Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover

Lea A. Frey, Tim Vleugels, Tom Ruttink, Franz X. Schubiger, Marie Pégard, Leif Skøt, Christoph Grieder, Bruno Studer, Isabel Roldán-Ruiz, Roland Kölliker*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Downloads (Pure)


Key message
High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding.

Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.
Original languageEnglish
Pages (from-to)4337-4349
Number of pages13
JournalTheoretical and Applied Genetics
Issue number12
Early online date25 Sept 2022
Publication statusPublished - 01 Dec 2022


  • Biological Variation, Population
  • Disease Resistance/genetics
  • Genome-Wide Association Study
  • Medicago/genetics
  • Plant Breeding
  • Plant Diseases/genetics
  • Quantitative Trait Loci
  • Trifolium/genetics


Dive into the research topics of 'Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover'. Together they form a unique fingerprint.

Cite this