Improved resolution of Fusarium head blight resistance quantitative trait loci in tetraploid wheat using a high density genetic map

Fusarium head blight (FHB) is a threat to durum wheat yield and quality worldwide. Breeding for FHB resistance in durum wheat is slow because of the weak and quantitative expression of resistance. Combining genes from the domesticated gene pool with sources from related tetraploid species is one strategy to improve genetic resistance in durum wheat. This can be aided through marker-­‐‑assisted selection using DNA markers tightly linked to the genes conferring resistance. High density genotyping platforms based single nucleotide polymorphism (SNP) markers have the potential to better identify and resolve QTL. Major stable FHB QTLs have been reported: one from T. carthlicum cultivar Blackbird chromosome 1A and two from durum line DT696 on 5A (Singh et al. 2008). In this study, we genotyped with the 90K Infinium iSelect SNP array 90 lines of the A0022 (Strongfield x Blackbird) and 121 lines of the A0132 (DT707 x DT606) doubled haploid mapping populations. Individual component maps were generated for each population using polymorphic SNP markers with simple sequence repeat (SSR) and Diversity Array Technology (DArT) markers used in the original mapping. A consensus map of the two populations was generated by combining the component maps using LPmerge software. This enabled mapping of 14,241 markers spanning 3,047 cM of all 14 chromosomes. The average genetic distance between markers was 0.4 cM. Analysis conducted using the component maps for each population and the multi-­‐‑location FHB field ratings acquired by Singh et al. (2008) revealed the same QTL but with additional SNP markers within the interval. The 1A QTL intervals calculated from five out of six phenotypic data was from 5.9 to 11.1 cM shorter than those reported by Sing et al. (2008). Two unlinked QTL was detected on 5A chromosome (5A1 and 5A2), confirming the previous results on the presence of two unlinked loci (gwm156 and wmc110) associated with the trait. Intervals obtained for 5A1 using five out of ten A0132 FHB data sets harbored the SSR marker gwm156, however in only one instance wmc110 was within 5A2 intervals. Several SNPs, localized to the centre of the QTL, converted to Kompetitive Allele Specific PCR (KASP) markers were tested on a subset of lines representative of observed haplotypes in the mapping population to assure that the KASP markers reproduce the results obtained from Infinium analysis. About 90% of KASP markers mimic the genotyping output obtained from infinium analysis. We are currently further validating these markers as tools for marker assisted selection in our durum breeding programs.