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Adaptation of the quantitative PCR method for the detection of the main representatives of cereal grain mycobiota


The content of fungal DNA and mycotoxins in cereal crops (31 varieties of wheat, oats, and barley) was quantitatively determined and used for comparative characterization of grains. The quantitative PCR has been adapted for the analysis of the target DNA of Alternaria spp., Bipolaris sorokiniana (B. sorokiniana), Fusarium graminearum (F. graminearum), F. culmorum, and F. sporotrichioides fungi, which are often present in mycobiota of small grain cereals. The content of DNA of aggressive pathogen B. sorokiniana was determined using quantitative PCR for the first time.
The DNA of Alternaria fungi was found abundantly in all grain samples, but its content in the oat was significantly higher compared to barley and wheat (5 and 9 times higher, respectively). In barley grain, the content of B. sorokiniana DNA was on average significantly higher than in the grains of oats and wheat. The presence of F. graminearum DNA was established in all the analyzed grain samples while the F. culmorum DNA was found in 70% of the oat’s samples and in all samples of barley and wheat. Mycotoxin deoxynivalenol (DON) produced by these fungi was detected in all analyzed cereal grains in a range from 77 to 4133 μg/kg. The DNA of F. sporotrichioides was detected in 70% of oats and 50% of barley samples but was not found in wheat. The T-2 toxin produced by this fungus was detected in 45% of all samples within the range from 2 to 89 μg/kg.
The statistically significant positive correlation with the Pearson correlation coefficient (r) equal to 0.49 (p<0.05) was observed between the amount of F. graminearum DNA and DON in the grain samples. Another significant positive correlation (r = 0.72, p<0.01) was found between DNA contents of Alternaria fungi and F. sporotrichioides in the grain samples. This leads to the suggestion that conditions for growth of these fungi in grain substrates are similar.

About the Authors

A. S. Orina
All-Russian Institute of Plant Protection
Russian Federation

Aleksandra Orina

St. Petersburg, Pushkin

O. P. Gavrilova
All-Russian Institute of Plant Protection
Russian Federation
St. Petersburg, Pushkin

T. Yu. Gagkaeva
All-Russian Institute of Plant Protection
Russian Federation
St. Petersburg, Pushkin


1. Yli-Mattila T, Paavanen-Huhtala S, Jestoi M, Parikka P, Hietaniemi V, Gagkaeva T, Sarlin T, Haikara A, Laaksonen S, Rizzo A. Real-time PCR detection and quantification of Fusarium poae, F. graminearum, F. sporotrichioides and F. langsethiae in cereal grains in Finland and Russia. Arch Phytopathol Plant Protect, 2008; 41(4). 243–60. doi: 10.1080/03235400600680659.

2. Шипилова НП, Гаврилова ОП, Гагкаева ТЮ. Влияние зараженности грибами рода Fusarium на качественные характеристики зерна озимой пшеницы. Вестник защиты растений, 2014; (4), 27–31.

3. Nicholson P, Simpson DR, Weston G, Rezanoor HN, Lees AK, Parry DW, Joyce D. Detection and quantification of Fusarium culmorum and Fusarium graminearum in cereals using PCR assays. Physiol Mol Plant Pathol, 1998; 53, 17–37. doi: 10.1006/ pmpp.1998.0170.

4. Stakheev A, Ryazantsev DYu, Gagkaeva TYu, Zavrieva SK. PCR detection of Fusarium fungi with similar profiles of the produced mycotoxins. Food Control, 2011; (22), 462–8. doi: 10.1016/j.foodcont.2010.09.028.

5. Gagkaeva TYu, Gavrilova OP, Orina AS, Blinova EV, Loskutov IG. Response of wild Avena species to fungal infection of grain. The Crop Journal, 2017; 5(6), 499–508. doi: 10.1016/j.cj.2017.04.005.

6. Орина АС, Гаврилова ОП, Гагкаева ТЮ. Колонизация культурных и дикорастущих злаковых растений грибами родов Alternaria, Cladosporium и Fusarium. Защита и карантин растений, 2017; (6), 25–7.

7. Ellis MB. Dematiaceos hyphomycetes. Kew: Commonwealth Mycological Institute; 1971.

8. Yli-Mattila T, Paavanen-Huhtala S, Parikka P, Konstantinova P, Gagkaeva TY. Molecular and morphological diversity of Fusarium fungi in Finland and north-western Russia. Eur J Plant Pathology, 2004; 110, 573–85. doi: 10.1023/B:EJ PP.0000032397.65710.69.

9. Pavón MÁ, González I, Martín R, García Lacarra T. ITS-based detection and quantification of Alternaria spp. in raw and processed vegetables by real-time quantitative PCR. Food Microbiol; 2012; 32(1), 165–71. doi: 10.1016/

10. Matusinsky P, Frei P, Mikolasova R, Svacinovaa I, Tvaruzeka L, Spitzera T. Species-specific detection of Bipolaris sorokiniana from wheat and barley tissues. Crop Protection, 2010; 29, 1325–30. doi: 10.1016/j.cropro.2010.07.013.

11. СанПиН «Гигиенические требования безопасности и пищевой ценности пищевых продуктов»; 2002.

12. Hofgaard IS, Aamot HU, Torp T, Jestoi M, Lattanzio VMT, Klemsdal SS, Waalwijk C, van der Lee T, Brodal G. Associations between Fusarium species and mycotoxins in oats and spring wheat from farmers’ fields in Norway over a six-year period. World Mycotoxin J, 2016; 9(3), 365–78. doi: 10.3920/WMJ2015.2003.

13. Desjardins AE. Fusarium Mycotoxins. Chemistry, Genetics, and Biology. St. Paul: American Phytopathological Society; 2006. doi: 10.1111/j.1365-3059.2006.01505.x.

14. Орина AC, Гаврилова ОП, Гагкаева ТЮ, Лоскутов ИГ. Симбиотические взаимоотношения грибов рода Fusarium и Alternaria, колонизирующих зерно овса. Сельскохозяйственная биология, 2017; 52(5), 986–94. doi: 10.15389/agrobiology.2017.5.986rus.


For citations:

Orina A.S., Gavrilova O.P., Gagkaeva T.Yu. Adaptation of the quantitative PCR method for the detection of the main representatives of cereal grain mycobiota. Microbiology Independent Research Journal (MIR Journal). 2018;5(1):71-77. (In Russ.)

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