Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16


Kassa, M.T., You, F.M., Hiebert, C.W., Pozniak, C.J., Fobert, P.R., Sharpe, A.G., Menzies, J.G., Humphreys, D.G., Rezac Harrison, N., Fellers, J.P., McCallum, B.D., McCartney, C.A. (2017). Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16. BMC Plant Biology, [online] 17(1), http://dx.doi.org/10.1186/s12870-017-0993-7

Plain language summary

Leaf rust is an important foliar disease of wheat in Canada that reduces grain yield. Leaf rust can be controlled by growing leaf rust resistant wheat varieties. In this study, researchers developed DNA markers that are predictive of the presence of a leaf rust resistance gene called Lr16. This gene is common in Canadian wheat varieties and provides a high level of leaf rust resistance when a variety carries both Lr16 and another common leaf rust resistance gene called Lr34. These DNA markers will enable wheat breeders to accurately determine whether Lr16 is present in a wheat variety. Similar DNA markers already exist for Lr34. There is some evidence that the combination of Lr16 and Lr34 may provide a so-called ‘durable’ leaf rust resistance, which would be a major breakthrough. Disease resistance frequently becomes ineffective after long term use of specific resistance genes in farmers’ fields. This phenomenon is similar to the buildup of antibiotic resistance in bacteria after prolonged use of a specific antibiotic. The researchers also precisely located Lr16 on a single wheat chromosome, which will lead to DNA sequencing of Lr16 in the future. The chromosomal location also provides wheat breeders with knowledge needed to develop wheat varieties with Lr16 and other genes of interest found on the same wheat chromosome, such as the wheat midge resistance gene Sm1. The DNA markers from this study will facilitate the development of leaf rust resistant wheat varieties, which is important to farmers, the wheat industry, and consumers.


Background: Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS). Results: Forty-three SNP markers were developed and mapped on chromosome 2BS tightly linked with the resistance gene Lr16 across four mapping populations representing a total of 1528 gametes. Kompetitive Allele Specific PCR (KASP) assays were designed for all identified SNPs. Resistance gene analogs (RGAs) linked with the Lr16 locus were identified and RGA-based SNP markers were developed. The diagnostic potential of the SNPs co-segregating with Lr16 was evaluated in a diverse set of 133 cultivars and breeding lines. Six SNP markers were consistent with the Lr16 phenotype and are accurately predictive of Lr16 for all wheat lines/cultivars in the panel. Conclusions:Lr16 was mapped relative to SNP markers in four populations. Six SNP markers exhibited high quality clustering in the KASP assay and are suitable for MAS of Lr16 in wheat breeding programs.