Fusarium head blight (FHB), caused by Fusarium graminearum, is a serious disease of wheat (Triticum aestivum L.) associated with contamination by the mycotoxin deoxynivalenol (DON). The FHB-resistant wheat cultivar ‘Sumai 3’ has been used extensively around the world. The existence of variation in FHB resistance among ‘Sumai 3’ accessions has been discussed. In this study, genetic variation among ‘Sumai 3’ accessions collected from six countries were identified using SSR markers; our results demonstrate unique chromosome regions in Sumai 3-AUT and Sumai 3-JPN (‘Sumai 3’ accessions from Austria and Japan, respectively). Field evaluation indicated strong resistance to FHB in Sumai 3-AUT. The polymorphic rate (number of polymorphic markers/number of available markers × 100) based on a DArT array was 12.5% between the two ‘Sumai 3’ accessions. Genotyping for DNA markers flanking FHB-resistant quantitative trait loci (QTLs) revealed genetic variations for the QTL regions on 5AS and 2DS; however, no variation was observed for the QTL regions on 3BS and 6B. Thus, the variation in FHB resistance among ‘Sumai 3’ accessions in the field is due to genetic diversity.

Background: Fusarium head blight (FHB) resistance in wheat (Triticum aestivum L.) has been enhanced by combining resistant alleles with transgressive segregation. In Japan, intensive FHB resistance breeding was initiated in 1970s in Kyushu and in 1990s in Hokkaido. The breeding objectives for climatic adaptation are different between Kyushu and Hokkaido. The objective of this study is to determine how and what type of alleles should be introduced into current cultivars by characterizing the track of allelic selection in both breeding lineages.Results: Herein, we traced haplotype of SSR markers for allelic selection of FHB resistance-related quantitative trait loci (QTLs) in the Japanese breeding lineages of Kyushu and Hokkaido where the climatic adaptations of wheat are dissimilar. In Kyushu, resistant haplotypes on chromosomes 3BS, 5AS, and 6BS were frequently found in old cultivars, and those on 3BS and 5AS were transmitted to modern cultivars with incorporating the resistant allele on 2DL. The winter cultivars of Hokkaido lacked the resistant allele set of the markers at 3BS, but the resistant haplotypes at 2DL and 5AS were predominantly retained. The resistant allele combinations at 6BS and 2DS were mostly excluded from Kyushu and the winter cultivars of Hokkaido. The susceptible haplotype on 2DS was co-inherited with the semi-dwarfing allele at Xgwm261 which is diagnostic for the presence of the dwarfing gene Rht8 and the allele of the photoperiod insensitive at Ppd-D1 in Kyushu, indicating a linkage drag between a FHB resistance allele and ones underling agronomic characters. In Hokkaido, six cultivars were found to have the resistant haplotype on 2DS with the semi-dwarfing allele of Xgwm261. Conclusions:Our results suggest that a trade-off between FHB resistance and quality or agronomic traits has contributed to the history of Japanese FHB resistance breeding. To enhance FHB resistance in current cultivars, introducing the resistant allele of QTL on 2DS should be a promising option. The six winter cultivars found in the Hokkaido lineage can be used as new donors for introducing FHB resistance alleles of QTL on 2DS into modern cultivars together with the semi-dwarfing allele at Xgwm261.

The wheat landraces collected by Dr Hitoshi Kihara et al. from Afghanistan, the place of secondary origin of wheat, are an untapped genetic resource for mining novel alleles. In this study, approximately 400 landraces were collected from seven agroecological zones and characterized using diversity array technology and single-nucleotide polymorphism markers, as well as diagnostic molecular markers at important loci controlling vernalization (Vrn), photoperiod response (Ppd), grain colour (R), leaf rust (Lr), yellow rust (Yr), stem rust (Sr) and Fusarium head blight (Fhb). A genome-wide marker array revealed a large amount of genetic diversity among the landraces, 53% of which were winter types, 43% were either spring types or facultative and 4% were either unknown or had Vrn-A1c – a rare spring allele that needs to be confirmed with additional genotyping and phenotyping. At Ppd, 97% of the lines carried a photosensitive allele. In the case of grain colour, classification based on dominant or recessive allelic combinations revealed that approximately 39% of the population is characterized by white grain. Four gene-specific markers that were targeted to identify loci for rust and Fhb resistance enabled us to identify 17 unique landraces with known resistance genes.