RGA-ILP, a new type of functional molecular markers in bread wheat

Markers targeting intron length polymorphism of resistance gene analogues (RGA-ILP) are not only expected to be more polymorphic than those designed from conserved exons, but also have potential resistance gene function. Based on known domains of resistance genes, more than 900 wheat RGAs were mined from public databases. Two hundred and seventy-eight intron-containing RGA candidates were predicted based on rice genomic DNA information, and 50 of them were selected for evaluation and mapping. A total of 150 RGA-ILP primer pairs, consisting of exon-primed intron-crossing primers to amplify the intronic regions of RGAs were designed. One hundred and thirty-five pairs were successfully amplified with similar or larger than expected product lengths. Three mapping populations (SOpop, NYpop and WSpop) were screened and 28 pairs of RGA-ILP primers gave reproducible polymorphic amplifications between the mapping parents. Sixteen, 14 and five loci were integrated into SOpop, NYpop and WSpop maps, respectively. The results demonstrated that this method provides an efficient approach for developing polymorphic markers.