Bt-transformed maize contains genes from Bacillus thuringiensis encoding for insecticidal crystal proteins. Less insect damage on Bt maize stalks can cause a reduced infection by Fusarium species through plant injuries. This could affect the presence of plant-pathogenic Fusarium species on maize residues which serve as an inoculum source for subsequent crops. We collected overwintered maize stalks of four different Bt maize hybrids and their corresponding non-Bt lines in two consecutive years in a field trial in Germany. Fusarium spp. were isolated from 67% of 648 collected maize stalks. Identification with new multiplex PCR assays showed that F. graminearum, F. avenaceum, and F. proliferatum were the most abundant Fusarium species, isolated from 42%, 26%, and 15% of the stalks, respectively. Species abundances varied between varieties and collection years. No consistent difference was found between Bt and non-Bt stalks. Fusariumgraminearum isolates were subject to a population genetic structure analysis with eight newly developed microsatellites. Significant association of loci and overrepresentation of repeated multilocus haplotypes indicated a substantial asexual component of reproduction, supporting selection of haplotypes. The data suggested selection of particular F. graminearum haplotypes by collection years but not by maize Bt transformation. Haplotypic changes between years caused no divergence in the distribution of alleles, suggesting that gene flow beyond the field scale prevented substructuring. We present evidence for gene flow between our saprophytic F.graminearum population on maize residues and a wheat-pathogenic population from a field 100km distan
