Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix

PLoS One. 2016 Dec 21;11(12):e0168776. doi: 10.1371/journal.pone.0168776. eCollection 2016.


An earlier identified major quantitative trait locus for resistance towards the willow leaf rust fungus Melampsora larici-epitea in a Salix viminalis x (S. viminalis × S. schwerinii) population was used to identify potential resistance genes to the rust pathogen. Screening a genomic bacterial artificial chromosome library with markers from the peak position of the QTL region revealed one gene with TIR-NBS-LRR (Toll Interleukin1 Receptor-Nucleotide Binding Site-Leucine-Rich Repeat) domain structure indicative of a resistance gene. The resistance gene analog was denoted RGA1 and further analysis revealed a number of non-synonymous single nucleotide polymorphisms in the LRR domain between the resistant and susceptible Salix genotypes. Gene expression levels under controlled conditions showed a significantly lower constitutive expression of RGA1 in the susceptible genotype. In addition, the susceptible genotype showed a significantly reduced expression level of the RGA1 gene at 24 hours post inoculation with M. larici-epitea. This indicates that the pathogen may actively suppress RGA1 gene expression allowing a compatible plant-pathogen interaction and causing infection.

MeSH terms

  • Amino Acid Sequence
  • Basidiomycota / pathogenicity
  • Chromosomes, Artificial, Bacterial / genetics
  • Chromosomes, Artificial, Bacterial / metabolism
  • Disease Resistance / genetics*
  • Gene Expression Regulation, Plant
  • Genotype
  • Molecular Sequence Data
  • Plant Diseases / genetics
  • Plant Diseases / microbiology
  • Plant Leaves / genetics
  • Plant Leaves / microbiology
  • Plant Proteins / chemistry
  • Plant Proteins / genetics
  • Plant Proteins / metabolism*
  • Polymorphism, Single Nucleotide
  • Protein Structure, Tertiary
  • Quantitative Trait Loci
  • Salix / genetics*
  • Salix / microbiology
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Toll-Like Receptor 1 / chemistry
  • Toll-Like Receptor 1 / genetics
  • Toll-Like Receptor 1 / metabolism*


  • Plant Proteins
  • Toll-Like Receptor 1

Grant support

This research was supported by the governmental Swedish Energy Agency (JS) ( and The NLfaculty at the Swedish University of Agricultural Sciences (JS) ( The two funders above had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The SNP Technology Platform, Uppsala, Sweden (JS) ( performed the high-throughput sequencing.