New Genetic Markers Reveal Wheat Breeding Has Never Used a Key Rust Resistance Gene

Wheat leaf rust, caused by the fungus Puccinia triticina, remains one of the most serious threats to global wheat production, and breeders have long relied on resistance genes to keep the disease in check. A new study in BMC Plant Biology reports a surprising finding: one of the most widely cited leaf rust resistance genes, Lr21, appears to have never been deployed in functional form in wheat breeding. Researchers developed diagnostic molecular markers that distinguish functional Lr21 alleles from non-functional ones, and used them to trace how the non-functional versions spread through cultivated wheat.

The team assayed twenty-five wheat cultivars previously reported to carry Lr21, testing each for the hypersensitive response triggered by the AvrLr21 protein, which signals a working resistance gene. None of the cultivars showed the response, indicating that all twenty-five carry non-functional Lr21 alleles. Sequence comparisons then sorted these non-functional alleles into two distinct haplotypes, labeled H1 and H2, found in fourteen and eleven cultivars respectively, and pinpointed six polymorphic sites that separate functional from non-functional versions of the gene.

Building on those six sites, the researchers designed a CAPS marker that diagnoses whether a plant carries a functional Lr21 allele, along four single-sequence-polymorphism markers that distinguish the H1 and H2 haplotypes. When applied to the panel, the markers confirmed that every one of the twenty-five cultivars carries a non-functional haplotype. Pedigree tracing of these cultivars led back to eight core parental germplasm accessions that carried only non-functional Lr21 haplotypes, supporting the conclusion that functional Lr21 has never entered wheat breeding programs.