Validation of exome capture sequence facilitated marker improvement for ergot resistance screening in durum wheat

Ergot is an important disease of durum wheat caused by the ascomycete Claviceps purpurea (Fr.) Tul. Initial symptoms of ergot infection are droplets of honeydew on immature spikes. Honeydew, a sticky exudate containing asexual spores, attracts insects that can transmit and spread disease to healthy plants. Dark purple coloured sclerotia or ergot bodies follow in place of honeydew, replacing healthy kernels resulting in yield loss and grade reduction. Of greater concern is the harmful cocktail of alkaloid compounds contained in the ergot bodies which are deleterious to both human and animal health when consumed. Resistant durum wheat (Triticum turgidum var. durum) genotypes are rare and there are no registered varieties currently available in Canada. Development of cultivars with resistance to ergot is an important integrated management strategy for its reduction. We previously identified a quantitative trait locus (QTL) on chromosome 2A associated with reduced honeydew production in durum wheat. The objective of this study was to develop and validate KASP markers for this QTL for use in marker assisted selection (MAS). Reduced exome capture sequencing was performed on breeding lines with low and high honeydew production. A physical interval was defined by anchoring wheat microsatellite markers associated with the 2A honeydew resistance locus. Polymorphisms in the target region were identified and used for KASP marker design. Markers were initially assessed against a small phenotyped test population and then applied to a panel of breeding lines characterised for honeydew resistance. Based on breeding panel results, a subset of markers showing polymorphism between parents of the doubled haploid breeding population CDC Carbide (ergot susceptible) / A0709-BX05 (ergot resistant) were validated on 150 progeny. The markers show a strong relationship to honeydew resistance, validating our strategy of designing KASP markers for variants detected from reduced exome capture sequences. The markers will be valuable for use in MAS to select for ergot resistant durum breeding lines harbouring the 2A QTL for reduced honeydew production.