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Background  Fusarium head blight (FHB) of wheat caused by  Fusarium graminearum  species complex (FGSC) is a devastating disease worldwide. The pathogens not only reduce the yield of wheat, but also impact the quality of wheat by contamination with trichothecene mycotoxins. A systematic investigation on the pathogens of FHB in Taiwan is lacking. Here, molecular and morphological approaches were used to identify species of the Taiwanese FGSC isolates and determine their trichothecene genotypes.    Results  In this study, a total of 195 isolates of FGSC from diseased wheat were collected from 8 areas of northern and central Taiwan. All isolates were subjected to seedling inoculation for verification of pathogenicity. The pathogenic isolates were genetically characterized by sequence characterized amplified region (SCAR), PCR- restriction fragment length polymorphism (RFLP), phylogenetic analysis and fixed nucleotides to clarify their phylogenetic species, and by PCR assays of  TRI  genes to determine trichothecene genotypes. They were identified as  F. asiaticum ,  F. graminearum  sensu stricto,  F. meridionale  and an unknown species. Isolates of  F. asiaticum  were the major causal agents (98%) in this investigated population and were comprised of SCAR type 5 (75%), SCAR type 4 (21%) and SCAR type 3 (2%). Their trichothecene genotypes were either 15-acetyl-deoxynivalenol (15-ADON) (83%) or nivalenol (NIV) genotype (17%). These genetic characterizations indicated that  F. asiaticum  (15-ADON SCAR type 5) accounts for 60% of this Taiwanese population. Virulence assay on wheat heads indicated virulence of  F. asiaticum  isolates in subpopulations divided by SCAR types or trichothecene genotypes were comparable, suggesting other factors influence the unequal subpopulation sizes.    Conclusions  This is the first study that FGSC isolates in Taiwan were systematically collected and characterized. In addition to  F. graminearum  sensu stricto and  F. meridionale ,  F. asiaticum  with 15-ADON genotype was identified as the predominate species in Taiwan. In contrast to Chinese and Japanese populations that  F. asiaticum  isolates were typically of 3-ADON or NIV genotype, the predominate 15-ADON genotype in Taiwanese population was unique among  F. asiaticum  populations and represented the southernmost 15-ADON genotype population in East Asia.    Electronic supplementary material  The online version of this article (doi:10.1186/s40529-016-0156-4) contains supplementary material, which is available to authorized users.

Identification and trichothecene genotypes of Fusarium graminearum species complex from wheat in Taiwan