAAACAGGCTCTTCACC | 220 | [23] |
FP82R (rev) | SCAR | TGTTCCACCTCAGTGACAGGTT | ||||
PoaeIGS-R (fwd) | IGS | F. poae + F. kyushuense + F. langsethiae | CAAGCTCTCCTCGGAGAGTCGAA | 306 | [24] | |
CNL12 (rev) | IGS | CTGAACGCCTCTAAGTCAG | ||||
Fps-F (fwd) | IGS | specific | CGCACGTATAGATGGACAAG | |||
Fpo-R (rev) | IGS | CAGCGCACCCCTCAGAGC | 400 | |||
F. sporotrichioides | AF330109CF (fwd) | TRI13 | specific | AAAAGCCCAAATTGCTGATG | 332 | [25] |
AF330109CR (rev) | TRI13 | TGGCATGTTCATTGTCACCT | ||||
FspITS2K (fwd) | ITS | specific | CTTGGTGTTGGGATCTGTCTGCAA | 288 | [26] | |
P28SL (rev) | ITS | ACAAATTACAACTCGGGCCCGAGA | ||||
Fps-F (fwd) | IGS | specific | CGCACGTATAGATGGACAAG | 400 | [21] | |
Fsp-R (rev) | IGS | GTCAGAAGAGACGCATCCGCC | ||||
F. pseudograminearum | FP1-1 (fwd) | degenerate | CGGGGTAGTTTCACATTTCYG | 523 | [27] | |
FP1-2 (rev) | GAGAATGTGATGASGACAATA | |||||
F. cerealis | CRO-AF (fwd) | specific | CTCAGTGTCCACCGCGTTGCGTAG | 842 | [28] | |
CRO-AR (rev) | CTCAGTGTCCCATCAAATAGTCC |
Technique | Advantages | Disadvantages | TRI Toxin | References |
---|---|---|---|---|
Enzyme-Linked Immunosorbent Assay (ELISA) |
|
| DON, T-2, T-2/HT-2 | [50,51,52,53,54,55,56,57] |
Liquid chromatography-mass spectrometry (LC-MS) or tandem mass spectrometry (LC-MS/MS); LC-MS/MS followed by structure confirmation via Q-TOF LC/MS, 1H- and 13C-NMR; LC-MS-based methods—LC with efficient electrospray (ESI) or atmospheric pressure chemical ionization (APCI); Columns: DON-NIV™ WB immunoaffinity columns isolate DON and NIV simultaneously in a single sample extract; Myco 6-in-1 is a quantitative method for the simultaneous detection of six mycotoxins |
|
| NIV, DON, 3-Ac-DON, 15-Ac-DON, HT-2, T-2 toxin (maize); LC-ESI-MS/MS: NIV, DON, 3-Ac-DON, 15-Ac-DON, HT-2 toxin, T-2 toxin, DAS, neosolaniol, monoacetoxyscirpenol, T-2 triol, and T-2 tetraol (wheat and oat); LC-APCI-MS- DOM-1, HT-2 toxin, T-2 toxin, acetyl T-2 toxin, DAS, monoacetoxyscirpenol, neosolaniol (oats, maize, barley and wheat); T-2 and HT-2 and their glucosylated and acetylated derivatives (T2 toxin-3-glucoside, 3-acetyl-T-2 toxin and 3-acetyl-HT-2 toxin) in staple flours, barley, maize, oats, rye, and wheat | [58,59,60,61,62,63] |
High Performance Liquid Chromatography (HPLC); Columns: T-2/HT-2™ HPLC columns -T-2 and HT-2 toxins |
|
| HT-2 toxin, T-2 toxin, DON (cereals and grains) | [58,59,60,64] |
HPLC with a specific detector—fluorescence (FL), ultraviolet (UV), diode array (DAD), or MS; Ultra HPLC-MS/MS (UHPLC-MS/MS) | HPLC-FL- highly specific and sensitive, lower cost than LC-MS methods; method validation performed according to Commission Decision 2002/657/EC (EC, 2002, 2014, 2017), revealed precision | HPLC-FL—specificity for fluorescing compounds which must be well separated on column for reliable quantification | HPLC-FL- DON, NIV, T-2 toxin, HT-2 toxin, NEO, DAS, 3-Ac-DON, 15-Ac-DON (wheat and corn); HPLC-MS- DON; DON and its acetylated and glucosylated metabolites, HT-2 and T-2 toxins in maize | [62,65,66,67] |
Combination of immunological capture and HPLC-MS/MS | monoclonal antibody developed against DON for purification of cereal extract, before the follow-up HPLC-MS/MS analysis | N/A | DON, 3-ADON, and 15-ADON from wheat, oatmeal, and maize | [68] |
Competitive immunochromatographic assay or lateral flow immunoassay | N/A | N/A | DON in maize extracts | [69] |
Fusarium Species | Host Species | Country | TRI Gene Target | Chemotype | Reference |
---|---|---|---|---|---|
F. asiaticum | Triticum sp. (wheat) | China | TRI3, TRI12 | 3-ADON | [73] |
F. asiaticum | Hordeum vulgare (barley) | Japan | TRI3, TRI12 | NIV | [73] |
F. asiaticum | Triticum sp. (wheat) | Taiwan | TRI13 | 15-ADON and NIV | [74] |
F. austroamericanum | Zea mays (maize) | Brazil | TRI3, TRI12 | 3-ADON | [73] |
F. austroamericanum | herbaceous vine | Venezuela | TRI3, TRI12 | NIV | [73] |
F. cerealis | potato tuber | Netherlands | TRI3, TRI12 | NIV | [75] |
F. cerealis | Azalea | New Zeland | TRI3, TRI12 | NIV | [75] |
F. culmorum | Ammophila arenaria (European beachgrass) | Netherlands | TRI3, TRI12 | NIV | [75] |
F. culmorum | Triticum sp. (wheat) | France | TRI3, TRI12 | 3-ADON | [75] |
F. culmorum | Populus nigra (European black poplar) | Portugal | TRI3, TRI12 | 3-ADON | [75] |
F. culmorum | Ammophila arenaria (European beachgrass) | Netherlands | TRI3, TRI12 | NIV | [75] |
F. culmorum | Hordeum vulgare (barley) | Denmark | TRI3, TRI12 | 3-ADON | [73] |
F. culmorum | Avena sativa (oat) | Canada | TRI3, TRI12 | 3-ADON | [76] |
F. culmorum | Hyacinthus orientalis (Hyacinth) | Netherlands | TRI3, TRI12 | NIV | [75] |
F. culmorum | Triticum sp. (wheat) | Poland | TRI3, TRI12 | NIV and 3-ADON | [77] |
F. culmorum | Triticum sp. (wheat) | UK | TRI3, TRI7, TRI13 | DON and NIV | [78] |
F. culmorum | Triticum sp. (wheat) | Tunisia | TRI3, TRI5, TRI7, TRI13 | DON, NIV | [79] |
F. graminearum | Zea mays (maize) | Iran | TRI3, TRI12 | NIV | [73] |
F. graminearum | Triticum sp. (wheat) | South Africa | TRI3, TRI12 | 15-ADON | [75] |
F. graminearum | Rumohra adiantiformis (leatherleaf fern) | Netherlands | TRI3, TRI12 | NIV | [73] |
F. graminearum | Triticum sp. (Louisiana, wheat) | USA | TRI3, TRI12 | 15-ADON | [80] |
F. graminearum | Triticum sp. (Ohio, wheat) | USA | TRI3, TRI12 | 3-ADON | [75] |
F. graminearum | Zea mays (Michigan, maize) | USA | TRI3, TRI12 | 15-ADON | [73] |
F. graminearum | Zea mays (Ohio, maize) | USA | TRI3, TRI12 | 15-ADON | [73] |
F. graminearum | Triticum sp. (Kansas, wheat) | USA | TRI3, TRI12 | 15-ADON | [73] |
F. graminearum | Sorghum bicolor (sorghum) | Ethiopia | TRI3, TRI12 | 15-ADON | [75] |
F. graminearum | Zea mays (maize) | Nepal | TRI3, TRI12 | NIV | [73] |
F. graminearum | Avena sativa (oat) | Sweden | TRI3, TRI12 | 3-ADON | [75] |
F. graminearum | Zea mays (maize) | South Africa | TRI3, TRI12 | 15-ADON | [75] |
F. graminearum | Triticum sp. (wheat) | England | TRI3, TRI12 | 15-ADON | [75] |
F. graminearum | Triticum sp. (wheat) | Poland | TRI3, TRI12 | 3-ADON, 15-ADON and NIV | [75] |
F. graminearum | Zea mays (maize) | Korea | TRI3, TRI4, TRI5, TRI7, TRI8, TRI11 | DON and NIV | [81] |
F. graminearum | Hordeum vulgare (barley) | Korea | TRI3, TRI4, TRI5, TRI7, TRI8, TRI11 | DON and NIV | [81] |
F. graminearum | Triticum sp. (wheat) | Taiwan | TRI13 | 15-ADON and NIV | [74] |
F. graminearum | Triticum sp. (wheat) | Canada | TRI1, TRI8, TRI12, TRI3 | 3-ADON, 15-ADON and 3-ANX | [82] |
F. graminearum | Zea mays (maize) | Canada | TRI1, TRI8, TRI12, TRI3 | 3-ADON, 15-ADON and 3-ANX | [82] |
F. graminearum | Triticum sp. (wheat) | Brazil | TRI3, TRI12 | 15-ADON, NIV and 3-ADON | [83] |
F. graminearum | potato tuber | USA | TRI7, TRI13 | DON, NIV | [35] |
F. graminearum | Triticum sp. (wheat) | Canada | TRI1 | DON, NIV, NX-2 | [84] |
F. graminearum | Multiple | USA | TRI1 | NX-2 | [85] |
F. graminearum | Galium aparine, Triticum sp. Zea mays | Germany, France | TRI7, TRI13, TRI5-TRI6 | 3-ADON, 15-ADON, DON, NIV | [86] |
F. graminearum + 21 related species of the F. sambucinum s.c. | cereals | USA (north) + Canada (south) | TRI1 | NX-2 | [40] |
F. graminearum s.c. | Zea mays (maize) | Argentina | TRI7, TRI13 | DON, NIV | [87] |
F. graminearum s.c. | Triticum sp. (wheat), wild grass | USA (New York) | TRI1 | NX-2 | [88] |
F. graminearum s.c. F. boothii, F. asiaticum, F. meridionale | Zea mays (maize) | Nepal | TRI13 | DON, NIV | [89] |
F. graminearum s.c. F. pseudograminearum, and F. poae | Hordeum vulgare (barley) | Uraguay | TRI1 | 15-ADON, NX-2 | [17] |
F. graminearum s.s. | Triticum sp. (wheat) | Argentina | TRI3, TRI7, TRI13 | 15-ADON, DON, NIV | [90] |
F. graminearum s.s. | Triticum sp. (wheat) | Argentina | TRI3, TRI7, TRI13 | 3-ADON, 15-ADON, DON, NIV | [19] |
F. graminearum s.s. | Triticum sp. (wheat) | Italy | TRI5, TRI7, TRI3 | NIV | [91] |
F. graminearum s.s. | Triticum sp. (wheat) | Uraguay | TRI3, TRI5, TRI7, TRI13 | 15-ADON, DON | [92] |
F. graminearum s.s. F. culmorum, F. poae | Triticum sp. (wheat) | Italy | TRI5, TRI7, TRI12 | 3-ADON, 15-ADON, NIV | [20] |
F. graminearum s.s. F. meridionale | Glycine max (soybean) | Argentina | TRI3, TRI5, TRI7 | 15-ADON, DON, NIV | [93] |
F. graminearum s.s. F. meridionale, F. austroamericanum | Triticum sp. (wheat) | Brazil | TRI3, TRI12 | 3-ADON, 15-ADON, NIV | [94] |
F. graminearum, F. meridionale | Triticum sp. (wheat) | Brazil | TRI3, TRI12, TRI13 | 15-ADON, DON | [95] |
F. meridionale | orange twig | New Caledonia | TRI3, TRI12 | NIV | [73] |
F. meridionale | Zea mays (maize) | Nepal | TRI3, TRI12 | NIV | [73] |
F. meridionale | Triticum sp. (wheat) | Taiwan | TRI13 | NIV | [74] |
F. mesoamericanum | Musa sp. (banana) | Honduras | TRI3, TRI12 | NIV | [73] |
F. mesoamericanum | Acaciae mearnsii (black wattle) | South Africa | TRI3, TRI12 | NIV | [75] |
F. pseudograminearum | Hordeum vulgare (barley) | Australia | TRI3, TRI12 | 3-ADON | [73] |
F. sporotrichioides | Zea mays (maize) | Korea | TRI3, TRI4, TRI5, TRI8, TRI11 | NIV | [81] |
F. sporotrichioides | Hordeum vulgare (barley) | Korea | TRI3, TRI4, TRI5, TRI8, TRI11 | NIV | [81] |
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Villafana, R.T.; Ramdass, A.C.; Rampersad, S.N. TRI Genotyping and Chemotyping: A Balance of Power. Toxins 2020, 12, 64. https://doi.org/10.3390/toxins12020064
Villafana RT, Ramdass AC, Rampersad SN. TRI Genotyping and Chemotyping: A Balance of Power. Toxins. 2020; 12(2):64. https://doi.org/10.3390/toxins12020064
Chicago/Turabian StyleVillafana, Ria T., Amanda C. Ramdass, and Sephra N. Rampersad. 2020. "TRI Genotyping and Chemotyping: A Balance of Power" Toxins 12, no. 2: 64. https://doi.org/10.3390/toxins12020064
APA StyleVillafana, R. T., Ramdass, A. C., & Rampersad, S. N. (2020). TRI Genotyping and Chemotyping: A Balance of Power. Toxins, 12(2), 64. https://doi.org/10.3390/toxins12020064