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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-017-0993-7) contains supplementary material, which is available to authorized users.

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