Tracking haplotype for QTLs associated with Fusarium head blight resistance in Japanese wheat (Triticum aestivum L.) lineage

Abstract 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.