GWAS Pinpoints Candidate Genes Behind Wheat Stripe Rust Resistance

A new genome-wide association study has now mapped the genetic basis of adult-plant resistance to this disease, identifying recurrent marker associations, prioritized candidate genes and favorable haplotypes that could guide resistance breeding in wheat.

The research team evaluated 120 wheat accessions for stripe rust resistance at the adult-plant stage in four field environments spread across three sites during 2022 to 2024. This multi-environment design allowed the researchers to assess how consistently resistance signals appeared across different growing conditions rather than relying on a single season or location.

Genotyping was carried out with a wheat 50 K liquid-phase SNP chip, from which 54,636 markers were retained for analysis. The team then applied a mixed linear model that incorporated both population structure and kinship, an approach designed to reduce false associations arising from relatedness among the accessions.

Disease severity varied continuously across the panel, and broad-sense heritability was estimated at 0.90, indicating that a large share of the observed variation in severity is attributable to genetic factors. The researchers analyzed five phenotypic datasets: disease severity in each individual environment and across-environment best linear unbiased predictions, known as BLUPs.

The association scan detected twelve recurrent marker records, representing eleven unique physical positions, on chromosomes 1A, 6B and 7B at a significance threshold of P < 0.001 in at least three phenotypic datasets, including the BLUP analysis. Using subgenome-specific linkage disequilibrium decay distances, the team grouped these marker records into five provisional association regions.

On the basis of functional annotation, seven candidate genes were prioritized within these regions. The authors emphasize that these recurrent associations and candidate genes provide targets for further genetic validation rather than confirmed resistance genes.

Haplotype analysis of four selected SNP-containing blocks identified haplotypes associated with lower disease severity. One marker in particular, AX-111,091,126, was detected in the 23YL and 24TS environments as well as in the BLUP analysis. Within its block, the Hap1 haplotype showed lower disease severity than Hap3 under the BLUP analysis.

To make this finding practically useful, the researchers developed a KASP assay for AX-111,091,126. The assay successfully distinguished A/G genotypes in an independent panel of 221 wheat accessions, demonstrating that it can serve as a genotyping tool for evaluating the associated allele in wheat resistance breeding programs.

The study’s combination of multi-environment field phenotyping, high heritability, recurrent statistical associations and a validated breeder-friendly marker assay offers a concrete starting point for further validation work. The favorable haplotypes and the KASP assay together provide tools that breeding programs can use to track and select alleles associated with reduced stripe rust severity as adult-plant resistance is refined in wheat germplasm.

Subject of Research: Genetic loci associated with adult-plant resistance to stripe rust in wheat

Article Title: Genome-wide association study identifies candidate genes for stripe rust resistance in wheat across multiple environments

Article References: Luo, Z., Zhang, F., Ababaikere, M., He, W., Jiao, W., Geng, H., & Cheng, Y. (2026). Genome-wide association study identifies candidate genes for stripe rust resistance in wheat across multiple environments. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10229-x

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10229-x

Keywords: wheat, stripe rust, GWAS, SNP chip, candidate genes, haplotype analysis, KASP assay, plant breeding, disease resistance, heritability, Puccinia striiformis, Genome-wide