Ryegrass Stem Rust Resistance Genes Mapped Through Combined GWAS and QTL Analysis

Stem rust, caused by the fungal pathogen Puccinia graminis, is a major biotic stress in perennial ryegrass (Lolium perenne L.) and can cause severe seed yield losses. As restrictions on fungicide use increase, developing cultivars with durable resistance has become critical for sustainable disease management, yet the genetic basis of stem rust resistance in this forage grass has remained poorly understood. A study published in BMC Plant Biology has now mapped the genomic architecture of this resistance, combining two complementary mapping approaches to identify both common and rare resistance variants.

The research team began by characterizing the pathogen itself. Using simple sequence repeat (SSR) markers, they genotyped a collection of Puccinia graminis isolates and found that the fungal population fell into three main phylogenetic groups. This classification allowed the researchers to select representative isolates for resistance testing, so that the plant material could be challenged against the breadth of pathogen diversity represented in the study rather than a single strain.

With pathogen diversity defined, the team assembled a substantial plant resource: a diversity panel of 390 perennial ryegrass genotypes, plus two biparental F₂ populations of 216 individuals each, derived from four genotypes of the diversity panel. Resistance phenotyping was carried out under controlled conditions using isolates representing each of the three phylogenetic groups, and under field conditions with natural infections. This dual strategy captured both controlled, isolate-specific responses and resistance expression under natural disease pressure.

The first analytical approach was a genome-wide association study (GWAS) on the diversity panel. GWAS scans the genomes of many individuals for DNA variants that statistically co-occur with differences in disease response, and is well suited to detecting common variants. In this study, GWAS identified three genomic regions associated with stem rust resistance, with the quantitative trait loci together explaining between 9.5 and 18.6 percent of the observed phenotypic variation.

Among the candidate genes within these regions was one encoding a Ser/Thr protein kinase. The second approach, quantitative trait locus (QTL) mapping in the two F₂ populations, was designed to identify potential rare variants that GWAS did not detect. The QTL mapping identified five genomic regions associated with resistance to European stem rust isolates, and these loci explained considerably more of the phenotypic variance within the mapping populations, jointly accounting for 58.3 to 64.3 percent.

The candidate genes uncovered by QTL mapping point to several components of the molecular machinery behind rust resistance. Shared across the two mapping populations were genes encoding a sugar transporter, a lipid-binding protein, components of nucleotide-binding site and leucine-rich repeat (NBS-LRR) proteins, a reverse transcriptase, and a 2S seed storage protein 5-like protein. A central conclusion of the study is that biparental QTL mapping complements GWAS by identifying rare resistance variants that would otherwise remain undetected.

Because the two approaches were applied to overlapping plant material drawn from the same diversity panel, the combined results give a fuller picture of the genetic architecture of stem rust resistance in perennial ryegrass than either method alone. From a breeding perspective, the authors note that the mapped genomic regions and favorable haplotypes represent valuable resources for marker-assisted selection and genomic selection, approaches aimed at accelerating the development of perennial ryegrass cultivars with stem rust resistance.

Subject of Research: Genetic architecture of stem rust resistance in perennial ryegrass revealed by GWAS and QTL mapping

Article Title: Genetic architecture of stem rust (Puccinia graminis Pers.) resistance in perennial ryegrass (Lolium perenne L.) revealed by GWAS and QTL mapping

Article References: Ollivier, R., Rodriguez-Algaba, J., Kristensen, P. S., Nielsen, B., Larsen, M. W., Malinowska, M., Lenk, I., Boelt, B., Patpour, M., Hovmøller, M. S., Justesen, A. F., & Asp, T. (2026). Genetic architecture of stem rust (Puccinia graminis Pers.) resistance in perennial ryegrass (Lolium perenne L.) revealed by GWAS and QTL mapping. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10083-x

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10083-x

Keywords: perennial ryegrass, stem rust, Puccinia graminis, GWAS, QTL mapping, candidate genes, marker-assisted selection, genomic selection, disease resistance, forage grass breeding, NBS-LRR, plant pathology