Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance

Natural plant populations encounter strong pathogen pressure and defense-associated genes are known to be under selection dependent on the pressure by the pathogens. Here we use populations of the wild tomato Solanum chilense to investigate natural resistance against Cladosporium fulvum, a well-known ascomycete pathogen of domesticated tomatoes. Host populations used are from distinct geographical origins and share a defined evolutionary history. We show that distinct populations of S. chilense differ in resistance against the pathogen. Screening for major resistance gene mediated pathogen recognition throughout the whole species showed clear geographical differences between populations and complete loss of pathogen recognition in the south of the species range. In addition, we observed high complexity in a homologues of Cladosporium resistance (Hcr) locus, underlying the recognition of C. fulvum, in central and northern populations. Our findings show that major gene mediated recognition specificity is diverse in a natural plant-pathosystem. We place major gene resistance in a geographical context that also defined the evolutionary history of that species. Data suggest that the underlying loci are more complex than previously anticipated, with small-scale gene recombination being possibly responsible for maintaining balanced polymorphisms in the populations that experience pathogen pressure.

Methods
Additional data for the manuscript "Population studies in the wild tomato species Solanum chilense reveal maintenance and loss of resistance at geographically distinct locations"

Contains:

METADATA MICROSCOPY

jpg and xml metadata files for the microscopy images used in our study

SNP DATA

Alignment files (fasta) for the genes mentioned in the study

    3chil*.fa

Intermediate files used for the generation of above fasta files

    Coreceptors*

Solanum lycopersicum gene sequences used in the analysis above

    Solyc*.fa

Description of the pipeline used to identify the coreceptors and their mutations

    Pipeline_fv.txt

OTHERS

R scripts used for graphs

    *.R

Tables with raw qPCR data as used in the study

    qpcrdata.csv

Details on the populations used in this study

    Population-details.ods

Details on the populations used in this study

    Avrmix.csv

Dualfigure.csv