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

Stem rust caused by Puccinia graminis ( Pg ) is a major biotic stress in perennial ryegrass ( Lolium perenne L.) and can result in severe seed yield losses. Increasing restrictions on fungicide use, developing cultivars with durable resistance is critical for sustainable disease management. However, the genetic basis of Pg resistance in perennial ryegrass remains poorly understood. To identify representative isolates for exploring stem rust resistance in perennial ryegrass, the genotypic diversity of different Pg isolates was investigated with SSR markers and revealed three main phylogenetic groups. The stem rust resistance variability was investigated in a diversity panel of 390 L. perenne genotypes and two biparental F₂ populations (216 individuals each) derived from four genotypes of the diversity panel. Phenotyping for stem rust resistance was conducted under controlled conditions using Pg isolates representing the three phylogenetic groups, as well as under field conditions with natural infections. A genome-wide association study (GWAS) was performed on the diversity panel to dissect the common variants involved in the resistance to stem rust, while quantitative trait locus (QTL) mapping was conducted on the two F₂ populations to identify potential rare variants non-identified by GWAS. GWAS identified three genomic regions, with QTLs explaining altogether 9.5–18.6% of the observed phenotypic variation, with candidate genes including a Ser/Thr protein kinase. QTL mapping identified five genomic regions associated with resistance to European stem rust isolates, with QTLs explaining altogether 58.3–64.3% of the phenotypic variance. Shared candidate genes across the two mapping populations encode a sugar transporter, a lipid-binding protein, components of nucleotide-binding site and leucine-rich repeat proteins, a reverse transcriptase, and a 2 S seed storage protein 5-like. By integrating GWAS and biparental QTL mapping, this study provides new insights into the genetic architecture of stem rust resistance in perennial ryegrass. Our results demonstrate that biparental QTL mapping complements GWAS by identifying rare resistance variants that would otherwise remain undetected. From a breeding perspective, these genomic regions and favorable haplotypes represent valuable resources for marker-assisted and genomic selection aimed at accelerating the development of perennial ryegrass cultivars with stem rust resistance.