Development and deployment of KASP markers for multiple alleles of Lr34 in wheat

<jats:title>Abstract</jats:title><jats:sec> <jats:title>Key message</jats:title> <jats:p>Heterogeneous Lr34 genes for leaf rust in winter wheat cultivar ‘Duster’ and KASP markers for allelic variation in exon 11 and exon 22 of Lr34.</jats:p> </jats:sec><jats:sec> <jats:title>Abstract</jats:title> <jats:p>Wheat, <jats:italic>Triticum aestivum</jats:italic> (2<jats:italic>n</jats:italic> = 6<jats:italic>x</jats:italic> = 42, AABBDD), is a hexaploid species, and each of three homoeologous genomes A, B, and D should have one copy for a gene in its ancestral form if the gene has no duplication. Previously reported leaf rust resistance gene <jats:italic>Lr34</jats:italic> has one copy on the short arm of chromosome 7D in hexaploid wheat, and allelic variation in <jats:italic>Lr34</jats:italic> is in intron 4, exon 11, exon 12, or exon 22. In this study, we discovered that Oklahoma hard red winter wheat cultivar ‘Duster’ (PI 644,016) has two copies of the <jats:italic>Lr34</jats:italic> gene, the resistance allele <jats:italic>Lr34a</jats:italic> and the susceptibility allele <jats:italic>Lr34b</jats:italic>. Both <jats:italic>Lr34a</jats:italic> and <jats:italic>Lr34b</jats:italic> were mapped in the same linkage group on chromosome 7D in a doubled-haploid population generated from a cross between Duster and a winter wheat cultivar ‘Billings’ which carries the susceptibility allele <jats:italic>Lr34c</jats:italic>. A chromosomal fragment including <jats:italic>Lr34</jats:italic> and at least two neighboring genes on its proximal side but excluding genes on its distal side was duplicated in Duster. The Duster <jats:italic>Lr34ab</jats:italic> allele was associated with tip necrosis and increased resistance against leaf rust at adult plants in the Duster × Billings DH population tested in the field, demonstrating the function of the Duster <jats:italic>Lr34ab</jats:italic> allele in wheat. We have developed KASP markers for allelic variation in exon 11 and exon 22 of <jats:italic>Lr34</jats:italic> in wheat. These markers can be utilized to accelerate the selection of <jats:italic>Lr34</jats:italic> in wheat.</jats:p> </jats:sec>