Marker Development for Wheat Leaf Rust Resistance Gene Lr16 and Wheat Midge Resistance Gene Sm1 in Canadian Wheat Cultivars

Wheat midge is a serious insect pest of spring wheat in Canada that causes significant economic loss. Sm1 is the major wheat midge resistance gene that has been shown to express antibiotic properties that kill the larvae of wheat midge. Similarly, wheat leaf rust, caused by the fungus Puccinia triticina, is one of the serious diseases of wheat worldwide. Lr16 is a widely deployed leaf rust resistance gene that is effective against the North American P. triticina population when in combination with Lr34. A comparative genomic analysis, using the reference genome, Brachypodium distachyon, identified molecular markers linked to the Lr16 locus on wheat chromosome 2BS. For Sm1, which is also located on wheat chromosome 2BS, SNP markers mapped in the vicinity of the gene (from 9K SNP Wheat Infinium Assay) were validated using the KBioscience Competitive Allele-Specific polymerase chain reaction (KASPar) assay. We developed and mapped KASP markers which are linked to Sm1, of which 5 (kwm23, kwm29, kwm30, cd01 and cd02) are mapped within 3.9 cM of Sm1. Similarly for Lr16, additional markers which are also in close proximity to the gene Lr16 were developed using the KASPar assay. These markers will be useful for marker assisted selection for Lr16 and Sm1 in wheat breeding programs. The markers are also targeted for the on-going efforts of fine mapping these genes. The genotyping platform of the KASP assay is efficient and well-suited for marker-assisted selection in breeding programs.