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.

To put the functional gene to use, the researchers crossed TcLr21, a line carrying functional Lr21, with ZKPm36, a line carrying the powdery mildew resistance gene Pm36, aiming to stack both resistance genes in a single genetic background. The resulting F2 progeny segregated in the expected 9:3:3:1 ratio, consistent with independent inheritance of the two genes. Resistance assays of the pyramided lines showed moderate resistance to leaf rust, high resistance to powdery mildew, and moderate resistance to root rot, demonstrating that the combined material carries multi-disease resistance.

Beyond the immediate breeding value, the study provides both a practical tool and a cautionary lesson for marker-assisted selection. The diagnostic CAPS marker allows breeders to screen germplasm directly for functional Lr21 rather than relying on historical records that may reflect non-functional alleles, while the haplotype markers clarify which version of the gene a line carries. The pyramided Lr21-Pm36 material offers a genetic resource for further improvement of multi-disease resistance in bread wheat, and the finding that a widely credited resistance gene has circulated in breeding as a non-functional allele underscores the importance of verifying gene functionality at the sequence level before deploying it in breeding programs.

Subject of Research: Development of diagnostic markers for functional Lr21 and pyramiding with Pm36 in bread wheat

Article Title: Development of diagnostic marker for functional Lr21 and its validation in pyramiding with Pm36 in bread wheat

Article References: Jin, Y., Liu, Y., Shen, S., Yuan, S., Liu, C., Xu, P., Yan, C., & Wang, H. (2026). Development of diagnostic marker for functional Lr21 and its validation in pyramiding with Pm36 in bread wheat. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10232-2

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10232-2

Keywords: wheat, leaf rust, Lr21, Pm36, diagnostic markers, marker-assisted selection, haplotypes, disease resistance, gene pyramiding, Puccinia triticina, powdery mildew, breeding