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

Abstract

Natural plant populations encounter strong pathogen pressure and defence-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.

Keywords: Cladosporium fulvum; Solanum chilense; loss of resistance; major gene resistance; tomato.

Figure 1.

Tomato leaves inoculated with 2 × 10⁴ conidia ml⁻¹. (a) i–iv inoculated leaves harvested at 14 dpi of MM-Cf-9, MM-Cf-5, and S. chilense population LA3111 and LA4330. (b) Microscopic pictures of bleached leaves (scale bar = 20 µm), after staining with ink (mycelium of pathogen indicated with red arrows). (c) Quantification of C. fulvum DNA load in pg/ng of plant DNA after 14 dpi of inoculation in three plants per MM control and five plants per S. chilense population. All the plants were evaluated in three technical replicates and each data point shows pathogen load per technical replicate. (Online version in version.)

Figure 2.

Infiltration of AF in populations of S. chilense. Leaf of an individual plant with no recognition of components present in the infiltrated AF (a) and leaf of an individual plant recognizing at least one component present in the AF (b). The infiltrated areas are indicated with white dotted lines. The map on the right shows the geographical distribution of AF component perception in S. chilense. The map shows the geographically distinct populations of S. chilense and their response to infiltration with AF. Each pie chart indicates one population with 8 to 17 individuals (c). The brick red fraction represents plants that respond to C. fulvum AF, whereas green indicates the fraction of non-responding plants. (Online version in colour.)

Figure 3.

(a–d) Geographical distribution of Avr9 and Avr4 perception in S. chilense. The map shows populations of S. chilense and their response to infiltration with Avr9 and Avr4 (purple when there is an HR-associated response to both), Avr9 (blue when there is an HR-associated response), and Avr4 (red when there is an HR-associated response). White sectors indicate plants showing no recognition of either Avr9 or Avr4. The infiltrated areas are indicated with red dotted lines. Each pie chart indicates one population with 8 to 17 individuals. (Online version in colour.)

Figure 4.

Amplification of the canonical Cf-9, 9DC, and Cf-4 region in geographically distinct populations of S. chilense. (a) The CS5-CS1 primer pair was used to amplify a fragment of Cf-9 (378 bp), the DS1-CS1 primer pair for 9DC (507 bp), and the PSK047/PSK050 primer pair for Cf-4 (728 bp). As a PCR control, part of the coding region of elongation factor 1 alpha (EF-1α) was amplified using the primer pair RS003/RS004 (400 bp). MM-Cf-9 and MM-CF-4, and LP12 (9DC) were used as controls (electronic supplementary material, figure S2). + or – are indicative of Avr9 and Avr4 responsiveness upon infiltration of these effectors (figure 2). (b) Map shows the populations used in the analysis. (Online version in colour.)